Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acinetobacter qingfengensis ANC 4671, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_MKKK0100000128427662295,745RefSeq:NZ_MKKK01000001
NZ_MKKK0100001218117371179,525RefSeq:NZ_MKKK01000012
NZ_MKKK0100002317516726176,927RefSeq:NZ_MKKK01000023
NZ_MKKK0100003414413860170,482RefSeq:NZ_MKKK01000034
NZ_MKKK0100004516215543156,565RefSeq:NZ_MKKK01000045
NZ_MKKK0100005613212804144,070RefSeq:NZ_MKKK01000056
NZ_MKKK0100006714413743143,168RefSeq:NZ_MKKK01000067
NZ_MKKK0100007312612042128,264RefSeq:NZ_MKKK01000073
NZ_MKKK0100007410510410115,898RefSeq:NZ_MKKK01000074
NZ_MKKK010000021019911105,244RefSeq:NZ_MKKK01000002
NZ_MKKK0100000377723280,056RefSeq:NZ_MKKK01000003
NZ_MKKK0100000475741076,728RefSeq:NZ_MKKK01000004
NZ_MKKK0100000567650274,083RefSeq:NZ_MKKK01000005
NZ_MKKK0100000671665072,279RefSeq:NZ_MKKK01000006
NZ_MKKK0100000760600071,792RefSeq:NZ_MKKK01000007
NZ_MKKK0100000867634070,028RefSeq:NZ_MKKK01000008
NZ_MKKK0100000964631065,218RefSeq:NZ_MKKK01000009
NZ_MKKK0100001059536062,604RefSeq:NZ_MKKK01000010
NZ_MKKK0100001148480059,019RefSeq:NZ_MKKK01000011
NZ_MKKK0100001341410046,404RefSeq:NZ_MKKK01000013
NZ_MKKK0100001452492145,522RefSeq:NZ_MKKK01000014
NZ_MKKK0100001635341044,976RefSeq:NZ_MKKK01000016
NZ_MKKK0100001758580044,192RefSeq:NZ_MKKK01000017
NZ_MKKK0100001540400044,033RefSeq:NZ_MKKK01000015
NZ_MKKK0100001928280042,231RefSeq:NZ_MKKK01000019
NZ_MKKK0100001839370241,896RefSeq:NZ_MKKK01000018
NZ_MKKK0100002142390333,673RefSeq:NZ_MKKK01000021
NZ_MKKK0100002034304031,704RefSeq:NZ_MKKK01000020
NZ_MKKK0100002418180030,098RefSeq:NZ_MKKK01000024
NZ_MKKK0100002733280529,981RefSeq:NZ_MKKK01000027
NZ_MKKK0100002516160028,860RefSeq:NZ_MKKK01000025
NZ_MKKK0100002222210128,318RefSeq:NZ_MKKK01000022
NZ_MKKK0100002622182227,239RefSeq:NZ_MKKK01000026
NZ_MKKK0100002926231223,123RefSeq:NZ_MKKK01000029
NZ_MKKK0100002817170022,582RefSeq:NZ_MKKK01000028
NZ_MKKK0100003018180019,851RefSeq:NZ_MKKK01000030
NZ_MKKK0100003217160119,580RefSeq:NZ_MKKK01000032
NZ_MKKK0100003117170018,979RefSeq:NZ_MKKK01000031
NZ_MKKK0100003513110216,751RefSeq:NZ_MKKK01000035
NZ_MKKK0100003315150016,437RefSeq:NZ_MKKK01000033
NZ_MKKK0100003612110116,036RefSeq:NZ_MKKK01000036
NZ_MKKK0100003715150015,212RefSeq:NZ_MKKK01000037
32 Undisplayed Contigs/Replicons15815626205,398
Total:2,9362,81767523,140,771
Ortholog data available?Yes
Database Contents
Genes2,936
Pathways253
Enzymatic Reactions1,277
Transport Reactions50
Polypeptides2,840
Protein Complexes61
Enzymes701
Transporters267
Compounds934
Transcription Units1,956
tRNAs58
Protein Features3,646
GO Terms228
Database Version29.0
Sequence SourceGCF_001753595.1
Synonyms Acinetobacter sp. 2BJ-1
Acinetobacter sp. 2C-3-1
Acinetobacter sp. HF5-2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter qingfengensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05846377
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1262585
Environmentcanker bark of Populus
Geographic LocationChina
Collection Date2011-09
Annotation ProviderNCBI RefSeq
Annotation Date2021-10-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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