Database Authors
Carol A Fulcher1, Anamika Kothari1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 14-Nov-2016 by the PathoLogic [Karp10, Karp11, Caspi14] component of Pathway Tools software version 20.5 and MetaCyc version 20.5. The primary data source for this dataset was the whole genome shotgun sequencing project for [Clostridium] symbiosum WAL-14163 derived from NCBI Reference Sequence: NZ_ADLQ00000000.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GL834305760742315907,173RefSeq:NZ_GL834305
NZ_GL834306588562620663,795RefSeq:NZ_GL834306
NZ_GL834307305288710364,314RefSeq:NZ_GL834307
NZ_GL83430830629916337,964RefSeq:NZ_GL834308
NZ_GL834309296279215329,697RefSeq:NZ_GL834309
NZ_GL834310347330512328,026RefSeq:NZ_GL834310
NZ_GL83431126925829316,306RefSeq:NZ_GL834311
NZ_GL83431224623097260,611RefSeq:NZ_GL834312
NZ_GL83431323322607232,044RefSeq:NZ_GL834313
NZ_GL83431419719232224,808RefSeq:NZ_GL834314
NZ_GL83431518617583188,374RefSeq:NZ_GL834315
NZ_GL83431616316003187,384RefSeq:NZ_GL834316
NZ_GL83431714313544176,465RefSeq:NZ_GL834317
NZ_GL83431814514005164,403RefSeq:NZ_GL834318
NZ_GL83431912411347149,583RefSeq:NZ_GL834319
NZ_GL83432012812134116,518RefSeq:NZ_GL834320
NZ_GL834321948932101,261RefSeq:NZ_GL834321
NZ_GL83432248460257,061RefSeq:NZ_GL834322
NZ_GL83432353520156,578RefSeq:NZ_GL834323
NZ_GL83432455459150,963RefSeq:NZ_GL834324
NZ_GL83432534310335,631RefSeq:NZ_GL834325
NZ_GL83432620180226,601RefSeq:NZ_GL834326
NZ_GL83432730290125,833RefSeq:NZ_GL834327
29 Undisplayed Contigs/Replicons413291051,105
Total:4,8214,592781515,352,498
Ortholog data available?Yes
Database Contents
Genes4,813
Pathways192
Enzymatic Reactions1,121
Transport Reactions107
Polypeptides4,617
Protein Complexes45
Enzymes960
Transporters489
Compounds883
Transcription Units3,025
tRNAs65
Protein Features5,602
GO Terms28,041
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Lachnospirales
Lachnospiraceae
Lachnoclostridium
[Clostridium] symbiosum
[Clostridium] symbiosum WAL-14163
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA224116
NCBI-Taxonomy742740
Environmentbiological product [ENVO:02000043]
Relationship to Oxygenanaerobe
Temperature Rangemesophile
HostHomo sapiens
Human Microbiome Body Sitegastrointestinal-tract
Copyright SRI International 2016. All Rights Reserved.

References

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

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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