ViewGene

Locus Name:
GeneID:
Location:

GeneID:4409
TrivialName: PA14_41060
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_41060
PAO1 Ortholog Locus:PA1815
Sequence Length:447
Protein Length:148
Start: 3661719
Stop: 3661273
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05204.1|AE004608_3 (AE004608) ribonuclease H [Pseudomonas aeruginosa PAO1]
Identities = 148/148 (100%), Positives = 148/148 (100%)
Sequence:
ATGACAGATAAAGAACAGGTAGTGATCTATACCGACGGCGCCTGCAAGGGCAACCCTGGGCGCGGCGGCTGG
GGGGCGTTGCTCCTCTACAAGGGCGCCGAGCGAGAGCTTTGGGGCGGCGAGCCGGACACCACCAACAACCGC
ATGGAGCTGATGGCGGCGATCCAGGCGCTGGCGGCACTCAAGCGTTCCTGTCCGATCCGTCTGATCACCGAC
TCGGAATACGTGATGCGCGGCATCACCGAATGGTTGCCGAACTGGAAGAAGCGCGGCTGGAAGACCGCCAGC
AAGCAGCCTGTCAAGAATGCCGACCTCTGGCAGGCCCTGGATGAACAGGTCGCCCGGCACCAGGTGGAGTGG
CAGTGGGTCCGCGGGCATACCGGCGACCCCGGCAACGAGCGGGCCGACCAGTTGGCCAACCGTGGCGTCGCC
GAATTGCCGCGCTGA
Translation:
MTDKEQVVIYTDGACKGNPGRGGWGALLLYKGAERELWGGEPDTTNNRMELMAAIQALAALKRSCPIRLITD
SEYVMRGITEWLPNWKKRGWKTASKQPVKNADLWQALDEQVARHQVEWQWVRGHTGDPGNERADQLANRGVA
ELPR*
AnnotationID:4415GeneID:4409
AnnotatorUID: diggins
Modification Date/Time: 2005-04-28 13:01:20
Gene Name:rnhA
Confidence Code:2
GeneProduct:ribonuclease H
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(11) DNA replication, recombination, modification and repair
Alternate Gene Product Name:ribonuclease HI
Functional Category Confidence Code:5
COGs:COG0328,pfam00075
Secondary Functional Category(ies):
EC Number:3.1.26.4
Status:ACTIVE
Pathway:
Homology:
>gb|AAN69724.1|AE016608_10 (AE016789) ribonuclease HI [Pseudomonas putida KT2440]
          Length = 148

 Score =  238 bits (606), Expect = 1e-62
 Identities = 105/142 (73%), Positives = 122/142 (85%)

>gb|AAO57181.1| (AE016869) ribonuclease HI [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 150

 Score =  237 bits (604), Expect = 2e-62
 Identities = 105/142 (73%), Positives = 122/142 (85%)

>emb|CAE34642.1| (BX640450) ribonuclease HI [Bordetella bronchiseptica]
          Length = 155

 Score =  216 bits (550), Expect = 3e-56
 Identities = 96/141 (68%), Positives = 115/141 (81%)

Structural Features:
COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]
CD-Length = 154 residues,  91.6% aligned
Score =  185 bits (471), Expect = 2e-48
Identities = 86/141 (60%), Positives = 101/141 (71%), Gaps = 3/141 (2%)

pfam00075, RnaseH, RNase H. 
CD-Length = 126 residues,  98.4% aligned
Score =  125 bits (315), Expect = 3e-30
Identities = 61/139 (43%), Positives = 80/139 (57%), Gaps = 15/139 (10%)

Genomic Context:
Comment:
ReferenceID:8819
Author/Investigator(s): GenNotator
Title:
PubMed:
MedLine:
Source:
Reference Type:BLASTP
Data:
URL:
ReferenceID:25962
Author/Investigator(s): GenNotator
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:RPSBLAST
Data:
URL:
ReferenceID:36520
Author/Investigator(s):
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:Misc (text/plain)
Data:4409_cdd.html
URL:
ReferenceID:36588
Author/Investigator(s): Itaya M, Kondo K.
Title: Molecular cloning of a ribonuclease H (RNase HI) gene from an extreme thermophile Thermus thermophilus HB8: a thermostable RNase H can functionally replace the Escherichia coli enzyme in vivo.
PubMed: 1653414
MedLine:
Source:
Nucleic Acids Res. 1991 Aug 25;19(16):4443-9.
Reference Type:Journal
Data:
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1653414
ReferenceID:36589
Author/Investigator(s): Dawes SS, Crouch RJ, Morris SL, Mizrahi V.
Title: Cloning, sequence analysis, overproduction in Escherichia coli and enzymatic characterization of the RNase HI from Mycobacterium smegmatis.
PubMed: 7489919
MedLine:
Source:
Gene. 1995 Nov 7;165(1):71-5.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7489919
ReferenceID:36590
Author/Investigator(s): Ohtani N, Haruki M, Morikawa M, Kanaya S.
Title: Heat labile ribonuclease HI from a psychrotrophic bacterium: gene cloning, characterization and site-directed mutagenesis.
PubMed: 11809928
MedLine:
Source:
Protein Eng. 2001 Dec;14(12):975-82.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11809928
Homologs By Global Alignment
Gene ID:4409

Identity:

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
HomologID Accession Description Length PctIdentity PctSimilarity Gaps Score
6746 PA1815_tr translation of PA1815 148 99.99 99.99 0 808.0
180898 gb|AAG05204.1|AE004608_3 (AE004608) ribonuclease H [Pseudomonas aeruginosa PAO1] 148 99.99 99.99 0 808.0
180899 gb|AAN69724.1|AE016608_10 (AE016789) ribonuclease HI [Pseudomonas putida KT2440] 150 71.33 82.66 4 602.0
180900 gb|AAO57181.1| (AE016869) ribonuclease HI [Pseudomonas syringae pv. tomato str. DC3000] 152 70.39 81.57 6 599.0
180904 gb|AAQ58931.1| (AE016914) ribonuclease H [Chromobacterium violaceum ATCC 12472] 149 65.10 79.19 3 540.0
GC ORFID: 47411How Found: BLASTX
GC_TrimmedSeqID: 69Blast Result ID
Subject Sequence Name: t_PA1815Glimmer Score:
Start: 1292191Stop: 1292637
Length: 447
Start Codon: ATGTruncated Start:
Stop Codon: TGATruncated Stop:
Homolog: t_PA1815 translation of PA1815Homolog Bit Score 315.0
Other Homologs: psyr_15may02_Scaffold1_revised_gene787 (ORF: BLASTX 237.0)
GC ORF Sequence
ATGACAGATAAAGAACAGGTAGTGATCTATACCGACGGCGCCTGCAAGGGCAACCCTGGGCGCGGCGGCTGG
GGGGCGTTGCTCCTCTACAAGGGCGCCGAGCGAGAGCTTTGGGGCGGCGAGCCGGACACCACCAACAACCGC
ATGGAGCTGATGGCGGCGATCCAGGCGCTGGCGGCACTCAAGCGTTCCTGTCCGATCCGTCTGATCACCGAC
TCGGAATACGTGATGCGCGGCATCACCGAATGGTTGCCGAACTGGAAGAAGCGCGGCTGGAAGACCGCCAGC
AAGCAGCCTGTCAAGAATGCCGACCTCTGGCAGGCCCTGGATGAACAGGTCGCCCGGCACCAGGTGGAGTGG
CAGTGGGTCCGCGGGCATACCGGCGACCCCGGCAACGAGCGGGCCGACCAGTTGGCCAACCGTGGCGTCGCC
GAATTGCCGCGCTGA