ViewGene

Locus Name:
GeneID:
Location:

GeneID:3613
TrivialName: PA14_06570
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_06570
PAO1 Ortholog Locus:PA0504
Sequence Length:687
Protein Length:228
Start: 573522
Stop: 574208
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG03893.1|AE004487_7 (AE004487) dethiobiotin synthase [Pseudomonas aeruginosa PAO1]
Identities = 224/228 (98%), Positives = 224/228 (98%)
Sequence:
ATGCCGGCGTTCTTCGTCACCGGTACCGACACCGAGATCGGCAAGACCACCATCGCCGCCGGCCTGCTCCAC
GCGGCCCGGCGTGCCGGCCTGAGCACCGCCGCGGCGAAGCCGGTGGCCTCCGGCTGCGAGCCCACGGCGCAA
GGCCTGCGCAATGGCGACGCGCTGGCGTTGCTCGGCCAGTGTTCGCTGGCGCTGGCCTACGAGCAGGTCAAC
CCGCTGGCCTTCGCGCCGGCCATCGCCCCGCACCTGGCGGCGCGCGAGGCCGGCGTCGAACTGAGCGCCGCA
CGCTTGCACGAGGCGGTGCGCGAGGTGCTGGCGCTACAGGCCGATCTCACCCTGGTGGAGGGCGCCGGCGGT
TGGCGCGTGCCGTTGCAGGGTCGCGAGAACCTCTCCGACCTGGCGCGCCTGCTGGCGCTGCCGGTGGTGCTG
GTGGTCGGCGTGCGCCTGGGCTGTATCAACCATGCGCTGCTCAGCGCCGAGGCGATCCTAGGCGACGGCCTG
GCGCTGGCCGGCTGGGTGGCCAACGTGGTCGACCCGGCTACCTCGCGCCTGGAGGAGAACCTGGCGACCCTC
GCCGAGCGCCTGCCGGCGCCCTGCCTGGGCCGGGTACCGCGCCTGGAGGAAGCCACTCCCGCGGCCGTGGCC
GCGCACCTCGACCTGCGGCCCCTGGGCATCGGGCTATAA
Translation:
MPAFFVTGTDTEIGKTTIAAGLLHAARRAGLSTAAAKPVASGCEPTAQGLRNGDALALLGQCSLALAYEQVN
PLAFAPAIAPHLAAREAGVELSAARLHEAVREVLALQADLTLVEGAGGWRVPLQGRENLSDLARLLALPVVL
VVGVRLGCINHALLSAEAILGDGLALAGWVANVVDPATSRLEENLATLAERLPAPCLGRVPRLEEATPAAVA
AHLDLRPLGIGL*
AnnotationID:3621GeneID:3613
AnnotatorUID: diggins
Modification Date/Time: 2005-03-28 04:04:03
Gene Name:bioD
Confidence Code:2
GeneProduct:dethiobiotin synthase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(4) Biosynthesis of cofactors, prosthetic groups and carriers
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0132
Secondary Functional Category(ies):
EC Number:6.3.3.3
Status:ACTIVE
Pathway:
Homology:
>gb|AAO54042.1| (AE016857) dethiobiotin synthetase [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 226

 Score =  312 bits (800), Expect = 9e-85
 Identities = 160/222 (72%), Positives = 182/222 (81%)

>gb|AAN65997.1|AE016228_10 (AE016775) dethiobiotin synthetase [Pseudomonas putida KT2440]
          Length = 226

 Score =  305 bits (780), Expect = 2e-82
 Identities = 155/219 (70%), Positives = 178/219 (81%)

>gb|AAN55765.1|AE015712_9 (AE015712) dethiobiotin synthase [Shewanella oneidensis MR-1]
          Length = 231

 Score =  223 bits (568), Expect = 7e-58
 Identities = 120/227 (52%), Positives = 155/227 (68%), Gaps = 6/227 (2%)

Structural Features:
COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism]
CD-Length = 223 residues,  98.7% aligned
Score =  226 bits (577), Expect = 2e-60
Identities = 103/224 (45%), Positives = 135/224 (60%), Gaps = 4/224 (1%)

Genomic Context:
Comment:
ReferenceID:7229
Author/Investigator(s): GenNotator
Title:
PubMed:
MedLine:
Source:
Reference Type:BLASTP
Data:
URL:
ReferenceID:24371
Author/Investigator(s): GenNotator
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:RPSBLAST
Data:
URL:
ReferenceID:33815
Author/Investigator(s):
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:Misc (text/plain)
Data:3613_cdd.html
URL:
ReferenceID:35313
Author/Investigator(s): Kiyasu T, Nagahashi Y, Hoshino T.
Title: Cloning and characterization of biotin biosynthetic genes of Kurthia sp.
PubMed: 11255013
MedLine:
Source:
Gene. 2001 Mar 7;265(1-2):103-13.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11255013
ReferenceID:35314
Author/Investigator(s): Wu CH, Bao YY, Shao CP, Shiuan D.
Title: Molecular cloning and nucleotide sequencing of bioF (7-keto-8-amino pelargonic acid synthetase), bioC and bioD (dethiobiotin synthetase) genes of Erwinia herbicola.
PubMed: 9063571
MedLine:
Source:
Biochem Mol Biol Int. 1997 Feb;41(2):311-5.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9063571
ReferenceID:35315
Author/Investigator(s): Sakurai N, Akatsuka H, Kawai E, Imai Y, Komatsubara S.
Title: Complete sequence and organization of the Serratia marcescens biotin operon.
PubMed: 8969526
MedLine:
Source:
Microbiology. 1996 Nov;142 ( Pt 11):3295-303.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8969526
ReferenceID:35316
Author/Investigator(s): Bower S, Perkins JB, Yocum RR, Howitt CL, Rahaim P, Pero J.
Title: Cloning, sequencing, and characterization of the Bacillus subtilis biotin biosynthetic operon.
PubMed: 8763940
MedLine:
Source:
J Bacteriol. 1996 Jul;178(14):4122-30.
Reference Type:Journal
Data:
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8763940
ReferenceID:35317
Author/Investigator(s): Hatakeyama K, Hohama K, Vertes AA, Kobayashi M, Kurusu Y, Yukawa H.
Title: Genomic organization of the biotin biosynthetic genes of coryneform bacteria: cloning and sequencing of the bioA-bioD genes from Brevibacterium flavum.
PubMed: 8161820
MedLine:
Source:
DNA Seq. 1993;4(3):177-84.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8161820
ReferenceID:35318
Author/Investigator(s): Gloeckler R, Ohsawa I, Speck D, Ledoux C, Bernard S, Zinsius M, Villeval D, Kisou T, Kamogawa K, Lemoine Y.
Title: Cloning and characterization of the Bacillus sphaericus genes controlling the bioconversion of pimelate into dethiobiotin.
PubMed: 2110099
MedLine:
Source:
Gene. 1990 Mar 1;87(1):63-70.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2110099
ReferenceID:35327
Author/Investigator(s): Otsuka AJ, Buoncristiani MR, Howard PK, Flamm J, Johnson C, Yamamoto R, Uchida K, Cook C, Ruppert J, Matsuzaki J.
Title: The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon.
PubMed: 3058702
MedLine:
Source:
J Biol Chem. 1988 Dec 25;263(36):19577-85.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3058702
Homologs By Global Alignment
Gene ID:3613

Identity:

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
HomologID Accession Description Length PctIdentity PctSimilarity Gaps Score
5795 PA0504_tr translation of PA0504 228 98.24 98.24 0 1113.0
161760 gb|AAG03893.1|AE004487_7 (AE004487) dethiobiotin synthase [Pseudomonas aeruginosa PAO1] 228 98.24 98.24 0 1113.0
161761 gb|AAO54042.1| (AE016857) dethiobiotin synthetase [Pseudomonas syringae pv. tomato str. DC3000] 229 69.86 79.47 4 798.0
161762 gb|AAN65997.1|AE016228_10 (AE016775) dethiobiotin synthetase [Pseudomonas putida KT2440] 229 68.12 78.16 4 776.0
161763 gb|AAN55765.1|AE015712_9 (AE015712) dethiobiotin synthase [Shewanella oneidensis MR-1] 235 52.76 68.08 11 570.0
GC ORFID: 46615How Found: BLASTX
GC_TrimmedSeqID: 69Blast Result ID
Subject Sequence Name: t_PA0504Glimmer Score:
Start: 6374864Stop: 6375550
Length: 687
Start Codon: ATGTruncated Start:
Stop Codon: TAATruncated Stop:
Homolog: t_PA0504 translation of PA0504Homolog Bit Score 433.0
Other Homologs: t_PA0504 (ORF: GLIMMER)
GC ORF Sequence
ATGCCGGCGTTCTTCGTCACCGGTACCGACACCGAGATCGGCAAGACCACCATCGCCGCCGGCCTGCTCCAC
GCGGCCCGGCGTGCCGGCCTGAGCACCGCCGCGGCGAAGCCGGTGGCCTCCGGCTGCGAGCCCACGGCGCAA
GGCCTGCGCAATGGCGACGCGCTGGCGTTGCTCGGCCAGTGTTCGCTGGCGCTGGCCTACGAGCAGGTCAAC
CCGCTGGCCTTCGCGCCGGCCATCGCCCCGCACCTGGCGGCGCGCGAGGCCGGCGTCGAACTGAGCGCCGCA
CGCTTGCACGAGGCGGTGCGCGAGGTGCTGGCGCTACAGGCCGATCTCACCCTGGTGGAGGGCGCCGGCGGT
TGGCGCGTGCCGTTGCAGGGTCGCGAGAACCTCTCCGACCTGGCGCGCCTGCTGGCGCTGCCGGTGGTGCTG
GTGGTCGGCGTGCGCCTGGGCTGTATCAACCATGCGCTGCTCAGCGCCGAGGCGATCCTAGGCGACGGCCTG
GCGCTGGCCGGCTGGGTGGCCAACGTGGTCGACCCGGCTACCTCGCGCCTGGAGGAGAACCTGGCGACCCTC
GCCGAGCGCCTGCCGGCGCCCTGCCTGGGCCGGGTACCGCGCCTGGAGGAAGCCACTCCCGCGGCCGTGGCC
GCGCACCTCGACCTGCGGCCCCTGGGCATCGGGCTATAA