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. P8-3-8 P8-3-8, 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_AFIE0100000122521519263,928RefSeq:NZ_AFIE01000001
NZ_AFIE0100000222521906230,441RefSeq:NZ_AFIE01000002
NZ_AFIE0100000316616240173,549RefSeq:NZ_AFIE01000003
NZ_AFIE0100000413613501141,939RefSeq:NZ_AFIE01000004
NZ_AFIE0100000510810503133,501RefSeq:NZ_AFIE01000005
NZ_AFIE0100000611010712121,795RefSeq:NZ_AFIE01000006
NZ_AFIE0100000710610411120,238RefSeq:NZ_AFIE01000007
NZ_AFIE010000081009541104,717RefSeq:NZ_AFIE01000008
NZ_AFIE0100000996858393,075RefSeq:NZ_AFIE01000009
NZ_AFIE0100001081780390,803RefSeq:NZ_AFIE01000010
NZ_AFIE0100001184794183,689RefSeq:NZ_AFIE01000011
NZ_AFIE0100001275740180,933RefSeq:NZ_AFIE01000012
NZ_AFIE0100001384784274,502RefSeq:NZ_AFIE01000013
NZ_AFIE0100001465640170,339RefSeq:NZ_AFIE01000014
NZ_AFIE0100001561543468,367RefSeq:NZ_AFIE01000015
NZ_AFIE0100001660571260,636RefSeq:NZ_AFIE01000016
NZ_AFIE0100001756533058,717RefSeq:NZ_AFIE01000017
NZ_AFIE0100001850460458,619RefSeq:NZ_AFIE01000018
NZ_AFIE0100001962610156,315RefSeq:NZ_AFIE01000019
NZ_AFIE0100002058560253,213RefSeq:NZ_AFIE01000020
NZ_AFIE0100002160581152,314RefSeq:NZ_AFIE01000021
NZ_AFIE0100002248471051,167RefSeq:NZ_AFIE01000022
NZ_AFIE0100002346430349,062RefSeq:NZ_AFIE01000023
NZ_AFIE0100002446410548,969RefSeq:NZ_AFIE01000024
NZ_AFIE0100002552466048,325RefSeq:NZ_AFIE01000025
NZ_AFIE0100002644401346,672RefSeq:NZ_AFIE01000026
NZ_AFIE0100002742410146,097RefSeq:NZ_AFIE01000027
NZ_AFIE0100002840390145,355RefSeq:NZ_AFIE01000028
NZ_AFIE0100002936350144,455RefSeq:NZ_AFIE01000029
NZ_AFIE0100003043410243,975RefSeq:NZ_AFIE01000030
NZ_AFIE0100003138353040,181RefSeq:NZ_AFIE01000031
NZ_AFIE0100003234321139,237RefSeq:NZ_AFIE01000032
NZ_AFIE0100003341400139,130RefSeq:NZ_AFIE01000033
NZ_AFIE0100003433320138,828RefSeq:NZ_AFIE01000034
NZ_AFIE0100003533310237,154RefSeq:NZ_AFIE01000035
NZ_AFIE0100003632311036,808RefSeq:NZ_AFIE01000036
NZ_AFIE0100003740390136,510RefSeq:NZ_AFIE01000037
NZ_AFIE0100003831300135,187RefSeq:NZ_AFIE01000038
NZ_AFIE0100003937350234,032RefSeq:NZ_AFIE01000039
NZ_AFIE0100004028271033,714RefSeq:NZ_AFIE01000040
NZ_AFIE0100004133320132,865RefSeq:NZ_AFIE01000041
NZ_AFIE0100004230300030,258RefSeq:NZ_AFIE01000042
NZ_AFIE0100004323230026,628RefSeq:NZ_AFIE01000043
NZ_AFIE0100004433270625,406RefSeq:NZ_AFIE01000044
NZ_AFIE0100004524230125,150RefSeq:NZ_AFIE01000045
NZ_AFIE0100004620200024,473RefSeq:NZ_AFIE01000046
NZ_AFIE0100004718160222,458RefSeq:NZ_AFIE01000047
NZ_AFIE0100004814120222,248RefSeq:NZ_AFIE01000048
NZ_AFIE0100004919190022,246RefSeq:NZ_AFIE01000049
NZ_AFIE0100005019163021,683RefSeq:NZ_AFIE01000050
NZ_AFIE0100005119180121,292RefSeq:NZ_AFIE01000051
NZ_AFIE0100005219170220,917RefSeq:NZ_AFIE01000052
NZ_AFIE0100005317170020,289RefSeq:NZ_AFIE01000053
NZ_AFIE0100005432310120,174RefSeq:NZ_AFIE01000054
NZ_AFIE0100005521210019,780RefSeq:NZ_AFIE01000055
NZ_AFIE0100005615150019,137RefSeq:NZ_AFIE01000056
NZ_AFIE0100005720181117,900RefSeq:NZ_AFIE01000057
NZ_AFIE0100005820180217,662RefSeq:NZ_AFIE01000058
NZ_AFIE0100005919190016,738RefSeq:NZ_AFIE01000059
NZ_AFIE0100006413120113,632RefSeq:NZ_AFIE01000064
NZ_AFIE0100006513130013,326RefSeq:NZ_AFIE01000065
NZ_AFIE010000661390413,162RefSeq:NZ_AFIE01000066
NZ_AFIE0100006914104012,334RefSeq:NZ_AFIE01000069
NZ_AFIE0100007014130112,234RefSeq:NZ_AFIE01000070
NZ_AFIE0100007115150012,090RefSeq:NZ_AFIE01000071
NZ_AFIE0100007312102011,571RefSeq:NZ_AFIE01000073
NZ_AFIE0100007514130110,708RefSeq:NZ_AFIE01000075
NZ_AFIE0100007711110010,569RefSeq:NZ_AFIE01000077
NZ_AFIE010000792017039,348RefSeq:NZ_AFIE01000079
NZ_AFIE010000831414007,563RefSeq:NZ_AFIE01000083
134 Undisplayed Contigs/Replicons2532441183351,996
Total:3,7183,463701853,892,325
Ortholog data available?Yes
Database Contents
Genes3,716
Pathways220
Enzymatic Reactions1,351
Transport Reactions68
Polypeptides3,495
Protein Complexes33
Enzymes723
Transporters268
Compounds1,082
Transcription Units2,730
tRNAs62
GO Terms13
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter sp. P8-3-8
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02470194
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1029823
Annotation ProviderNCBI
Annotation Date2017-04-6
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
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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