Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter sp. WC-743 WC-743, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [Caspi18]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AMFQ0100009017216318186,714RefSeq:NZ_AMFQ01000090
NZ_AMFQ0100010118917784183,405RefSeq:NZ_AMFQ01000101
NZ_AMFQ0100013214713809171,512RefSeq:NZ_AMFQ01000132
NZ_AMFQ0100001314914234166,843RefSeq:NZ_AMFQ01000013
NZ_AMFQ0100009715414815153,621RefSeq:NZ_AMFQ01000097
NZ_AMFQ0100011810610222123,205RefSeq:NZ_AMFQ01000118
NZ_AMFQ0100007611511500120,192RefSeq:NZ_AMFQ01000076
NZ_AMFQ0100004610810503115,881RefSeq:NZ_AMFQ01000046
NZ_AMFQ0100002211010541115,495RefSeq:NZ_AMFQ01000022
NZ_AMFQ0100007811410761114,034RefSeq:NZ_AMFQ01000078
NZ_AMFQ01000085112101101111,428RefSeq:NZ_AMFQ01000085
NZ_AMFQ010001251019704109,117RefSeq:NZ_AMFQ01000125
NZ_AMFQ01000152939012106,977RefSeq:NZ_AMFQ01000152
NZ_AMFQ01000096969303106,772RefSeq:NZ_AMFQ01000096
NZ_AMFQ01000139999603105,571RefSeq:NZ_AMFQ01000139
NZ_AMFQ0100007194876198,400RefSeq:NZ_AMFQ01000071
NZ_AMFQ0100000981770495,587RefSeq:NZ_AMFQ01000009
NZ_AMFQ0100015180752395,412RefSeq:NZ_AMFQ01000151
NZ_AMFQ0100001888825192,151RefSeq:NZ_AMFQ01000018
NZ_AMFQ0100006092920089,894RefSeq:NZ_AMFQ01000060
NZ_AMFQ0100014888860289,234RefSeq:NZ_AMFQ01000148
NZ_AMFQ0100014276731287,503RefSeq:NZ_AMFQ01000142
NZ_AMFQ0100003989798286,887RefSeq:NZ_AMFQ01000039
NZ_AMFQ0100011385831185,244RefSeq:NZ_AMFQ01000113
NZ_AMFQ0100009995904184,394RefSeq:NZ_AMFQ01000099
NZ_AMFQ0100009881747083,831RefSeq:NZ_AMFQ01000098
NZ_AMFQ0100004382745382,410RefSeq:NZ_AMFQ01000043
NZ_AMFQ0100007580770379,851RefSeq:NZ_AMFQ01000075
NZ_AMFQ0100006774692377,781RefSeq:NZ_AMFQ01000067
NZ_AMFQ0100000676760076,777RefSeq:NZ_AMFQ01000006
NZ_AMFQ0100006165620376,684RefSeq:NZ_AMFQ01000061
NZ_AMFQ0100004170618175,001RefSeq:NZ_AMFQ01000041
NZ_AMFQ0100002366651072,336RefSeq:NZ_AMFQ01000023
NZ_AMFQ0100010458560260,764RefSeq:NZ_AMFQ01000104
NZ_AMFQ0100006965620357,542RefSeq:NZ_AMFQ01000069
NZ_AMFQ0100003449430655,049RefSeq:NZ_AMFQ01000034
NZ_AMFQ0100007941400154,620RefSeq:NZ_AMFQ01000079
NZ_AMFQ0100001148460254,578RefSeq:NZ_AMFQ01000011
NZ_AMFQ0100003144400452,116RefSeq:NZ_AMFQ01000031
NZ_AMFQ0100003741410046,806RefSeq:NZ_AMFQ01000037
NZ_AMFQ0100012852500245,959RefSeq:NZ_AMFQ01000128
NZ_AMFQ0100011444385145,693RefSeq:NZ_AMFQ01000114
NZ_AMFQ0100002546440244,909RefSeq:NZ_AMFQ01000025
NZ_AMFQ0100001060570341,887RefSeq:NZ_AMFQ01000010
NZ_AMFQ0100012646400640,903RefSeq:NZ_AMFQ01000126
NZ_AMFQ0100001938362038,959RefSeq:NZ_AMFQ01000019
NZ_AMFQ0100014947431337,351RefSeq:NZ_AMFQ01000149
NZ_AMFQ0100007429280135,583RefSeq:NZ_AMFQ01000074
NZ_AMFQ0100010621200130,535RefSeq:NZ_AMFQ01000106
NZ_AMFQ0100006224230130,424RefSeq:NZ_AMFQ01000062
NZ_AMFQ0100007726240229,805RefSeq:NZ_AMFQ01000077
NZ_AMFQ0100011729280129,666RefSeq:NZ_AMFQ01000117
NZ_AMFQ0100004418180028,967RefSeq:NZ_AMFQ01000044
NZ_AMFQ0100003828233226,440RefSeq:NZ_AMFQ01000038
NZ_AMFQ0100014132300225,530RefSeq:NZ_AMFQ01000141
NZ_AMFQ0100013432300223,400RefSeq:NZ_AMFQ01000134
NZ_AMFQ0100000317151122,292RefSeq:NZ_AMFQ01000003
NZ_AMFQ0100010725230222,236RefSeq:NZ_AMFQ01000107
NZ_AMFQ0100005627260121,703RefSeq:NZ_AMFQ01000056
NZ_AMFQ0100013125211320,754RefSeq:NZ_AMFQ01000131
NZ_AMFQ0100011514131020,097RefSeq:NZ_AMFQ01000115
NZ_AMFQ0100000218160219,957RefSeq:NZ_AMFQ01000002
NZ_AMFQ0100010314120219,771RefSeq:NZ_AMFQ01000103
NZ_AMFQ0100005217160118,683RefSeq:NZ_AMFQ01000052
NZ_AMFQ0100012721190218,362RefSeq:NZ_AMFQ01000127
NZ_AMFQ0100009420120816,891RefSeq:NZ_AMFQ01000094
NZ_AMFQ010000841595116,533RefSeq:NZ_AMFQ01000084
NZ_AMFQ0100000712110113,019RefSeq:NZ_AMFQ01000007
NZ_AMFQ0100001716130312,347RefSeq:NZ_AMFQ01000017
NZ_AMFQ0100000418130510,934RefSeq:NZ_AMFQ01000004
NZ_AMFQ0100011012110110,600RefSeq:NZ_AMFQ01000110
NZ_AMFQ0100010915140110,319RefSeq:NZ_AMFQ01000109
NZ_AMFQ010001401514019,687RefSeq:NZ_AMFQ01000140
81 Undisplayed Contigs/Replicons105901574160,555
Total:4,7254,3691202364,902,370
Ortholog data available?Yes
Database Contents
Genes4,725
Pathways258
Enzymatic Reactions1,592
Transport Reactions11
Polypeptides4,387
Protein Complexes28
Enzymes769
Transporters371
Compounds1,234
Transcription Units3,454
tRNAs89
GO Terms48
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter sp. WC-743
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761217
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903945
Geographic LocationUSA
Collection Date2008-06-27
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.2
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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