Database Authors
Pallavi Subhraveti1, Quang Ong1, Tim Holland1, Anamika Kothari1, Ingrid Keseler1, 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 Acidithiobacillus sp. GGI-221 NIL as obtained from RefSeq.

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
NZ_AEFB01000322 contig10100012,633RefSeq:NZ_AEFB01000322
NZ_AEFB01000267 contig13130012,235RefSeq:NZ_AEFB01000267
NZ_AEFB01001066 contig11110012,094RefSeq:NZ_AEFB01001066
NZ_AEFB01000025 contig14140011,089RefSeq:NZ_AEFB01000025
NZ_AEFB01000787 contig1212007,719RefSeq:NZ_AEFB01000787
NZ_AEFB01000699 contig1010007,211RefSeq:NZ_AEFB01000699
NZ_AEFB01001427 contig1111007,133RefSeq:NZ_AEFB01001427
NZ_AEFB01000782 contig1211104,842RefSeq:NZ_AEFB01000782
NZ_AEFB01000240 contig1321103,701RefSeq:NZ_AEFB01000240
NZ_AEFB01000012 contig2051503,347RefSeq:NZ_AEFB01000012
1,592 Undisplayed Contigs/Replicons2,1922,1415103,092,930
Total:2,3182,2407803,174,934
Ortholog data available?Yes
Database Contents
Genes2,318
Pathways251
Enzymatic Reactions1,106
Transport Reactions9
Polypeptides4,010
Protein Complexes0
Enzymes819
Transporters282
Compounds753
Transcription Units3,113
tRNAs75
Protein Features1,727
GO Terms4,436
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Acidithiobacillia
Acidithiobacillales
Acidithiobacillaceae
Acidithiobacillus
Acidithiobacillus sp. GGI-221
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0008778
NCBI-Taxonomy872330
Environmentmine water
Geographic LocationIndia

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(D1);D742-D753. 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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