Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 08-Apr-2022 from the annotated genome of Acinetobacter rongchengensis WCHAc060115, 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_RAXT0100000127426914281,980RefSeq:NZ_RAXT01000001
NZ_RAXT0100000223022541249,724RefSeq:NZ_RAXT01000002
NZ_RAXT0100000319018811220,878RefSeq:NZ_RAXT01000003
NZ_RAXT0100000416816332171,545RefSeq:NZ_RAXT01000004
NZ_RAXT0100000512712313137,978RefSeq:NZ_RAXT01000005
NZ_RAXT0100000612111380123,846RefSeq:NZ_RAXT01000006
NZ_RAXT01000007110100100112,535RefSeq:NZ_RAXT01000007
NZ_RAXT01000008959401110,618RefSeq:NZ_RAXT01000008
NZ_RAXT0100000998970198,639RefSeq:NZ_RAXT01000009
NZ_RAXT0100001081791188,250RefSeq:NZ_RAXT01000010
NZ_RAXT0100001192884086,321RefSeq:NZ_RAXT01000011
NZ_RAXT0100001280790184,090RefSeq:NZ_RAXT01000012
NZ_RAXT0100001368670181,118RefSeq:NZ_RAXT01000013
NZ_RAXT0100001473675170,728RefSeq:NZ_RAXT01000014
NZ_RAXT0100001572693068,584RefSeq:NZ_RAXT01000015
NZ_RAXT0100001660580268,539RefSeq:NZ_RAXT01000016
NZ_RAXT0100001758561165,058RefSeq:NZ_RAXT01000017
NZ_RAXT0100001852520064,695RefSeq:NZ_RAXT01000018
NZ_RAXT0100001958551262,556RefSeq:NZ_RAXT01000019
NZ_RAXT0100002049480153,592RefSeq:NZ_RAXT01000020
NZ_RAXT0100002145431152,131RefSeq:NZ_RAXT01000021
NZ_RAXT0100002235340147,825RefSeq:NZ_RAXT01000022
NZ_RAXT0100002343393147,348RefSeq:NZ_RAXT01000023
NZ_RAXT0100002435340146,197RefSeq:NZ_RAXT01000024
NZ_RAXT0100002527240344,086RefSeq:NZ_RAXT01000025
NZ_RAXT0100002636340243,568RefSeq:NZ_RAXT01000026
NZ_RAXT0100002738370142,400RefSeq:NZ_RAXT01000027
NZ_RAXT0100002841383042,375RefSeq:NZ_RAXT01000028
NZ_RAXT0100002936300641,908RefSeq:NZ_RAXT01000029
NZ_RAXT0100003032291238,841RefSeq:NZ_RAXT01000030
NZ_RAXT0100003139380137,906RefSeq:NZ_RAXT01000031
NZ_RAXT0100003236360037,441RefSeq:NZ_RAXT01000032
NZ_RAXT0100003339354036,664RefSeq:NZ_RAXT01000033
NZ_RAXT0100003432320036,209RefSeq:NZ_RAXT01000034
NZ_RAXT0100003538325134,030RefSeq:NZ_RAXT01000035
NZ_RAXT0100003626260033,332RefSeq:NZ_RAXT01000036
NZ_RAXT0100003731301032,936RefSeq:NZ_RAXT01000037
NZ_RAXT0100003826241132,740RefSeq:NZ_RAXT01000038
NZ_RAXT0100003930300032,600RefSeq:NZ_RAXT01000039
NZ_RAXT0100004029290032,365RefSeq:NZ_RAXT01000040
NZ_RAXT0100004125241031,354RefSeq:NZ_RAXT01000041
NZ_RAXT0100004221210029,950RefSeq:NZ_RAXT01000042
NZ_RAXT0100004324200427,084RefSeq:NZ_RAXT01000043
NZ_RAXT0100004422210126,621RefSeq:NZ_RAXT01000044
NZ_RAXT0100004523220126,341RefSeq:NZ_RAXT01000045
NZ_RAXT0100004628270126,293RefSeq:NZ_RAXT01000046
NZ_RAXT0100004724230124,530RefSeq:NZ_RAXT01000047
NZ_RAXT0100004832310123,477RefSeq:NZ_RAXT01000048
NZ_RAXT0100004919180122,842RefSeq:NZ_RAXT01000049
NZ_RAXT0100005026260022,399RefSeq:NZ_RAXT01000050
NZ_RAXT0100005119170222,041RefSeq:NZ_RAXT01000051
NZ_RAXT0100005222220021,561RefSeq:NZ_RAXT01000052
NZ_RAXT0100005316150120,635RefSeq:NZ_RAXT01000053
NZ_RAXT0100005420200019,838RefSeq:NZ_RAXT01000054
NZ_RAXT0100005519180119,501RefSeq:NZ_RAXT01000055
NZ_RAXT0100005620190118,882RefSeq:NZ_RAXT01000056
NZ_RAXT0100005714140018,624RefSeq:NZ_RAXT01000057
NZ_RAXT0100005814130118,520RefSeq:NZ_RAXT01000058
NZ_RAXT0100005919180118,167RefSeq:NZ_RAXT01000059
NZ_RAXT0100006017160117,623RefSeq:NZ_RAXT01000060
NZ_RAXT0100006115141017,518RefSeq:NZ_RAXT01000061
NZ_RAXT0100006211110017,391RefSeq:NZ_RAXT01000062
NZ_RAXT0100006317160117,360RefSeq:NZ_RAXT01000063
NZ_RAXT0100006413130016,638RefSeq:NZ_RAXT01000064
NZ_RAXT0100006515130215,357RefSeq:NZ_RAXT01000065
NZ_RAXT0100006610100015,221RefSeq:NZ_RAXT01000066
NZ_RAXT0100006915150011,833RefSeq:NZ_RAXT01000069
NZ_RAXT0100007313120110,180RefSeq:NZ_RAXT01000073
NZ_RAXT010000761110019,400RefSeq:NZ_RAXT01000076
NZ_RAXT010000841210027,856RefSeq:NZ_RAXT01000084
178 Undisplayed Contigs/Replicons295289675412,917
Total:3,7763,562701444,102,130
Ortholog data available?Yes
Database Contents
Genes3,776
Pathways259
Enzymatic Reactions1,337
Transport Reactions57
Polypeptides3,702
Protein Complexes5
Enzymes793
Transporters340
Compounds958
Transcription Units2,862
tRNAs63
Protein Features4,157
GO Terms263
Database Version29.0
Sequence SourceGCF_003611475.1
Synonyms Acinetobacter sp. WCHAc060115
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter rongchengensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09842375
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2419601
EnvironmentSewage
Geographic LocationChina
Collection Date2018
Annotation ProviderNCBI RefSeq
Annotation Date2021-06-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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