Updates to the Pto DC3000 chromosome sequence and annotation:

  LocusDate: Nature of changeSource
2901-3360  

06-16-10: Qualifiers of 460 CDS features changed to reflect both RNA transcript and peptide sequencing
Qualifiers added:
/experiment="RNA sequencing"
/experiment="peptide sequencing"
/note="see PMID:20190049 for expression data"

Product names for 33 "conserved hypothetical protein" changed to "conserved protein of unknown function"
Product names for 5 "hypothetical protein" changed to "protein of unknown function"

M. Filiatrault
USDA-ARS
345-2900  

06-16-10: Qualifiers of 2555 CDS features changed to reflect RNA transcript sequencing
Qualifiers added:
/experiment="RNA sequencing"
/note="see PMID:20190049 for expression data"

Product names for 486 "conserved hypothetical protein" changed to "conserved protein of unknown function"
Product names for 214 "hypothetical protein" changed to "protein of unknown function"

M. Filiatrault
USDA-ARS
344 PSPTO_5671

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(4170293..4170371)
FT                   /locus_tag="PSPTO_5671"
FT                   /product=”rsmX”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="similar to RNA sequence, ncRNA:GenBank:DQ137846.1"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
343 PSPTO_5670

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(373131..373014)
FT                   /locus_tag="PSPTO_5670"
FT                   /product=”Spot42”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00021"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
342 PSPTO_5669

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(1778751..1778383)
FT                   /locus_tag="PSPTO_5669"
FT                   /product=”Psr2”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing, Northern blot"
FT                   /inference="nucleotide motif:PMID 17621584:gamma-150"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
341 PSPTO_5668

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(1046951..1046593)
FT                   /locus_tag="PSPTO_5668"
FT                   /product=”Psr1”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing, Northern blot"
FT                   /inference="nucleotide motif:PMID 17621584:gamma-150"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
340 PSPTO_5671

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(4170293..4170371)
FT                   /locus_tag="PSPTO_5671"
FT                   /product=”rsmX”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="similar to RNA sequence, ncRNA:GenBank:DQ137846.1"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
339 PSPTO_5670

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(373131..373014)
FT                   /locus_tag="PSPTO_5670"
FT                   /product=”Spot42”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00021"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
338 PSPTO_5669

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(1778751..1778383)
FT                   /locus_tag="PSPTO_5669"
FT                   /product=”Psr2”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing, Northern blot"
FT                   /inference="nucleotide motif:PMID 17621584:gamma-150”
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
337 PSPTO_5668

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(1046951..1046593)
FT                   /locus_tag="PSPTO_5668"
FT                   /product=”Psr1”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing, Northern blot"
FT                   /inference=" nucleotide motif:PMID 17621584:gamma-150”
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
336 PSPTO_5667

03-23-10: Gene/ncRNA feature added
FT   ncRNA           6038511..6038690
FT                   /locus_tag="PSPTO_5667"
FT                   /product=”P1”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00623"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
335 PSPTO_5666

03-23-10: Gene/ncRNA feature added
FT   ncRNA           5949055..5949233
FT                   /locus_tag="PSPTO_5666"
FT                   /product=”6S”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00013"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
334 PSPTO_5665

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(5648734..5648630)
FT                   /locus_tag="PSPTO_5665"
FT                   /product=”TPP”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00059"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
333 PSPTO_5664

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(5433294..5433053)
FT                   /locus_tag="PSPTO_5664"
FT                   /product=”P24”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00629"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
332 PSPTO_5663

03-23-10: Gene/ncRNA feature added
FT   ncRNA           5086183..5086569
FT                   /locus_tag="PSPTO_5663"
FT                   /product=”tmRNA”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00023"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
331 PSPTO_5662

03-23-10: Gene/ncRNA feature added
FT ncRNA           complement(5055007..5054896)
FT                   /locus_tag="PSPTO_5662"
FT                   /product=”S15”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00114"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
330 PSPTO_5661

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(4986712..4986420)
FT                   /locus_tag="PSPTO_5661"
FT                   /product=”RNaseP_bact_a”
FT                   /ncRNA_class=”RNaseP_RNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00010"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
329 PSPTO_5660

03-23-10: Gene/ncRNA feature added
FT   ncRNA           4332812..4333007
FT                   /locus_tag="PSPTO_5660"
FT                   /product=”P16”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00628"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
328 PSPTO_5659

03-23-10: Gene/ncRNA feature added
FT   ncRNA           4116112..4116013
FT                   /locus_tag="PSPTO_5659"
FT                   /product=”SRP_bact”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00169"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
327 PSPTO_5658

03-23-10: Gene/ncRNA feature added
FT   ncRNA           3679925..3680123
FT                   /locus_tag="PSPTO_5658"
FT                   /product=”Cobalamin-4”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00174"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
326 PSPTO_5657

03-23-10: Gene/ncRNA feature added
FT   ncRNA           3549457..3549603
FT                   /locus_tag="PSPTO_5657"
FT                   /product=”prrF2”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00444"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
325 PSPTO_5656

03-23-10: Gene/ncRNA feature added
FT   ncRNA           3542594..3542808
FT                   /locus_tag="PSPTO_5656"
FT                   /product=”Cobalamin-3”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00174"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
324 PSPTO_5655

03-23-10: Gene/ncRNA feature added
FT   ncRNA           complement(3542313..3542537)
FT                   /locus_tag="PSPTO_5655"
FT                   /product=”Cobalamin-2”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00174"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
323 PSPTO_5654

03-23-10: Gene/ncRNA feature added
FT  ncRNA           complement(2009078..2008912)
FT                   /locus_tag="PSPTO_5654"
FT                   /product=”FMN”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00050"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
322 PSPTO_5653

03-23-10: Gene/ncRNA feature added
FT   ncRNA           1878136..1878350
FT                   /locus_tag="PSPTO_5653"
FT                   /product=” Cobalamin-1”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00174"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
321 PSPTO_5652

03-23-10: Gene/ncRNA feature added
FT   ncRNA           1728406..1728566
FT                   /locus_tag="PSPTO_5652"
FT                   /product=”PrrB_RsmZ”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00174"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
320 PSPTO_5651

03-23-10: Gene/ncRNA feature added
FT   ncRNA           1693384..1693536
FT                   /locus_tag="PSPTO_5651"
FT                   /product=”t44”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00127"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
319 PSPTO_5650

03-23-10: Gene/ncRNA feature added
FT  ncRNA           complement(1255819..1255678)
FT                   /locus_tag="PSPTO_5650"
FT                   /product=”yybP-ykoY”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00080"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
318 PSPTO_5649

03-23-10: Gene/ncRNA feature added
FT   ncRNA           1059034..1058888
FT                   /locus_tag="PSPTO_5649"
FT                   /product=”prrF1”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00444"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
317 PSPTO_5648

03-23-10: Gene/ncRNA feature added
FT   ncRNA           678273..678338
FT                   /locus_tag="PSPTO_5648"
FT                   /product=“P26”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00630"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
316 PSPTO_5647 03-23-10: Gene/ncRNA feature added
FT   ncRNA           555344..555465
FT                   /locus_tag="PSPTO_5647"
FT                   /product=”rsmY”
FT                   /ncRNA_class=”scRNA”
FT                   /experiment="RNA sequencing"
FT                   /inference="nucleotide motif:RFAM:RF00195"
FT                   /note="see PMID:20190049 for expression data"
M. Filiatrault
USDA-ARS
315 PSPTO_5646

03-23-10: Gene/CDS feature added
FT   CDS             complement(6174382..6174792)
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5646"
FT                   /product="protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
314 PSPTO_5645

03-23-10: Gene/CDS feature added
FT   CDS             complement(6174792..6175730)
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5645"
FT                   /product="protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
313 PSPTO_5644

03-23-10: Gene/CDS feature added
FT   CDS             4862483..4862680
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5644"
FT                   /product="protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
312 PSPTO_5643

03-23-10: Gene/CDS feature added
FT   CDS             complement(3476773..3477240)
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5643"
FT                   /product="protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
311 PSPTO_5642

03-23-10: Gene/CDS feature added
FT   CDS             complement(3476622..3477131)
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5642"
FT                   /product="protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
310 PSPTO_5641

03-23-10: Gene/CDS feature added
FT   CDS             2978065..2978625
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5641"
FT                   /product="protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
309 PSPTO_5640

03-23-10: Gene/CDS feature added
FT  CDS             2910705..2911238
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5640"
FT                   /product="protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
308 PSPTO_5639

03-23-10: Gene/CDS feature added
FT   CDS             2777027..2777347
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5639"
FT                   /product="protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
307 PSPTO_5638

03-23-10: Gene/CDS feature added
FT   CDS             complement(2611919..2612308)
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5638"
FT                   /product="conserved protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
306 PSPTO_2108

03-23-10: Gene/CDS feature added
FT   CDS             complement(2283419..2284006)
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_2108"
FT                   /product="protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="RNA sequencing"
FT                   /experiment="peptide sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
305 PSPTO_5637

03-23-10: Gene/CDS feature added
FT   CDS             2006821..2007108
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5637"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
304 PSPTO_5635

03-23-10: Gene/CDS feature added
FT   CDS             1581112..1581555
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5635"
FT                   /product="conserved protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="RNA sequencing"
FT                   /experiment="peptide sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
303 PSPTO_5634

03-23-10: Gene/CDS feature added
FT   CDS             1244571..1244858
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5634"
FT                   /product="conserved protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="RNA sequencing"
FT                   /experiment="peptide sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
302 PSPTO_5636

03-23-10: Gene/CDS feature added
FT   CDS             1228041..1228448
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5636"
FT                   /product="conserved protein of unknown function"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
301 PSPTO_0391

03-23-10: Gene/CDS feature added
FT   CDS             complement(432379..432798)
FT                   /locus_tag="PSPTO_0391"
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /product="conserved protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="RNA sequencing"
FT                   /note="see PMID:20190049 for expression data"

M. Filiatrault
USDA-ARS
300 PSPTO_5633 03-23-10: Gene/CDS feature added
FT   CDS             15948..16421
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PSPTO_5633"
FT                   /product="conserved protein of unknown function"
FT                   /inference="ab initio prediction:Easygene 1.2"
FT                   /experiment="peptide sequencing"
FT                   /note="see PMID:20190049 for expression data"
M. Filiatrault
USDA-ARS
299 PSPTO_4705

03-23-10: CDS feature added
5331800..5333372
/codon_start=1
/transl_table=11
/locus_tag="PSPTO_4705"
/product="sensor histidine kinase CorS"
/note="PMID:18429999"

M. Filiatrault
USDA-ARS
298 PSPTO_3477 03-23-10: Gene/CDS feature changed
complement(3924034..3924501)
/product="protein of unknown function"
/inference="ab initio prediction:Easygene 1.2"
/experiment="RNA sequencing, peptide sequencing"FT                  
/note="PMID:20190049"
M. Filiatrault
USDA-ARS
297 PSPTO_2108 03-23-10: Gene/CDS feature changed
complement(2283419..2284006)
/product="protein of unknown function"
/inference="ab initio prediction:Easygene 1.2"
/experiment="RNA sequencing, peptide sequencing"FT                  
/note="PMID:20190049"
M. Filiatrault
USDA-ARS
296 PSPTO_1500 03-23-10: Gene/CDS feature changed
1657245..1658126
/product="protein of unknown function"
/inference="ab initio prediction:Easygene 1.2"
/experiment="RNA sequencing, peptide sequencing"FT                  
/note="PMID:20190049"
M. Filiatrault
USDA-ARS
295

PSPTO_0392

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
294

PSPTO_1113

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
293

PSPTO_1442

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
292

PSPTO_1837

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
291

PSPTO_2357

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
290

PSPTO_2512

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
289

PSPTO_2619

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
288

PSPTO_2682

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
287

PSPTO_3093

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
286

PSPTO_4311

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
285

PSPTO_5429

03-23-10: Gene/CDS feature deleted
gene call inconsistent with transcriptome mapping
M. Filiatrault
USDA-ARS
266-284 multiple 09-15-09: 19 PvdS box promoter features added
Formatting consistent with 2009 DDBJ/EMBL/Genbank guidelines:
/bound_moiety="PvdS"
/inference="nucleotide motif:PvdS_box_model_C_DC3000.hmm"
/experiment="PvdS-dependent reporter activity and/or RT-PCR "
/note=[PubMed ID]
B. Swingle
USDA-ARS
215-265 multiple

09-15-09: 51 Hrp box promoter features changed
qualifiers changed to the following format consistent with 2009 DDBJ/EMBL/Genbank guidelines:
/bound_moiety="HrpL"
/inference="nucleotide motif:HMM2"
/experiment="microarray and/or RT-PCR"
/note=[PubMed ID]

D. Schneider
USDA-ARS
214 PSPTO_1407 12-22-08: Gene/CDS feature restored
complement(1547545..1548381)
/locus_tag="PSPTO_1407"
/product="ISPssy transposase or derivative"
M. Lindeberg
Cornell University
213 PSPTO_1949 12-22-08: Gene name added
/gene="fliC"
M. Lindeberg
Cornell University
212 PSPTO_4655 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
211 PSPTO_0122 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
210 PSPTO_4085 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
209 PSPTO_4086 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
208 PSPTO_5042 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
207 PSPTO_3622 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
206 PSPTO_3623 03-19-08: Gene/CDS feature deleted M. Lindeberg
Cornell University
205 PSPTO_5269 03-19-08: Gene name, product name, and note changed
/gene="betT"
/product="choline transporter"
/note="see PMID: 18156257"
M. Lindeberg
Cornell University
Based on literature review
204 PSPTO_1378 03-19-08: Gene name, product name, and note changed
/gene="hrpH"
/product="membrane-bound lytic murein transglycosylase D"
/note="see PMID: 17827286"
M. Lindeberg
Cornell University
Based on literature review
203 PSPTO_4710 03-19-08: Gene name, product name, and note changed
/gene="cmaB"
/product="coronamic acid synthetase CmaB"
/note="member of the non-heme alpha-ketoglutarate-dependent enzyme superfamily; exhibits halogenase activity, chlorinating the gamma-position of L-allo-isoleucine during coronamic acid biosynthesis; see PMID: 16121186"
M. Lindeberg
Cornell University
Based on literature review
202 PSPTO_4711 03-19-08: Gene name, product name, and note changed
/gene="cmaC"
/product="coronamic acid synthetase CmaC"
/note="catalyses formation of the cyclopropyl ring from the gamma-Cl-L-allo-isoleucine product of the CmaB reaction during coronamic acid biosynthesis; see PMID: 16121186"
M. Lindeberg
Cornell University
Based on literature review
201 PSPTO_4707 03-19-08: Gene name, product name, and note changed
/gene="cmaD"
/product="coronamic acid synthetase CmaD"
/note="non-ribosomal peptide synthetase thiolation domain; aminoacylated by adenylation domain of CmaA in the presence of CmaE during coronamic acid biosynthesis; see PMID: 16121186"
M. Lindeberg
Cornell University
Based on literature review
200 PSPTO_4708 03-19-08: Gene name, product name, and note changed
/gene="cmaE"
/product="coronamic acid synthetase CmaED"
/note="acetyletransferase; shuttles amino acid group between thiolation domains of CmaA and CmaD during coronamic acid biosynthesis; see PMID: 16121186"
M. Lindeberg
Cornell University
Based on literature review
199 PSPTO_4709 03-19-08: Product name, and note changed
/product="coronamic acid synthetase CmaA"
/note="non-ribosomal peptide synthetase with adenylation and thiolation domains; reacts with the AMP derivative of L-allo-isoleucine to produce an aminoacyl thiolester intermediate during coronamic acid biosynthesis; see PMID: 14679222"

M. Lindeberg
Cornell University
Based on literature review
198 PSPTO_0442 03-19-08: Gene name, and note changed
/gene="betB"
/product="betaine aldehyde dehydrogenase BADH"

M. Lindeberg
Cornell University
Based on literature review
197 PSPTO_4794 03-19-08: CDS feature added and pseudogene designation removed
/gene="rluE"
/product="ribosomal large subunit pseudouridine synthase E"
/note="identified by similarity to SP:P75966; match to protein family HMM PF00849; match to protein family HMM TIGR00093"
G. Preston
Oxford University
196 PSPTO_1815 03-19-08: CDS feature added and pseudogene designation removed
/gene="rluB"
/product="ribosomal large subunit pseudouridine synthase B"
/note="identified by similarity to SP:P37765; match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093"
G. Preston
Oxford University
195 PSPTO_2349 03-19-08: CDS feature added and pseudogene designation removed
/product="RNA pseudouridine synthase family protein"
/note="identified by match to protein family HMM PF00849"
G. Preston
Oxford University
194 PSPTO_0160 11-26-07: Gene/CDS feature deleted D. Schneider,
USDA-ARS
193 PSPTO_4783 11-26-07: Gene/CDS feature deleted D. Schneider,
USDA-ARS
192 PSPTO_5631

11-26-07: Gene/CDS feature created
gene
5423493..5424341
/locus_tag="PSPTO_5631"
CDS
5423493..5424341
/locus_tag="PSPTO_5631"
/inference=”similar to AA sequence(same species):INSD:AAO57223.1”
/codon_start=1
/transl_table=11
/product="hypothetical protein"

D. Schneider,
USDA-ARS
191 PSPTO_5632 11-26-07: Gene/CDS feature created
gene
5376643..5378961
/locus_tag="PSPTO_5632"
CDS
5376643..5378961
/locus_tag="PSPTO_5632"
/inference=”similar to AA sequence:RefSeq: ZP_01715308.1"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
D. Schneider,
USDA-ARS
190 PSPTO_5457

11-26-07: Gene name, product name, and note changed - Inference added
/gene="mgoA"
/note="This enzyme consists of an amino acid activation and ligation domain followed by a thiolation domaintypical of non-ribosomal peptide synthetases; similar to the ornithine acetyl transferase inhibitor mangotoxin; see PMID:17506328"
/product="ornithine acetyl transferase inhibitor"
/inference="similar to AA sequence(same species):INSD:ABG00046.1"

M. Lindeberg
Cornell University
Based on literature review

189  

11-26-07: Miscellaneous feature created
misc_feature
899534..960280
/note="ICEland; putative integrative and conjugative element, degenerate; includes genes for type III effectors HopAJ1, HopAT1’, HopD1, HopQ1-1, and HopR1”
/inference=”similar to DNA sequence(same species):INSD:AJ870974.1”

M. Lindeberg
Cornell University
188 PSPTO_2828 11-26-07: Gene name, product name, and note changed
/gene="syrR"
/product="transcriptional regulator SyrR"
/note="required for syringofactin-induced swarming motility and droplet collapse. See PMID:17601782"

M. Lindeberg
Cornell University
Based on literature review
187 PSPTO_2829 11-26-07: Gene name, product name, and note changed
/gene="syfA"
/product="non-ribosomal peptide synthetase SyfA"
/note="This gene consists of three complete condensation, adenylation, thiolation domain modules.  The adenylation domains are specific for leucine, leucine and glutamine; together with PSPTO_2830 codes for proteins involved in production of lipopeptide syringofactins. See PMID:17601782"
M. Lindeberg
Cornell University
Based on literature review
186 PSPTO_2830 11-26-07: Gene name, product name, and note changed
/gene="syfB"
/product="non-ribosomal peptide synthetase SyfB"
/note="This gene consists of five complete condensation, adenylation, thiolation domain modules followed by two thioesterase domains.  The adenylation domains are specific for leucine, threonine, valine, leucine and leucine; together with PSPTO_2829 codes for proteins involved in production of lipopeptide syringofactins. See PMID:17601782"
M. Lindeberg
Cornell University
Based on literature review
185 PSPTO_2831 11-26-07: Gene name, product name, and note changed
/gene="syfC"
/product="syringolide efflux protein SyfC"
/note="see PMID:17601782"
M. Lindeberg
Cornell University
Based on literature review
184 PSPTO_2832 11-26-07: Gene name, product name, and note changed
/gene="syfD"
/product="syringolide efflux protein SyfD"
/note="see PMID:17601782"
M. Lindeberg
Cornell University
Based on literature review
183 PSPTO_4575 11-26-07: Gene name, product name, and note changed
/gene="opuCA"
/product="glycine betaine/choline OpuC ABC transporter, ATP-binding protein"
/note="see PMID:17660277"
M. Lindeberg
Cornell University
Based on literature review
182 PSPTO_3549 11-26-07: Gene name, product name, and note changed
/gene="aefR"
/product="transcriptional regulator AefR"
/note="see PMID:17400767"
M. Lindeberg
Cornell University
Based on literature review
181 PSPTO_4576 11-26-07: Product name, and note changed
/product="glycine betaine/choline OpuC ABC transporter, permease protein"
/note="see PMID:17660277"

M. Lindeberg
Cornell University
Based on literature review
180 PSPTO_4577 11-26-07: Product name, and note changed
/product="glycine betaine/choline OpuC ABC transporter, periplasmic substrate-binding protein"
/note="see PMID:17660277"
M. Lindeberg
Cornell University
Based on literature review
179 PSPTO_3332 11-26-07: Product name changed and inference added
/product="alkaline metalloendoprotease"
/inference="similar to AA sequence:RefSeq:YP_607222"

M. Lindeberg
Cornell University
178 PSPTO_4868 11-26-07: Product name changed and inference added
/product="sensor histidine kinase/response regulator RetS"
/inference="similar to AA sequence:INSD: AAG08241.1"
M. Lindeberg
Cornell University
177 PSPTO_3529 11-26-07: Product name changed and inference added
/product="capsular polysaccharide biosynthesis protein PslA"
/inference="similar to AA sequence:INSD:AAG05619.1"
M. Lindeberg
Cornell University
176 PSPTO_3530 11-26-07: Product name changed and inference added
/product="mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase PslB"
/inference="similar to AA sequence:INSD:AAG05620.1"
M. Lindeberg
Cornell University
175 PSPTO_3531 11-26-07: Product name changed and inference added
/product="lipoprotein PslD"
/inference="similar to AA sequence:INSD:AAG05622.1"
M. Lindeberg
Cornell University
174 PSPTO_3532 11-26-07: Product name changed and inference added
/product="exopolysaccharide biosythesis protein PslE"
/inference="similar to AA sequence:INSD:AAG05623.1"
M. Lindeberg
Cornell University
173 PSPTO_3533 11-26-07: Product name changed and inference added
/product="glycosyl transferase, group 1 family protein PslF"
/inference="similar to AA sequence:INSD:AAG05624.1"
M. Lindeberg
Cornell University
172 PSPTO_3534 11-26-07: Product name changed and inference added
/product="glycosyl hydrolase, family 5 PslG"
/inference="similar to AA sequence:INSD:AAG05625.1"
M. Lindeberg
Cornell University
171 PSPTO_3535 11-26-07: Product name changed and inference added
/product="glycosyl transferase, group 1 family protein PslH"
/inference="similar to AA sequence:INSD:AAG05626.1"
M. Lindeberg
Cornell University
170 PSPTO_3536 11-26-07: Product name changed and inference added
/product="glycosyl transferase, group 1 family protein PslI"
/inference="similar to AA sequence:INSD:AAG05627.1"
M. Lindeberg
Cornell University
169 PSPTO_3537 11-26-07: Product name changed and inference added
/product="membrane protein PslJ"
/inference="similar to AA sequence:INSD:AAG05628.1"
M. Lindeberg
Cornell University
168 PSPTO_3539 11-26-07: Product name changed and inference added
/product="membrane protein PslK"
/inference="similar to AA sequence:INSD:AAG05629.1"
M. Lindeberg
Cornell University
167 PSPTO_4574

9-06-07: Coordinates changed
Coordinates for PSPTO_4574 changed from 5170504..5171616 to 5169133..5171616. Translated product changed accordingly.

M. Lindeberg
Cornell University
166 PSPTO_4570 9-06-07: Product name and note fields changed
Product name changed from "hypothetical protein" to "binary cytotoxin component, putative". Note field changed to /note="similar to GP:80558284; identified by sequence similarity; putative"
M. Lindeberg
Cornell University
Based on literature review
165 PSPTO_4571 9-06-07: Product name and note fields changed
Product name changed from "hypothetical protein" to "binary cytotoxin component, putative". Note field changed to /note="similar to GP:80558283; identified by sequence similarity; putative"
M. Lindeberg
Cornell University
Based on literature review
164 PSPTO_4287 9-06-07: Product name and note fields changed
Product name changed from "hypothetical protein" to "binary cytotoxin component, putative". Note field changed to /note="similar to GP:80558284; identified by sequence similarity; putative"
M. Lindeberg
Cornell University
Based on literature review
163 PSPTO_5625 9-06-07: Gene and CDS features added
gene           
4827116..4828336
/locus_tag="PSPTO_5625"
CDS            
4827116..4828336
/locus_tag="PSPTO_5625"
/note="similar to GP:80558283; identified by sequence similarity; putative"
/codon_start=1
/transl_table=11
/product="binary cytotoxin component, putative"
/protein_id=""
/db_xref=""                     /translation="MLSQAALLENEDIARVTLKPVEYLSVILDDEKNGGRSAALILTREDILSLKRYERHALNI
PTSLPRVEQQLGFTKSGIPGLEPKDMLVTYQAINNHGKSWLGIEDGIKRSGFAIDLFAAQ
FSGQGQQIINYIEKMDFARQLDLTVADLTIEEVREKNPTPLGETDQKVCITLAAFLKKTA
SQIKNHQHAAGTLAQHIDTFSTVLSVQLIPGINDKVKLARRSGLDQQLKELEKDIEQLTK
EIEQKNKEYKFSMNNIAWGGFGGPIGVAITGGIFGAKAEKIRKEKNRMVDSKNQKVQTLK
EKVPLAAAVRSLQILFEDMNIRMMDAHQSATHLKDLWTMLAAYIDSSANELAAITDDQAL
MIFAMQFQGVVTPWLEIRGMTTQLLKIFDSALDQFQREQQPVVVVGR"
M. Lindeberg
Cornell University
Based on literature review
162 PSPTO_5626 9-06-07: Gene feature added
gene
5356088..5356525
/locus_tag="PSPTO_5626"
/note="this region is disrupted by an IS element insertion, interruption-N; this region is similar to the N-terminal region of a transposase protein; identified by sequence similarity; putative"

M. Lindeberg
Cornell University
161 PSPTO_5627 9-06-07: Gene feature added
gene
5358542..5359036
/locus_tag="PSPTO_5627"
/note="this region is disrupted by an IS element insertion, interruption-C; this region is similar to the C-terminal region of a transposase protein; identified by sequence similarity; putative"
/pseudo
M. Lindeberg
Cornell University
160 PSPTO_5628 9-06-07: Gene feature added
gene
5359162..5359782
/locus_tag="PSPTO_5628"
/note="This gene is disrupted by two IS element insertions; HopH protein, interruption-C; identified by sequence similarity; putative"
/pseudo
M. Lindeberg
Cornell University
159 PSPTO_5623

9-06-07: Coordinates and note field changed
gene          
5355978..5356022
/locus_tag="PSPTO_5623"
/note="This region contains an authentic frame shift and is not the result of a sequencing artifact; This gene is disrupted by an IS element insertion.; HopH protein, interruption-N; identified by sequence similarity; putative"
/pseudo


M. Lindeberg
Cornell University
158 PSPTO_5629 9-06-07: Gene and CDS features added
5334154..5335002
/locus_tag="PSPTO_5629"
CDS
complement(5328266..5329000)
/locus_tag="PSPTO_5629"
/note="residues 1-118 show similarity to ISPs1 OrfA and 84-237 to ISPsy13 OrfB; identified by sequence
similarity; putative"
/codon_start=1
/transl_table=11
/product="insertion sequence, putative"
M. Lindeberg
Cornell University
157 PSPTO_5630

9-06-07: Gene and CDS features added
gene
191660..192508
/locus_tag="PSPTO_5630"
CDS
191660..192508
/locus_tag="PSPTO_5630"
/note="similar to gb:AAO55966; identified by sequence similarity; putative"
/codon_start=1
/transl_table=11
/product="hypothetical protein"

M. Lindeberg
Cornell University
156 PSPTO_5162 9-06-07: Gene name corrected
Gene name for PSPTO_5162 changed from MgoG to MdoG
N. Panopoulos
Univ of Crete
Heraklion, Greece
155 PSPTO_2157

12-13-06: Change in coordinates and assignment of gene and product name
gene            2367818..2369452
/gene="pvdP"
/locus_tag="PSPTO_2157"
/old_locus_tag=PSPTO2157
CDS             2367818..2369452
/gene="pvdP"
/locus_tag="PSPTO_2157"
/note="similar to SP:Q9I188; identified
by sequence similarity; putative"
/codon_start=1
/transl_table=11
product="PvdP; Tat (twin-arginine translocation) pathway signal
sequence domain protein"
/protein_id="AAO53621.1"
/db_xref="GI:28850541"
/translation="MTISRRGFMAGLALTGAALPAAYYAHRELTRVEEPVTPGEATAGPADTATQR
LADKLRGVWTLRFEGRDAGLSGAPLQGLEMFLDIAPRGRGLRGYIDTAEQLRGEGMPRFR
VIGDLQPNAAKLYLRVMDGHAGNDPHSDTPDYEFSLTLDEVWGAFGNAGSGTLSGRVERL
DRPLALPELENRLIAIKQVFPEARERVALSPPFLAWLVSREHRLFHQLWHASRDKWHKLPE
DKRDARGIGWQPGPRDKERDARGPRKDRNGSGEDFFYMHRHMLIQARKIQDLPSWPRF
PLPQPEERDRLGFARYFDNHDGCALPPNWLAQGDEEYTQLVSDIKSHETYHTHFEVWES
QYRDPLSKLTLGQFGSQVELELHDWLHMRWASVARDPANGQPVPMARRSDDFAERWFE
PENDFDPFSSHVNPVFWMFHGWIDDRIDDWFRAHERFHPGEVKRLDVNGVPWFAPGRW
VEVSDPWLGPETHGCSTVPGQTAGTTMEMDPEVMKLALRITFAADDKLSNLLRRVPRRPW
YARNLLPERWF"


B. Swingle
USDA-ARS
154 PSPTO_1389 12-8-06: Coordinates corrected
Coordinates for hrcC changed from 1529049..1530989 to 1528890..1530989. Translated product adjusted accordingly
M. Lindeberg
Cornell University
153 PSPTO_0827

11-21-06: CDS feature added and pseudogene designation removed
/product="ribosomal large subunit pseudouridine synthase D"

G. Preston
Oxford University
152 PSPTO_3817 11-21-06: CDS feature added and pseudogene designation removed
/product="tRNA pseudouridine synthase A"
G. Preston
Oxford University
151 PSPTO_3840 11-21-06: CDS feature added and pseudogene designation removed
/product="ribosomal large subunit pseudouridine synthase C"
G. Preston
Oxford University
150 PSPTO_3875 11-21-06: CDS feature added and pseudogene designation removed
/product="ribosomal large subunit pseudouridine synthase A"
G. Preston
Oxford University
149 PSPTO_4247 11-21-06: CDS feature added and pseudogene designation removed
/product="ribosomal small subunit pseudouridine synthase A"
G. Preston
Oxford University
148 PSPTO_4488 11-21-06: CDS feature added and pseudogene designation removed
/product="tRNA pseudouridine synthase B"
G. Preston
Oxford University
147 PSPTO_0473 9-22-06: Change in feature designation
misc_feature changed to gene with name "hopAS1" and /pseudo field added

M. Lindeberg
Cornell University
146 PSPTO_0474 9-22-06: Expanded note field
/note="This region contains an authentic point mutation causing a premature stop and is not the result of a sequencing artifact; identified by sequence similarity to the N-terminal regions of HopAS1 in Pseudomonas syringae phaseolicola; previously known as ORF01152 (PMID 11854524; Fouts et al, 2002)”
M. Lindeberg
Cornell University
145 PSPTO_0904 9-22-06: CDS feature removed
M. Lindeberg
Cornell University
144 PSPTO_0904 9-22-06: Expanded note field for gene feature and addition of pseudo field
/note="This region is disrupted by an IS element insertion, interruption-C; region is similar to the C-terminal region of HopAG1 in Pseudomonas syringae pv syringae; identified by match to PFAM protein family HMM PF00293"

M. Lindeberg
Cornell University
143 PSPTO_4591 9-22-06: Change in feature designation
misc_feature changed to gene with name "hopO1-3" and /pseudo field added
M. Lindeberg
Cornell University
142 PSPTO_4597 9-22-06: Expanded note field
/note="Previously known as holPtoZ (PMID 11872842; Guttman et al, 2002), HopPtoS4 (PMID 14702323; Schechter, 2004) ORF26 (PMID 12032338; Petnicki-Ocwieja et al, 2002).;similar to GP:19071536; identified by sequence similarity; putative; possibly truncated by ISPssy insertion"

M. Lindeberg
Cornell University
141 PSPTO_4724 9-22-06: Gene name added
/gene="hopD"
M. Lindeberg
Cornell University
140 PSPTO_4724

9-22-06: New CDS feature
5350102..5350647
/gene="hopD"
/locus_tag="PSPTO_4724"
/note="This region contains an authentic frame shift and is not the result of a sequencing artifact; This gene is disrupted by an IS element insertion.; HopD protein, interruption-N; previously known as HopPtoD-related; similar to GP:11322461; identified by sequence similarity; putative"
/codon_start=1 /transl_table=11
/product="type III effector HopD"
/protein_id="ABI93937.1"
/db_xref="GI:115313959"
/translation="MNPLQSTQHSITTPLISGGRPLDAVGPQAQQSHPKRISPSQLSP GAHQALKRPSANAEHQRIASLVRNALQDGTLQFQSSNDKQVTYKAPVCLPADTSTDTD TDTVRTERLINNELTVQARLNDQSEYDIVSAHLHGSSRSISFDVPSPPPAHGSASSAL SERTHLGRRCKNSQLSPPLAH"

M. Lindeberg
Cornell University
139 PSPTO_4726 9-22-06: Addition of /pseudo field M. Lindeberg
Cornell University
138 PSPTO_1383 9-22-06: Nomenclature
Gene name changed to "hrpB", product name changed to "type III secretion protein HrpB"
M. Lindeberg
Cornell University
137 PSPTO_1376 9-22-06: Nomenclature
Gene name changed from "avrF" to "ShcE", product name changed from "type III chaperone AvrF" to "type III chaperone ShcE"
M. Lindeberg
Cornell University
136 PSPTO_1369 9-22-06: Geneand product name added
/gene="shcN", /product="type III chaperone protein ShcN"
M. Lindeberg
Cornell University
135 PSPTO_4993 9-22-06: Expanded note field
/note="This gene is disrupted by an IS element insertion, interruption-N; known as holPtoAC (PMID 12615215; Greenberg and Vinatzer, 2003) or HopAC (PMID 15828679;Lindeberg et al, 2005); not a type III effector"
M. Lindeberg
Cornell University
134 PSPTO_4996 9-22-06: Expanded note field
/note="This gene is disrupted by an IS element insertion, interruption-C; previously known as holPtoAC (PMID 12615215; Greenberg and Vinatzer, 2003) or HopAC (PMID 15828679; Lindeberg et al, 2005); not a type III effector"
M. Lindeberg
Cornell University
133 PSPTO_1569 8-18-06: Gene and CDS features deleted M. Lindeberg
Cornell University
132 PSPTO_4598 8-18-06 Gene and CDS features deleted M. Lindeberg
Cornell University
131 PSPTO_5623 8-18-06: Gene and CDS features added
misc_feature    5355978..5356064
                 /locus_tag="PSPTO_5623"
                 /note="This region contains an authentic frame shift and
                 is not the result of a sequencing artifact; This gene is
                 disrupted by an IS element insertion.; HopH protein,
                 interruption-N; identified by sequence similarity;
                 putative"
M. Lindeberg
Cornell University
130   8-8-06: Promoter feature added
promoter 1542129..1542182
/experiment="gel-shift assay"
/note="putative CorR binding site; identified by gel-shift assays
and sequence alignment; downstream gene(s) exhibit CorR-dependent
diffential expression; PMID: 16838789"
A. Sreedharen
Oklahoma State University
129   8-8-06: Promoter feature added
promoter 5330722..5330777
/note="putative CorR binding site; identified by
sequence alignment; downstream gene(s) exhibit CorR-dependent
diffential expression; PMID: 16838789"
A. Sreedharen
Oklahoma State University
128 PSPTO4732 8-8-06: Nomenclature
Gene name changed from "holQ1-2" to "hopQ1-2"
M. Lindeberg
Cornell University
127 PSPTO1376 8-8-06: Product name changed
Product name changed from "avirulence protein AvrF" to "Type III chaperone AvrF"
M. Lindeberg
Cornell University
126 PSPTO1374 5-06: Gene and product name added
Gene name "shcM" added. Product name changed from "conserved effector locus protein" to "type III chaperone ShcM"

M. Lindeberg
Cornell University

125 PSPTO4721 5-06: Gene and product name added
Gene name "shcV" added. Product name changed from "hypothetical protein" to "type III chaperone ShcV"

M. Lindeberg
Cornell University

124 PSPTO3576

5-06: Gene, product name, and functional information added
Gene name "tvrR" added. Product name changed from "transcriptional regulator, TetR family" to "TetR-like virulence regulator".

”mutations exhibit reduced disease symptoms and growth in planta; PMID 16267304 added to note qualifier

M. Lindeberg
Cornell University
Based on literature review

123 PSPTO5157

5-06: Functional information added

"mutations exhibit reduced virulence; PMID 16321949" added to note qualifier
M. Lindeberg
Cornell University
Based on literature review
122 PSPTO32923-06: Gene and product name added
Gene name "hopAH2-1" added. Product name changed from "hypothetical protein" to "type III effector HopAH2-1"
Reference (PMID: 17073301)
Lisa Schechter
University of Missouri, St. Louis
121 PSPTO32933-06: Gene and product name added
Gene name "hopAH2-2" added. Product name changed from "hypothetical protein" to "type III effector HopAH2-2"
Reference (PMID: 17073301)
Lisa Schechter
University of Missouri, St. Louis
120 PSPTO45893-06: Gene and product name added
Gene name "shcS2" added. Product name changed from "hypothetical protein" to "type III chaperone ShcS2"
Reference (PMID: 17073301)

M. Lindeberg
Cornell University
Based on literature review

119 PSPTO45993-06: Gene and product name added
Gene name "shcS1" added. Product name changed from "hypothetical protein" to "type III chaperone ShcS1"
Reference (PMID: 17073301)
M. Lindeberg
Cornell University
Based on literature review
118 PSPTO04733-06: Gene and CDS features replaced with misc_feature
Gene and CDS features for this locus were deleted and replaced with:

misc_feature complement(518079..521327)
/note="PSPTO0473; this region contains an authentic point
mutation causing a premature stop and is not the result of
a sequencing artifact; identified by similarity to the
C-terminal regions of HopAS1 in Pseudomonas syringae phaseolicola"

M. Lindeberg
Cornell University
117 PSPTO56163-06: Gene and CDS features added
gene
complement(522206..522316)
/locus_tag="PSPTO_5616"
CDS
complement(522206..522316)
/locus_tag="PSPTO_5616"
/note="similar to gene downstream of PSPPH4735"
/codon_start=1
/transl_table=11
/product="conserved hypothetical protein"
/protein_id="ABD93120.1"
/db_xref="GI:90295593"
/translation="MPPRQFEEVSPSAATALRTRFTHHRMRSVDYYHHLY"
D. Schneider,
USDA-ARS
116 PSPTO5618

3-06: Gene feature added
gene
complement(922509..922756)
/gene="hopAT1"
/locus_tag="PSPTO_5618"
/note="type III effector protein hopAT1; this region contains premature stop codons or frameshifts;
identified by sequence similarity, degenerate; similar to PSPPH_5225
(GI:76008346)"
/pseudo

D. Schneider,
USDA-ARS
115 PSPTO5621 3-06: Gene and CDS features added
gene
923360..923584
/locus_tag="PSPTO_5621"
/note="conserved hypothetical gene; identified by sequence
similarity"
CDS
923360..923584
/locus_tag="PSPTO_5621"
/note="identified by sequence similarity; N-terminus similar to carbon storage regulator proteins"
/codon_start=1
/transl_table=11
/product="PSPTO5621"
/protein_id="ABD93121.1"
/db_xref="GI:90295594"
/translation="MLLLTRREGENIVIGDGIQIQVLSVSEDTGDVRIQIEAPDVVEAQGRTAGNEVTDH
KPGPVITHKRRWRSLVTQ"
D. Schneider,
USDA-ARS
114 PSPTO5617 3-06: Gene feature added
gene
complement(938980..939307)
/locus_tag="PSPTO_5617"
/note="This region contains a gene with one or more premature stops or frameshifts;
conserved hypothetical gene; similar to GI:63255405, GI:68637911"
/pseudo
D. Schneider,
USDA-ARS
113 PSPTO5619 3-06: Gene and CDS features added
gene
981249..981500
/locus_tag="PSPTO_5619"
/note="hypothetical gene; identified by sequence
similarity"
CDS
981249..981500
/locus_tag="PSPTO_5619"
/note="identified by sequence similarity"
/codon_start=1
/transl_table=11
/product="PSPTO5619"
/protein_id="ABD93122.1"
/db_xref="GI:90295595"
/translation="MDYLESIISSAYWQYLVRSGNWLLILSCLLSPSVIQDSAEPESG
YVPREYRLTAVGPDNYHDACNAKDENSSRAPRRTRRSAQ"
D. Schneider,
USDA-ARS
112 PSPTO5622 3-06: Gene and CDS features added
gene
1548470..1548718
/locus_tag="PSPTO_5622"
/note="conserved gene; similar to PSTO_B0005.1"
CDS
1548470..1548718
/locus_tag="PSPTO_5622"
/note="similar to PSPTO_B005.1"
/codon_start=1
/transl_table=11
/product="PSPTO5622"
/protein_id="ABD93123.1"
/db_xref="GI:90295596"
/translation="MKLKDICSKTKFIALASFAVLSLQMPLVHADGGAQLSGAQGQGS
AALNSGSGQGGTAQSGSQSGSRDSSTCCTPTACITPCP"
D. Schneider,
USDA-ARS
111 PSPTO5620 3-06: Gene and CDS features added
gene
complement(1731272..1731397)
/locus_tag="PSPTO_5620"
/note="identified by sequence similarity"
CDS
complement(1731272..1731397)
/locus_tag="PSPTO_5620"
/note="identified by sequence similarity"
/codon_start=1
/transl_table=11
/product="PSPTO5620"
/protein_id="ABD93124.1"
/db_xref="GI:90295597"
/translation="MRVSNCSAPVIKHTIRTCAAHSTLSSVAIEIQVSHHKRKAN"
D. Schneider,
USDA-ARS
110 PSPTO05903-06: Gene and CDS features deletedD. Schneider,
USDA-AR
109 PSPTO08703-06: Gene and CDS features deletedD. Schneider,
USDA-AR
108 PSPTO15693-06: Gene and CDS features deletedD. Schneider,
USDA-AR
107 PSPTO45983-06: Gene and CDS features deletedD. Schneider,
USDA-AR
A tabular listing of the all hrp promoters added to the Pto DC3000 Genbank annotation can be viewed here
106  3-06: Promoter feature added
promoter complement(61504..61536)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
105  3-06: Promoter feature added
promoter 82447..82478
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
104  3-06: Promoter feature added
promoter 404752..404784
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
103  3-06: Promoter feature added
promoter complement(522444..522475)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
102  3-06: Promoter feature added
promoter complement(550602..550634)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
101  3-06: Promoter feature added
promoter 572473..572504
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
100  3-06: Promoter feature added
promoter complement(648424..648456)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
99  3-06: Promoter feature added
promoter complement(649735..649766)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
98  3-06: Promoter feature added
promoter 905339..905371
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
97  3-06: Promoter feature added
promoter complement(921879..921911)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
96  3-06: Promoter feature added
promoter complement(939413..939445)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
95  3-06: Promoter feature added
promoter 941100..941132
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
94  3-06: Promoter feature added
promoter 946154..946185
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
93  3-06: Promoter feature added
promoter complement(949826..949858)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
92  3-06: Promoter feature added
promoter 954203..954234
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
91  3-06: Promoter feature added
promoter 981177..981208
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
90  3-06: Promoter feature added
promoter complement(1116378..1116410)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
89  3-06: Promoter feature added
promoter 1504886..1504917
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
88  3-06: Promoter feature added
promoter 1505219..1505251
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
87  3-06: Promoter feature added
promoter 1507652..1507684
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
86  3-06: Promoter feature added
promoter complement(1510785..1510816)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
85  3-06: Promoter feature added
promoter 1510881..1510913
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
84  3-06: Promoter feature added
promoter complement(1519570..1519601)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
83  3-06: Promoter feature added
promoter 1519666..1519697
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
82  3-06: Promoter feature added
promoter 1524204..1524236
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
81  3-06: Promoter feature added
promoter 1528184..1528216
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
80  3-06: Promoter feature added
promoter complement(1536874..1536905)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
79  3-06: Promoter feature added
promoter complement(1542621..1542653)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
78  3-06: Promoter feature added
promoter 1543416..1543447
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
77  3-06: Promoter feature added
promoter 1548389..1548420
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
76  3-06: Promoter feature added
promoter complement(1731421..1731453)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
75  3-06: Promoter feature added
promoter 2279883..2279915
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
74  3-06: Promoter feature added
promoter 2973825..2973856
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
73  3-06: Promoter feature added
promoter complement(3470185..3470217)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
72  3-06: Promoter feature added
promoter complement(3939658..3939690)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
71  3-06: Promoter feature added
promoter complement(4515296..4515328)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
70  3-06: Promoter feature added
promoter 4621129..4621160
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
69  3-06: Promoter feature added
promoter 4881097..4881129
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
68  3-06: Promoter feature added
promoter complement(5186123..5186154)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
67  3-06: Promoter feature added
promoter complement(5192613..5192644)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
66  3-06: Promoter feature added
promoter 5305220..5305252
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
65  3-06: Promoter feature added
promoter 5330688..5330720
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
64  3-06: Promoter feature added
promoter complement(5344375..5344407)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
63  3-06: Promoter feature added
promoter complement(5348578..5348610)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
62  3-06: Promoter feature added
promoter 5350034..5350065
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
61  3-06: Promoter feature added
promoter complement(5355224..5355256)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
60  3-06: Promoter feature added
promoter 5355530..5355562
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
59  3-06: Promoter feature added
promoter complement(5361707..5361739)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
58  3-06: Promoter feature added
promoter complement(5418197..5418228)
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
57  3-06: Promoter feature added
promoter 6085756..6085788
/experiment="microarray and/or RT-PCR"
/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans; downstream gene(s) exhibit HrpL-dependent
diffential expression"
Reference (PMID: 17073300)
D. Schneider,
USDA-ARS
56 all tRNA loci11-05: product names added
A qualifier in the format: /product="[name]" has been added to all tRNA features in the annotation
Genbank
55 PSPTO3914

11-05: Gene name added
Gene name "copA" added. Based on experimental evidence in Pto DC3000

P. Bronstein, M. Lindeberg, Cornell University
54 PSPTO3648

11-05: Gene name added
Gene name "plcA1" added. Based on experimental evidence in Pto DC3000

P. Bronstein, M. Lindeberg, Cornell University
53 PSPTO1377

3-05: Nomenclature
Gene name changed from "avrE(Pto)" to "avrE1". Product name changed from "avirulence protein AvrE(Pto)" to "type III effector protein AvrE1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
52
PSPTO4001

3-05: Nomenclature
Gene name changed from "avrPto(DC3000)" to "avrPto1". Product name changed from "avirulence protein AvrPto(DC3000)" to "type III effector protein AvrPto1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
51
PSPTO5354

3-05: Nomenclature
Gene name changed from "hopPsyA(Pto)" to "hopA1". Product name changed from "type III effector HopPsyA(Pto)" to "type III effector HopA1"
Note changed to: "previously known as HrmA (PMID 8274770; Heu and Hutcheson, 1993) and HopPsyA (PMID 11854524; Fouts et al, 2002); similar to SP:Q08370, GB:L05500, SP:Q08828, and PID:349269; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
50
PSPTO1406

3-05: Nomenclature
Gene name changed from "hopPtoB1" to "hopB1". Product name changed from "type III effector HopPtoB1" to "type III effector HopB1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
49
PSPTO0589

3-05: Nomenclature
Gene name changed from "hopPtoC" to "hopC1". Product name changed from "type III effector HopPtoC" to "type III effector HopC1"
Note changed to: "previously known as HopPtoC (PMID 12032338; Petnicki-Ocwieja et al, 2002).. Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
48
PSPTO0876

3-05: Nomenclature
Gene name changed from "hopPtoD1" to "hopD1". Product name changed from "type III effector HopPtoD1" to "type III effector HopD1"
Note changed to: "previously known as HopPtoD1 (PMID 12032338; Petnicki-Ocwieja et al, 2002); similar to GP:14905934; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
47
PSPTO4724

3-05: Nomenclature
Note changed to: "This region contains an authentic frame shift and is not the result of a sequencing artifact; This gene is disrupted by an IS element insertion.; HopD protein, interruption-N; previously known as HopPtoD-related; similar to GP:11322461; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
46
PSPTO4726

3-05: Nomenclature
Note changed to: "This region contains an authentic frame shift and is not the result of a sequencing artifact; This gene is disrupted by an IS element insertion.; HopD protein, interruption-C; similar to GP:14905934; previously known as HopPtoD-related; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
45
PSPTO4331

3-05: Nomenclature
Gene name changed from "hopPtoE" to "hopE1". Product name changed from "type III effector HopPtoE" to "type III effector HopE1"
Note changed to: "previously known as HolPtoV (PMID 11872842; Guttman et
al, 2002) and HopPtoE (PMID 12032338; Petnicki-Ocwieja et al, 2002)." Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
44
PSPTO0502

3-05: Nomenclature
Gene name changed from "hopPtoF" to "hopF2". Product name changed from "type III effector HopPtoF" to "type III effector HopF2"
Note changed to: "This gene has an isoleucine start. Previously known as HolPtoAD (PMID 11872842; Guttman et al, 2002) and HopPtoF (PMID 11854524; Fouts et al, 2002); similar to GP:7677395; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
43
PSPTO4727

3-05: Nomenclature
Gene name changed from "hopPtoG" to "hopG1". Product name changed from "type III effector HopPtoG" to "type III effector HopG1"
Note changed to: "Previously known as HolPtoW (PMID 11872842; Guttman et
al, 2002) and HopPtoG (PMID 12032338; Petnicki-Ocwieja et al, 2002).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
42
PSPTO0588

3-05: Nomenclature
Gene name changed from "hopPtoH" to "hopH1". Product name changed from "type III effector HopPtoH" to "type III effector HopH1"
Note added: "Previously known as HopPtoH (PMID 12032338; Petnicki-Ocwieja et al, 2002).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
41
PSPTO4691

3-05: Nomenclature
Gene name changed from "hopPtoI" to "hopAD1". Product name changed from "type III effector HopPtoI" to "type III effector HopAD1"
Note changed to: "Previously known as and HolPtoS (PMID 11872842; Guttman et al, 2002) and HopPtoI (PMID 12032338; Petnicki-Ocwieja et al, 2002); identified by match to PFAM protein family HMM PF02918". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
40
PSPTO1568

3-05: Nomenclature
Gene name changed from "hopPtoJ" to "hopAF1". Product name changed from "type III effector HopPtoJ" to "type III effector HopAF1"
Note added: "Previously known as HolPtoN (PMID 11872842; Guttman et
al, 2002) and HopPToJ (PMID 12032338; Petnicki-Ocwieja et al, 2002)" . Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
39
PSPTO0044

3-05: Nomenclature
Gene name changed from "hopPtoK" to "hopK1". Product name changed from "type III effector HopPtoK" to "type III effector HopK1"
Note changed to: "Previously known as HopPtoK (PMID 12032338; Petnicki-Ocwieja et al, 2002) and HolPtoAB (PMID 11872842; Guttman et al, 2002); similar to GP:1008894; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
38
PSPTO2872

3-05: Nomenclature
Gene name changed from "hopPtoL" to "hopL1". Product name changed from "type III effector HopPtoL" to "type III effector HopL1"
Note added: "Previously known as HopPtoL (PMID 12032338; Petnicki-Ocwieja et al, 2002)". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
37
PSPTO1375

3-05: Nomenclature
Gene name changed from "hopPtoM" to "hopM1". Product name changed from "type III effector HopPtoM" to "type III effector HopM1"
Note changed to: "Previously known as CEL ORF3 (PMID 10781092; Alfano et
al, 2000), HolPtoX (PMID 11872842; Guttman et al,
2002), HopPtoM (PMID 12940984; Badel et al, 2003); similar to GP:8037794; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
36
PSPTO1370

3-05: Nomenclature
Gene name changed from "hopPtoN" to "hopN1". Product name changed from "type III effector HopPtoN" to "type III effector HopN1".
Note changed to: "Previously known as CEL ORF7 (PMID 10781092; Alfano et
al, 2000), HolPtoT (PMID 11872842; Guttman et al,
2002), and HopPtoN (PMID 15469508; Lopez-Solanilla, et al, 2004); identified by match to TIGR protein family HMM TIGR01586". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
35
PSPTO4592

3-05: Nomenclature
Gene name added: "hopO1-3"
Product name changed from "HopPtoO-related protein" to "type III effector HopO1-3"
Note added: "This region contains an authentic point mutation causing a premature stop and is not the result of a sequencing artifact; identified by similarity to the N-terminal regions of HopO1-1 and HopO1-2. ". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
34
PSPTO4591

3-05: Nomenclature
Region designated as: "misc_feature"
Note added: "This region contains an authentic point mutation causing a premature stop and is not the result of a sequencing artifact; identified by similarity to the C-terminal regions of HopO1-1 and HopO1-2. ". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
33
PSPTO4594

3-05: Nomenclature
Gene name changed from "hopPtoS3" to "hopO1-2". Product name changed from "type III effector HopPtoS3" to "type III effector HopO1-2"
Note changed to: "Previously known as HopPtoO2 (PMID 11872842; Guttman et
al, 2002) and HopPtoS3 (PMID 12032338; Petnicki-Ocwieja et al, 2002); identified by match to PFAM protein family HMM PF03496". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
32
PSPTO2678

3-05: Nomenclature
Gene name changed from "hopPtoP" to "hopP1". Product name changed from "type III effector HopPtoP" to "type III effector HopP1"
Note changed to: "previously known as HopPtoP (PMID 11872842; Guttman et
al, 2002) and HrpW-related (PMID 11854524; Fouts et al, 2002); similar to GP:3694999; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
31
PSPTO0877

3-05: Nomenclature
Gene name added: "hopQ1-1"
Product name changed from "candidate type III effector HolPtoQ" to " type III effector HopQ1-1"
Note changed to: "previously known as ORF19 (PMID 12032338;
Petnicki-Ocwieja et al, 2002) and HolPtoQ (PMID 11872842; Guttman et al, 2002); similar to GP:17427254,and GP:19071520; identified by sequence similarity;putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
30
PSPTO4732

3-05: Nomenclature
Gene name added: "hopQ1-2"
Product name changed from "HolPtoQ-like protein" to "type III effector HopQ1-2"
Note added: "previously known as HolPtoQ2 (PMID 12615215; Greenberg and Vinatzer, 2003) and HolPtoQ-like (PMID 12928499; Buell et al, 2003)". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
29
PSPTO0883

3-05: Nomenclature
Gene name changed from "hopPtoR" to "hopR1". Product name changed from "type III effector HopPtoR" to "type III effector HopR1"
Note changed to: "Previously known as HolPtoR; similar to GP:17431754, and GP:19071522; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
28
PSPTO4597

3-05: Nomenclature
Gene name added: "hopS1"
Product name changed from "candidate type III effector HolPtoZ" to "type III effector HopS1"
Note changed to: "Previously known as holPtoZ (PMID 11872842; Guttman et
al, 2002), HopPtoS4 (PMID 14702323; Schechter, 2004), ORF26 (PMID 12032338; Petnicki-Ocwieja et al, 2002).; similar to GP:19071536;identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
27
PSPTO4588

3-05: Nomenclature
Gene name added: "hopS2"
Product name changed from "candidate type III effector Hop protein" to "type III effector HopS2"
Note changed to: "Previously known as ORF15 (PMID: 12032338
Petnicki-Ocwieja et al 2002) and HolPtoZ2 (PMID 12615215; Greenberg and Vinatzer, 2003).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
26
PSPTO4593

3-05: Nomenclature
Gene name changed from "holPtoU2" to "hopT1-2". Product name changed from "type III effector HolPtoU2" to "type III effector HopT1-2"
Note changed to: "Previously known as HolPtoU2 (PMID 11872842; Guttman et
al, 2002); similar to GP:19071528; identified by sequence
similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
25
PSPTO4590

3-05: Nomenclature
Gene name added: "hopT2"
Product name changed from ="HolPtoU-related protein" to ="type III effector HopT2"
Note changed to: "previously known as HolPtoU3 and HolPtoU-related (PMID 12615215; Greenberg and Vinatzer, 2003); similar to GP:19071526, and GP:19071526; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
24
PSPTO0501

3-05: Nomenclature
Gene name changed from "hopPtoS2" to "hopU1". Product name changed from "type III effector HopPtoS2" to "type III effector HopU1"
Note added: "previously known as HopPtoS2 (PMID 12032338; Petnicki-Ocwieja et al, 2002)". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
23
PSPTO4720

3-05: Nomenclature
Gene name added: "hopV1"
Product name changed from "hypothetical protein" to "type III effector HopV1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
22
PSPTO0061

3-05: Nomenclature
Gene name added: "hopY1"
Product name changed from "candidate type III helper HolPtoY" to "type III effector HopY1"
Note changed to: "Previously known as HolPtoY (PMID 11872842; Guttman et
al, 2002) and ORF11 (PMID 11854524; Fouts et al,
2002).; similar to GP:19071534; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
21
PSPTO1372

3-05: Nomenclature
Gene name changed from "hopPtoA1" to "hopAA1-1". Product name changed from "type III effector hopPtoA1" to "type III effector hopAA1-1"
Note changed to: "previously known as HopPtoA1 (PMID 12437299; Badel et al,2002) and CEL ORF5 (PMID 10781092; Alfano et al, 2000); identified by match to PFAM protein family HMM PF02987". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
20
PSPTO4718

3-05: Nomenclature
Gene name changed from "hopPtoA2" to "hopAA1-2". Product name changed from "type III effector hopPtoA2" to "type III effector hopAA1-2"
Note changed to: "previously known as HopPtoA2 (PMID 12437299; Badel et al,2002); identified by match to PFAM protein family HMM PF02987". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
19
PSPTO3087

3-05: Nomenclature
Gene name changed from "avrPtoB" to "hopAB2". Product name changed from "avirulence protein AvrPtoB" to "type III effector HopAB2"
Note added: "also known as AvrPtoB". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
18
PSPTO4691

3-05: Nomenclature
Gene name changed from "hopPtoI" to "hopAD1". Product name changed from "type III effector HopPtoI" to "type III effector HopAD1"
Note changed to: "Previously known as HolPtoS (PMID 11872842; Guttman et
al, 2002).; HopPtoI; (PMID 12032338; Petnicki-Ocwieja et al, 2002).; identified by match to PFAM protein family HMM PF02918". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
17
PSPTO1568

3-05: Nomenclature
Gene name changed from "hopPtoJ" to "hopAF1". Product name changed from "type III effector HopPtoJ" to "type III effector HopAF1"
Note added: "Previously known as HolPtoN (PMID 11872842; Guttman et
al, 2002).; HopPtoJ; (PMID 12032338; Petnicki-Ocwieja et al, 2002).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
16
PSPTO0901

3-05: Nomenclature
Gene name added: "hopAG". Product name changed from "candidate type III effector Hop protein" to " type III effector HopAG"
Note changed to: "this region is disrupted by an IS element insertion, interruption-N; this region is similar to the N-terminal region of HopAG1 in Pseudomonas syringae syringae; previously known as ORF28 (PMID 12032338;Petnicki-Ocwieja et al, 2002).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
15
PSPTO0904

3-05: Nomenclature
Note changed to: "this region is disrupted by an IS element insertion, interruption-C; region is similar to the C-terminal region of HopAG1 in Pseudomonas syringae syringae; identified by match to PFAM protein family HMM PF00293". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
14
PSPTO0905

3-05: Nomenclature
Gene name added: "hopAH1". Product name changed from "glycosyl hydrolase, family 5" to "type III effector HopAH1"
Note added: "previously known as HolPtoAH (PMID 12615215; Greenberg and Vinatzer, 2003).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
13
PSPTO0906

3-05: Nomenclature
Gene name added: "hopAI1". Product name changed from "hypothetical protein" to "type III effector HopAI1"
Note changed to : "previously known as HolPtoAI (PMID 12615215; Greenberg and Vinatzer, 2003)". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
12
PSPTO0852

3-05: Nomenclature
Gene name added: "hopAJ1". Product name changed from "transglycosylase, putative" to "type III effector HopAJI1"
Note added: "previously known as hopPmaG (PMID 11872842; Guttman et al, 2002) ". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
11
PSPTO4817

3-05: Nomenclature
Gene name added: "hopAJ2". Product name changed from "transglycosylase, putative" to "type III effector HopAJI2". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
10
PSPTO4101

3-05: Nomenclature
Gene name changed from "hopPmaH(Pto)" to "hopAK1". Product name changed from "type III helper protein HopPmaH(Pto)" to "type III effector HopAK1"
Note changed to: "previously known as HopPmaH (PMID 11872842; Guttman et al, 2002); similar to GP:1783275, and GP:19071494; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
9
PSPTO1022

3-05: Nomenclature
Gene name changed from "avrPpiB1(Pto)" to "HopAM1-1". Product name changed from "avirulence protein AvrPpiB1(Pto)" to "type III effector HopM1-1"
Note changed to: "also known as avirulence protein AvrPpiB1; similar to GP:886702, and GP:886702; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
8
PSPTO5061

3-05: Nomenclature
Gene name added:"hopAN1". Product name changed from "candidate type III effector Hop protein" to " type III effector HopAN1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
7
PSPTO4722

3-05: Nomenclature
Gene name changed from "hopPtoD2" to ="hopAO1". Product name changed from "type III effector HopPtoD2" to "type III effector HopAO1"
Note changed to: "previously known as HopPtoD2 (PMID 12032338; Petnicki-Ocwieja et al, 2002); similar to GP:14994330; identified by sequence similarity; putative". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
6
PSPTO4703

3-05: Nomenclature
Gene name changed from "holPtoAA" to ="hopAQ1". Product name changed from "candidate type III effector HolPtoAA" to " type III effector HopAQ1"
Note added: "previously known as HopPtoAA (PMID 11872842; Guttman et al, 2002)". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
5
PSPTO0474

3-05: Nomenclature
Gene name added:"hopAS1". Product name changed from "hypothetical protein" to "type III effector HopAS1"
Note changed to: "previously known as OF01152" (PMID 11854524; Fouts et al, 2002).". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
4
PSPTO1381

3-05: Nomenclature
Gene name changed from "hrpA(Pto)" to ="hrpA1". Product name changed from "type III helper protein HrpA(Pto)" to "type III helper protein HrpA1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
3
PSPTO1405

3-05: Nomenclature
Gene name changed from "hrpK(Pto)" to ="hrpK1". Product name changed from "type III helper protein HrpK(Pto)" to "type III helper protein HrpK1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
2
PSPTO1373

3-05: Nomenclature
Gene name changed from "hrpW(Pto)" to ="hrpW1". Product name changed from "type III helper protein HrpW(Pto)" to "type III helper protein HrpW1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University
1
PSPTO1382

3-05: Nomenclature
Gene name changed from "hrpZ(Pto)" to ="hrpZ1". Product name changed from "type III helper protein HrpZ(Pto)" to "type III helper protein HrpZ1". Reference (PMID: 15828679)

M. Lindeberg,
Cornell University