Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Tim Holland1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp02, Dale10, Karp11, Caspi12] using Pathway Tools software version 18.5 and MetaCyc version 18.5 on 10-Aug-2014 18:43:19 from the annotated genome of Lactobacillus vaginalis ATCC 49540 as obtained from RefSeq downloaded on 21-May-2014.

This BioCyc Tier 3 PGDB was computationally generated. It has not undergone any manual curation nor manual review, and thus may contain errors. Development of this PGDB was supported by grant GM080746 from the NIH.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD1, whole genome shotgun sequence.616604120693,865RefSeq:NZ_GG693412
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD2, whole genome shotgun sequence.395372230409,041RefSeq:NZ_GG693413
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD4, whole genome shotgun sequence.290278120294,131RefSeq:NZ_GG693415
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD3, whole genome shotgun sequence.282271110258,163RefSeq:NZ_GG693414
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD5, whole genome shotgun sequence.959410115,457RefSeq:NZ_GG693416
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD6, whole genome shotgun sequence.68680041,209RefSeq:NZ_GG693417
Lactobacillus vaginalis ATCC 49540 genomic scaffold SCAFFOLD10, whole genome shotgun sequence.15141013,795RefSeq:NZ_GG693421
105 Undisplayed Contigs/Replicons25196051,671
Total:1,7861,7206601,877,332
Ortholog data available?Yes
Database Contents
Genes1,781
Pathways202
Enzymatic Reactions977
Transport Reactions56
Polypeptides1,871
Protein Complexes6
Enzymes553
Transporters195
Compounds658
Transcription Units1,210
tRNAs57
GO Terms2,623
Database Version29.0
Synonyms Lactobacillus vaginalis ATCC 49540 = DSM 5837
Lactobacillus vaginalis DSM 5837
Lactobacillus vaginalis DSM 5837 = ATCC 49540
Lactobacillus vaginalis strain ATCC 49540
Lactobacillus vaginalis ATCC 49540
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Lactobacillaceae
Lactobacillus
Lactobacillus vaginalis
Lactobacillus vaginalis DSM 5837 = ATCC 49540
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0004621
NCBI-Taxonomy1423814
Environmenturogenital_tract
Relationship to Oxygenmicroaerophilic
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract

References

Caspi12: Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 40(Database issue);D742-53. PMID: 22102576

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Karp02: Karp PD, Paley S, Romero P (2002). "The Pathway Tools software." Bioinformatics 18 Suppl 1;S225-32. PMID: 12169551

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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