Updates to the Psp 1448A chromosome sequence and annotation:

  Locus Date: Nature of change Source
14
PSPPH_1293 12-22-08: New product name
Product name changed to "type III secretion component protein HrpJ".
M. Lindeberg,
Cornell University
13
PSPPH_5227 12-22-08: New gene/CDS
Coordinates: 1494211..1494414. Gene name: "hrpT". Product name: "HrpT".
M. Lindeberg,
Cornell University
12
 

12-8-06: 84 promoter features added (view list of all promoters in tabular form)
(Feature properties based on data presented in PMID: 17073302 and PMID: 15701698)

Format for those promoters identified solely by bioinformatic approaches:

/note="hrp box; putative HrpL-dependent promoter; location identified by hidden Markov model and/or weight matrix scans (PMID: 17073302)”

Format for those promoters with experimental confirmation:

/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”
/experiment="RT-PCR (PMID: 17073302) and DFI screening (PMID: 15701698)"

(note that some /experiment fields are RT-PCR (PMID: 17073302) or DFI screening (PMID: 15701698) only)

M. Lindeberg,
Cornell University
(see literature cited)
11
PSPPH_2351 12-8-06: Coordinates corrected
Coordinates for hopV1 changed from complement(2725396..2727183) to complement(2725396..2727093) . Translated product adjusted accordingly
M. Lindeberg,
Cornell University
10
PSPPH1272 8-8-06: Nomenclature
Gene name changed from "hrpA1" to "hrpA2". Product name changed from "type III helper protein HrpA1" to "type III helper protein HrpA2" based on phylogenetic analysis of multiple HrpA sequences
M. Lindeberg,
Cornell University
9
PSPPH5226

6-21-06: New gene/CDS
Coordinates: complement(205082..205555). Product name: "HrpL-regulated protein".
Evidence reference (PubMed ID): 15701698

M. Lindeberg,
Cornell University (based on literature review).
8
all loci 11-05: change in locus tag format
Locus tag format for all loci has been changed from PSPTO#### to PSPTO_####
Genbank
7
all tRNA loci 11-05: product names added
A qualifier in the format: /product="[name]" has been added to all tRNA features in the annotation
Genbank
6
PSPPH1266 9-05: Nomenclature
Gene named changed from "hopM" to "hopM1"
M. Lindeberg,
Cornell University
5
PSPPH3028 9-05: Nomenclature
Gene named changed from "avrB4" to "avrB4-1". Product named changed from "AvrB4" to "AvrB4-1"
M. Lindeberg,
Cornell University
4
PSPPH0784 9-05: Nomenclature
Gene named added: "avrB4-2". Product named changed from "conserved hypothetical protein" to "type III effector AvrB4-2".
M. Lindeberg, Cornell University
3
PSPPH5225 9-05: New gene/CDS
Coordinates: complement(894856..895116). Gene name: "hopAT1". Product name: "type III effector HopAT1". New evidence reference (PubMed ID): 15701698
M. Lindeberg,
Cornell University (based on literature review).
2
PSPPH1525 9-05: Functional assignment
Product name changed from "shikimate kinase" to "hypothetical gene conserved among plant-associated proteobacteria".
D. Schneider, Cornell University
1
PSPPH0105 9-05: Functional assignment
Product name changed from "MloB" to "carbon storage regulator related".
D. Schneider, Cornell University