Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp10, Karp11, Caspi14] component of Pathway Tools software version 22.0 and MetaCyc version 22.0 on 22-May-2018 15:21:32.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_ALCB010001081019551114,867RefSeq:NZ_ALCB01000108
NZ_ALCB0100001678770183,922RefSeq:NZ_ALCB01000016
NZ_ALCB0100007271673182,243RefSeq:NZ_ALCB01000072
NZ_ALCB0100004265630277,175RefSeq:NZ_ALCB01000042
NZ_ALCB0100005269672070,470RefSeq:NZ_ALCB01000052
NZ_ALCB0100006867661069,885RefSeq:NZ_ALCB01000068
NZ_ALCB0100014162611061,143RefSeq:NZ_ALCB01000141
NZ_ALCB0100011648461155,243RefSeq:NZ_ALCB01000116
NZ_ALCB0100007050481152,724RefSeq:NZ_ALCB01000070
NZ_ALCB0100006544431047,630RefSeq:NZ_ALCB01000065
NZ_ALCB0100014339380146,148RefSeq:NZ_ALCB01000143
NZ_ALCB0100010438361145,026RefSeq:NZ_ALCB01000104
NZ_ALCB0100011428280041,083RefSeq:NZ_ALCB01000114
NZ_ALCB0100000732320039,854RefSeq:NZ_ALCB01000007
NZ_ALCB0100012927252039,153RefSeq:NZ_ALCB01000129
NZ_ALCB0100006927251136,499RefSeq:NZ_ALCB01000069
NZ_ALCB0100006730290136,411RefSeq:NZ_ALCB01000067
NZ_ALCB0100009534320233,294RefSeq:NZ_ALCB01000095
NZ_ALCB0100013129281033,200RefSeq:NZ_ALCB01000131
NZ_ALCB0100010526260031,716RefSeq:NZ_ALCB01000105
NZ_ALCB0100007330281129,827RefSeq:NZ_ALCB01000073
NZ_ALCB0100013729250428,994RefSeq:NZ_ALCB01000137
NZ_ALCB0100014421210028,608RefSeq:NZ_ALCB01000144
NZ_ALCB0100014029281027,852RefSeq:NZ_ALCB01000140
NZ_ALCB0100001517160126,705RefSeq:NZ_ALCB01000015
NZ_ALCB0100002919190026,099RefSeq:NZ_ALCB01000029
NZ_ALCB0100012423221025,830RefSeq:NZ_ALCB01000124
NZ_ALCB0100006322202025,810RefSeq:NZ_ALCB01000063
NZ_ALCB0100008819180125,355RefSeq:NZ_ALCB01000088
NZ_ALCB0100003313130025,079RefSeq:NZ_ALCB01000033
NZ_ALCB0100009616160024,109RefSeq:NZ_ALCB01000096
NZ_ALCB0100010027243023,457RefSeq:NZ_ALCB01000100
NZ_ALCB0100002525250022,943RefSeq:NZ_ALCB01000025
NZ_ALCB0100010319190022,857RefSeq:NZ_ALCB01000103
NZ_ALCB0100003915150022,730RefSeq:NZ_ALCB01000039
NZ_ALCB0100001026224022,019RefSeq:NZ_ALCB01000010
NZ_ALCB0100001112102021,403RefSeq:NZ_ALCB01000011
NZ_ALCB0100010713130020,777RefSeq:NZ_ALCB01000107
NZ_ALCB0100007919190020,772RefSeq:NZ_ALCB01000079
NZ_ALCB0100011812110117,819RefSeq:NZ_ALCB01000118
NZ_ALCB0100005916160016,363RefSeq:NZ_ALCB01000059
NZ_ALCB0100000919160316,087RefSeq:NZ_ALCB01000009
NZ_ALCB0100010614130115,142RefSeq:NZ_ALCB01000106
NZ_ALCB0100003214130114,835RefSeq:NZ_ALCB01000032
NZ_ALCB0100004515123014,755RefSeq:NZ_ALCB01000045
NZ_ALCB0100004318170114,593RefSeq:NZ_ALCB01000043
NZ_ALCB0100010213111114,064RefSeq:NZ_ALCB01000102
NZ_ALCB0100009813110214,056RefSeq:NZ_ALCB01000098
NZ_ALCB0100012313121013,592RefSeq:NZ_ALCB01000123
NZ_ALCB0100003613111112,618RefSeq:NZ_ALCB01000036
NZ_ALCB0100003513110212,473RefSeq:NZ_ALCB01000035
NZ_ALCB010001101253412,241RefSeq:NZ_ALCB01000110
NZ_ALCB0100001812100211,931RefSeq:NZ_ALCB01000018
NZ_ALCB0100002112110111,039RefSeq:NZ_ALCB01000021
NZ_ALCB0100006012120010,426RefSeq:NZ_ALCB01000060
91 Undisplayed Contigs/Replicons339330945476,710
Total:1,9641,82752852,267,656
Ortholog data available?Yes
Database Contents
Genes1,965
Pathways147
Enzymatic Reactions753
Transport Reactions45
Polypeptides1,857
Protein Complexes24
Enzymes407
Transporters189
Compounds653
Transcription Units1,283
tRNAs48
Protein Features2,254
GO Terms9,468
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. ICM39
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00828786
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1105029
Environmenthuman-associated habitat [ENVO:00009003]
HostHomo sapiens
Human Microbiome Body Sitenot-specified

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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