ViewGene

Locus Name:
GeneID:
Location:

GeneID:4903
TrivialName: PA14_36000
AnnotatorUID: ericdeziel
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_36000
PAO1 Ortholog Locus:
Sequence Length:1422
Protein Length:473
Start: 3204291
Stop: 3205712
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAK01495.1| (AF241171) propionate catabolism operon regulator prpR [Pseudomonas aeruginosa]
Identities = 469/473 (99%), Positives = 472/473 (99%) to gene #5 of PAGI-1 island.
Sequence:
CTGAGCGAAGACACTGCGCGCAAGGCGCTCGAGGAAGCCATGGGAGTCCTCGACAGCCAGCGCCTGGAGATC
GCCAAGCGGCGGCATCTGGACGCGGTGCTGCAACACATTCCAAGCGGTGTGGCAGCGGTCGACAACCAGGGT
GTGGTGCAATCGCTCAACCCTGCCCTTGCCCAGTTGCTGGAGTTGCCGGTCAGCTCGGCTCTGGGTCGACCG
TTACAGCAGCTATGCCCGGAGCTTGACCTGCAACAGGCGCTAGAGGATGGCGGTGGCGAGGAAAACCGGGTG
ATCCGGCTGGGCTCGCACGCCGTGGTCAGCAATCTCCTGCCGATCCTGGAGAATGGCGAGCGTACCGGCCTG
GTGCTCACCTGCCAGGACATCACCGCCGTGCAGCGCGCGGATCAACGCATCCGCTCCACTCGCCGTCCAGGT
GCCTTCACCGCGCGTTACCGGCTCGAACAACTCAACGGCGCGAGCAAGGCCAACCGTGAGATGTTGCAGCTG
GCCAAGCGCTTTGCCGCCAGCCATTCGACCATCCTGATCACTGGCGAAAGCGGCACCGGCAAGGAACTGCTC
GCCCAAGGGATCCATAACGAGAGCCCTCGCCGGCACGGGCCTTTCGTCGCCATCAACTGCGCGGCGTTTCCC
GAGTCGCTACTGGAAAGCGAACTGTTCGGCTACGAGGAAGGGGCCTTCAGCGGTTCGCGCAAAGGCGGCAAG
CCCGGCCTGTTCGAGGCGGCGCACCGTGGCACGCTGTTCCTCGACGAGATCGGCGACATGCCTGTGTCGCTG
CAGACTCGCCTCCTTCGTGTATTGCAGGAGCGAGAGGTCTTGCGCCTGGGCGGCACCGAGCCGATCTCCATC
GACGTGCGCATCGTCGCCGCCACCCACAAGGACCTGGGGGGCGCCATGAAGGATCGCGAGTTTCGCACCGAC
CTGTATTACCGGCTGAATATCCTGCGCTTGCAGACCACGCCCCTGCGCGAGCGGCCCGAGGACATCCCTCTG
ATTTGCCAGGGAATCAGCCAGCGCCTGCTGGTCCAGGGCCAGCCACCGGGTTCCGCAGGCATAACGACGCTC
CTGCTACCCTACCTCGTCCGCCATTCCTGGCCCGGAAACGTCAGGGAACTGGAGAATGTCATCGAACGGGCG
ATGCTCTCCGCCAGCGAAATCTTCCATGAGCACGGCGTGGATGAGCATTACCTGGCTCGCGTGCTGCCCGAG
CTATTCGAAGGCCAGCCTCAGCCCAGGTCCCGGAAAGAGCCATCGCGCACAAAGGATTTGCACGCCATCGGC
AAAACCGCGCAGTTGCGCTACATACAGGAGACGCTGGACAGCTGCCAGGGCAGCCTTGACGAGGCTGCGCGT
CGGCTCGGGATCAGCCGGACCACGCTGTGGCGGCGGCTTCGTTCGGCACGCTGA
Translation:
MSEDTARKALEEAMGVLDSQRLEIAKRRHLDAVLQHIPSGVAAVDNQGVVQSLNPALAQLLELPVSSALGRP
LQQLCPELDLQQALEDGGGEENRVIRLGSHAVVSNLLPILENGERTGLVLTCQDITAVQRADQRIRSTRRPG
AFTARYRLEQLNGASKANREMLQLAKRFAASHSTILITGESGTGKELLAQGIHNESPRRHGPFVAINCAAFP
ESLLESELFGYEEGAFSGSRKGGKPGLFEAAHRGTLFLDEIGDMPVSLQTRLLRVLQEREVLRLGGTEPISI
DVRIVAATHKDLGGAMKDREFRTDLYYRLNILRLQTTPLRERPEDIPLICQGISQRLLVQGQPPGSAGITTL
LLPYLVRHSWPGNVRELENVIERAMLSASEIFHEHGVDEHYLARVLPELFEGQPQPRSRKEPSRTKDLHAIG
KTAQLRYIQETLDSCQGSLDEAARRLGISRTTLWRRLRSAR*
AnnotationID:4908GeneID:4903
AnnotatorUID: danlee
Modification Date/Time: 2005-10-11 15:03:46
Gene Name:PAGI-1(5)
Confidence Code:3
GeneProduct:Probable propionate catabolism operon regulator prpR
Cell Localization:()
Synonyms:prpR
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG3829
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:
Homology:
gi|12698381|gb|AAK01495.1|  propionate catabolism operon regulator prpR [Pseudomonas aeruginosa]
      Length=650
      Score =  921 bits (2381),  Expect = 0.0
      Identities = 469/473 (99%), Positives = 472/473 (99%), Gaps = 0/473 (0%)

gi|24984381|gb|AAN68398.1|  sigma-54 dependent sensory box protein [Pseudomonas putida KT2440]
     Length=650
     Score =  804 bits (2077),  Expect = 0.0
     Identities = 408/472 (86%), Positives = 440/472 (93%), Gaps = 0/472 (0%)

Structural Features:
COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains.
             CD-Length = 560 residues,  81.6% aligned
             Score =  397 bits (1021), Expect = 2e-111

COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains.
             CD-Length = 464 residues, only  73.5% aligned
             Score =  287 bits (735), Expect = 2e-78

COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains.
             CD-Length = 550 residues, only  61.3% aligned
             Score =  264 bits (676), Expect = 2e-71

COG3283, TyrR, Transcriptional regulator of aromatic amino acids metabolism.
             CD-Length = 511 residues,  87.9% aligned
             Score =  245 bits (627), Expect = 7e-66
Genomic Context:
Predicted gene #5 of the PAGI-1 island absent in PAO1 but present in a majority of pathogenic P. aeruginosa isolates.   
The PA14 island at this locus, from PA14_35860 to PA14_36030, corresponds to PAGI-1 genes 17 through 2, respectively.
Comment:
The first half of the PA14 island (from PA14_35700 through PA14_35850) diverges from PAGI-1 such that 
genes 18 through 51 are absent.  PA14 has 31 ORFs in 35368 bp (from PA14_35700 to PA14_36030), 
whereas PAGI-1 contains 51 ORFs in 51300 bp.
ReferenceID:15210
Author/Investigator(s): GenNotator
Title:
PubMed:
MedLine:
Source:
Reference Type:BLASTP
Data:
URL:
ReferenceID:26947
Author/Investigator(s): GenNotator
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:RPSBLAST
Data:
URL:
Homologs By Global Alignment
Gene ID:4903

Identity:

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
HomologID Accession Description Length PctIdentity PctSimilarity Gaps Score
189939 gb|AAK01495.1| (AF241171) propionate catabolism operon regulator prpR [Pseudomonas aeruginosa] 650 72.30 72.61 177 2383.0
189940 gb|AAN68398.1|AE016472_5 (AE016784) sigma-54 dependent sensory box protein [Pseudomonas putida KT2440] 650 62.92 67.69 177 2079.0
189988 gb|AAN69949.1|AE016633_7 (AE016790) response regulator FleR [Pseudomonas putida KT2440] 508 36.22 50.19 92 644.0
189949 gb|AAG54679.1|AE005212_4 (AE005212) regulator for prp operon [Escherichia coli O157:H7 EDL933] 562 35.05 48.39 123 713.0
189950 dbj|BAB33807.1| (AP002551) regulator for prp operon [Escherichia coli O157:H7] 562 35.05 48.39 123 713.0
GC ORFID: 47905How Found: BLASTX
GC_TrimmedSeqID: 69Blast Result ID
Subject Sequence Name: t_PA1097Glimmer Score:
Start: 1749625Stop: 1748204
Length: 1422
Start Codon: CTGTruncated Start:
Stop Codon: TGATruncated Stop:
Homolog: t_PA1097 translation of PA1097Homolog Bit Score 240.0
Other Homologs: t_PA2449 (ORF: BLASTX 239.0), t_PA1099 (ORF: BLASTX 238.0), psyr_15may02_Scaffold8_revised_gene7914 (ORF: BLASTX 233.0), t_PA1945 (ORF: BLASTX 229.0), t_PA2359 (ORF: BLASTX 222.0), t_PA4726 (ORF: BLASTX 218.0), t_PA1663 (ORF: BLASTX 211.0), psyr_15may02_Scaffold2_revised_gene4053 (ORF: BLASTX 209.0), t_PA2665 (ORF: BLASTX 208.0), t_PA5511 (ORF: BLASTX 204.0), t_PA5166 (ORF: BLASTX 202.0), t_PA1196 (ORF: BLASTX 196.0), psyr_15may02_Scaffold14_revised_gene2286 (ORF: BLASTX 194.0), t_PA1097 (ORF: GLIMMER)
GC ORF Sequence
CTGAGCGAAGACACTGCGCGCAAGGCGCTCGAGGAAGCCATGGGAGTCCTCGACAGCCAGCGCCTGGAGATC
GCCAAGCGGCGGCATCTGGACGCGGTGCTGCAACACATTCCAAGCGGTGTGGCAGCGGTCGACAACCAGGGT
GTGGTGCAATCGCTCAACCCTGCCCTTGCCCAGTTGCTGGAGTTGCCGGTCAGCTCGGCTCTGGGTCGACCG
TTACAGCAGCTATGCCCGGAGCTTGACCTGCAACAGGCGCTAGAGGATGGCGGTGGCGAGGAAAACCGGGTG
ATCCGGCTGGGCTCGCACGCCGTGGTCAGCAATCTCCTGCCGATCCTGGAGAATGGCGAGCGTACCGGCCTG
GTGCTCACCTGCCAGGACATCACCGCCGTGCAGCGCGCGGATCAACGCATCCGCTCCACTCGCCGTCCAGGT
GCCTTCACCGCGCGTTACCGGCTCGAACAACTCAACGGCGCGAGCAAGGCCAACCGTGAGATGTTGCAGCTG
GCCAAGCGCTTTGCCGCCAGCCATTCGACCATCCTGATCACTGGCGAAAGCGGCACCGGCAAGGAACTGCTC
GCCCAAGGGATCCATAACGAGAGCCCTCGCCGGCACGGGCCTTTCGTCGCCATCAACTGCGCGGCGTTTCCC
GAGTCGCTACTGGAAAGCGAACTGTTCGGCTACGAGGAAGGGGCCTTCAGCGGTTCGCGCAAAGGCGGCAAG
CCCGGCCTGTTCGAGGCGGCGCACCGTGGCACGCTGTTCCTCGACGAGATCGGCGACATGCCTGTGTCGCTG
CAGACTCGCCTCCTTCGTGTATTGCAGGAGCGAGAGGTCTTGCGCCTGGGCGGCACCGAGCCGATCTCCATC
GACGTGCGCATCGTCGCCGCCACCCACAAGGACCTGGGGGGCGCCATGAAGGATCGCGAGTTTCGCACCGAC
CTGTATTACCGGCTGAATATCCTGCGCTTGCAGACCACGCCCCTGCGCGAGCGGCCCGAGGACATCCCTCTG
ATTTGCCAGGGAATCAGCCAGCGCCTGCTGGTCCAGGGCCAGCCACCGGGTTCCGCAGGCATAACGACGCTC
CTGCTACCCTACCTCGTCCGCCATTCCTGGCCCGGAAACGTCAGGGAACTGGAGAATGTCATCGAACGGGCG
ATGCTCTCCGCCAGCGAAATCTTCCATGAGCACGGCGTGGATGAGCATTACCTGGCTCGCGTGCTGCCCGAG
CTATTCGAAGGCCAGCCTCAGCCCAGGTCCCGGAAAGAGCCATCGCGCACAAAGGATTTGCACGCCATCGGC
AAAACCGCGCAGTTGCGCTACATACAGGAGACGCTGGACAGCTGCCAGGGCAGCCTTGACGAGGCTGCGCGT
CGGCTCGGGATCAGCCGGACCACGCTGTGGCGGCGGCTTCGTTCGGCACGCTGA