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 baumannii MSP4-16, 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_AODW0100003135834666385,402RefSeq:NZ_AODW01000031
NZ_AODW0100000533532357354,252RefSeq:NZ_AODW01000005
NZ_AODW0100002230229804319,813RefSeq:NZ_AODW01000022
NZ_AODW0100000729428653315,178RefSeq:NZ_AODW01000007
NZ_AODW01000027266252104254,343RefSeq:NZ_AODW01000027
NZ_AODW0100001222522014233,533RefSeq:NZ_AODW01000012
NZ_AODW0100001417417004192,388RefSeq:NZ_AODW01000014
NZ_AODW0100001518217480192,251RefSeq:NZ_AODW01000015
NZ_AODW0100002618317463188,258RefSeq:NZ_AODW01000026
NZ_AODW0100003017616673177,578RefSeq:NZ_AODW01000030
NZ_AODW0100001616616114174,215RefSeq:NZ_AODW01000016
NZ_AODW0100002812211705135,110RefSeq:NZ_AODW01000028
NZ_AODW0100000412111902129,545RefSeq:NZ_AODW01000004
NZ_AODW0100002313312751118,526RefSeq:NZ_AODW01000023
NZ_AODW0100003711811440111,594RefSeq:NZ_AODW01000037
NZ_AODW0100003493823890,465RefSeq:NZ_AODW01000034
NZ_AODW0100002194910385,106RefSeq:NZ_AODW01000021
NZ_AODW0100000958570163,246RefSeq:NZ_AODW01000009
NZ_AODW0100002458560263,061RefSeq:NZ_AODW01000024
NZ_AODW0100001049480156,521RefSeq:NZ_AODW01000010
NZ_AODW0100001749470248,065RefSeq:NZ_AODW01000017
NZ_AODW0100003340380244,270RefSeq:NZ_AODW01000033
NZ_AODW0100005041400142,396RefSeq:NZ_AODW01000050
NZ_AODW0100003531273138,080RefSeq:NZ_AODW01000035
NZ_AODW0100001129280126,465RefSeq:NZ_AODW01000011
NZ_AODW0100001832300221,997RefSeq:NZ_AODW01000018
NZ_AODW0100002013120114,044RefSeq:NZ_AODW01000020
NZ_AODW0100004414120211,679RefSeq:NZ_AODW01000044
NZ_AODW010000511414007,218RefSeq:NZ_AODW01000051
24 Undisplayed Contigs/Replicons483991649,943
Total:3,8343,66873933,944,542
Ortholog data available?Yes
Database Contents
Genes3,834
Pathways264
Enzymatic Reactions1,283
Transport Reactions102
Polypeptides3,687
Protein Complexes52
Enzymes775
Transporters357
Compounds1,054
Transcription Units2,647
tRNAs63
GO Terms1,295
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii MSP4-16
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469980
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1278070
Environmentmangrove soil
Geographic LocationIndia
Collection Date2010-11
Annotation ProviderNCBI
Annotation Date2017-11-24
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.3
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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