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 AB_1594-8, 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_AMHD0100000412212011126,323RefSeq:NZ_AMHD01000004
NZ_AMHD0100015711010352122,818RefSeq:NZ_AMHD01000157
NZ_AMHD0100021686850194,450RefSeq:NZ_AMHD01000216
NZ_AMHD0100013689843285,556RefSeq:NZ_AMHD01000136
NZ_AMHD0100008684821183,921RefSeq:NZ_AMHD01000086
NZ_AMHD0100009189890083,405RefSeq:NZ_AMHD01000091
NZ_AMHD0100015672701182,803RefSeq:NZ_AMHD01000156
NZ_AMHD0100010369660371,018RefSeq:NZ_AMHD01000103
NZ_AMHD0100016069661267,603RefSeq:NZ_AMHD01000160
NZ_AMHD0100016658560267,287RefSeq:NZ_AMHD01000166
NZ_AMHD0100018763620167,218RefSeq:NZ_AMHD01000187
NZ_AMHD0100016862620066,609RefSeq:NZ_AMHD01000168
NZ_AMHD0100016562581365,334RefSeq:NZ_AMHD01000165
NZ_AMHD0100005168660262,932RefSeq:NZ_AMHD01000051
NZ_AMHD0100021950453258,519RefSeq:NZ_AMHD01000219
NZ_AMHD0100004046442056,523RefSeq:NZ_AMHD01000040
NZ_AMHD0100017765612255,838RefSeq:NZ_AMHD01000177
NZ_AMHD0100014345450054,125RefSeq:NZ_AMHD01000143
NZ_AMHD0100018550470353,956RefSeq:NZ_AMHD01000185
NZ_AMHD0100018450480250,933RefSeq:NZ_AMHD01000184
NZ_AMHD0100019440390145,133RefSeq:NZ_AMHD01000194
NZ_AMHD0100017848480044,467RefSeq:NZ_AMHD01000178
NZ_AMHD0100015040390144,347RefSeq:NZ_AMHD01000150
NZ_AMHD0100020041400143,335RefSeq:NZ_AMHD01000200
NZ_AMHD0100015334320243,305RefSeq:NZ_AMHD01000153
NZ_AMHD0100022035331143,207RefSeq:NZ_AMHD01000220
NZ_AMHD0100014434330142,955RefSeq:NZ_AMHD01000144
NZ_AMHD0100019738380042,455RefSeq:NZ_AMHD01000197
NZ_AMHD0100014841383041,987RefSeq:NZ_AMHD01000148
NZ_AMHD0100007839370241,203RefSeq:NZ_AMHD01000078
NZ_AMHD0100022244440040,839RefSeq:NZ_AMHD01000222
NZ_AMHD0100013435350040,465RefSeq:NZ_AMHD01000134
NZ_AMHD0100017240380239,318RefSeq:NZ_AMHD01000172
NZ_AMHD0100017132310138,549RefSeq:NZ_AMHD01000171
NZ_AMHD0100014941380338,442RefSeq:NZ_AMHD01000149
NZ_AMHD0100019934340038,370RefSeq:NZ_AMHD01000199
NZ_AMHD0100021735330237,512RefSeq:NZ_AMHD01000217
NZ_AMHD0100009634330136,153RefSeq:NZ_AMHD01000096
NZ_AMHD0100006728270136,087RefSeq:NZ_AMHD01000067
NZ_AMHD0100009931300133,655RefSeq:NZ_AMHD01000099
NZ_AMHD0100021834340032,951RefSeq:NZ_AMHD01000218
NZ_AMHD0100016728270131,862RefSeq:NZ_AMHD01000167
NZ_AMHD0100004226250130,873RefSeq:NZ_AMHD01000042
NZ_AMHD0100000225250030,599RefSeq:NZ_AMHD01000002
NZ_AMHD0100017934294130,530RefSeq:NZ_AMHD01000179
NZ_AMHD0100018031300130,222RefSeq:NZ_AMHD01000180
NZ_AMHD0100014522220029,349RefSeq:NZ_AMHD01000145
NZ_AMHD0100011727251128,720RefSeq:NZ_AMHD01000117
NZ_AMHD0100013120200026,971RefSeq:NZ_AMHD01000131
NZ_AMHD0100020624240026,208RefSeq:NZ_AMHD01000206
NZ_AMHD0100020824231026,134RefSeq:NZ_AMHD01000208
NZ_AMHD0100021128270125,085RefSeq:NZ_AMHD01000211
NZ_AMHD0100001119190024,901RefSeq:NZ_AMHD01000011
NZ_AMHD0100001322191224,720RefSeq:NZ_AMHD01000013
NZ_AMHD0100015518180024,544RefSeq:NZ_AMHD01000155
NZ_AMHD0100010728271024,517RefSeq:NZ_AMHD01000107
NZ_AMHD0100017425230224,342RefSeq:NZ_AMHD01000174
NZ_AMHD0100004326250124,093RefSeq:NZ_AMHD01000043
NZ_AMHD0100005220190123,952RefSeq:NZ_AMHD01000052
NZ_AMHD0100020224230123,774RefSeq:NZ_AMHD01000202
NZ_AMHD0100012221200123,550RefSeq:NZ_AMHD01000122
NZ_AMHD0100005823220123,123RefSeq:NZ_AMHD01000058
NZ_AMHD0100011825231123,098RefSeq:NZ_AMHD01000118
NZ_AMHD0100000725231122,784RefSeq:NZ_AMHD01000007
NZ_AMHD0100021322210122,617RefSeq:NZ_AMHD01000213
NZ_AMHD0100003923230022,169RefSeq:NZ_AMHD01000039
NZ_AMHD0100001224220221,432RefSeq:NZ_AMHD01000012
NZ_AMHD0100009825222121,279RefSeq:NZ_AMHD01000098
NZ_AMHD0100001918170120,516RefSeq:NZ_AMHD01000019
NZ_AMHD0100014017170019,883RefSeq:NZ_AMHD01000140
NZ_AMHD0100005916140219,543RefSeq:NZ_AMHD01000059
NZ_AMHD0100020318170119,539RefSeq:NZ_AMHD01000203
NZ_AMHD0100004919150418,526RefSeq:NZ_AMHD01000049
NZ_AMHD0100018217151118,419RefSeq:NZ_AMHD01000182
NZ_AMHD0100004518160218,402RefSeq:NZ_AMHD01000045
NZ_AMHD0100001619170217,687RefSeq:NZ_AMHD01000016
NZ_AMHD0100018817150217,344RefSeq:NZ_AMHD01000188
NZ_AMHD0100001416150117,179RefSeq:NZ_AMHD01000014
NZ_AMHD0100021218160216,391RefSeq:NZ_AMHD01000212
NZ_AMHD0100021516113216,373RefSeq:NZ_AMHD01000215
NZ_AMHD0100006519180115,931RefSeq:NZ_AMHD01000065
NZ_AMHD0100004715150015,871RefSeq:NZ_AMHD01000047
NZ_AMHD0100003519180115,858RefSeq:NZ_AMHD01000035
NZ_AMHD0100010018170115,577RefSeq:NZ_AMHD01000100
NZ_AMHD0100004612111015,518RefSeq:NZ_AMHD01000046
NZ_AMHD0100004818162015,157RefSeq:NZ_AMHD01000048
NZ_AMHD0100002913110215,021RefSeq:NZ_AMHD01000029
NZ_AMHD0100001712120014,279RefSeq:NZ_AMHD01000017
NZ_AMHD0100000621210013,650RefSeq:NZ_AMHD01000006
NZ_AMHD0100017314140013,572RefSeq:NZ_AMHD01000173
NZ_AMHD0100006412120012,420RefSeq:NZ_AMHD01000064
NZ_AMHD0100022114120212,315RefSeq:NZ_AMHD01000221
NZ_AMHD0100005613120111,777RefSeq:NZ_AMHD01000056
NZ_AMHD0100002015130211,716RefSeq:NZ_AMHD01000020
NZ_AMHD0100000112110111,670RefSeq:NZ_AMHD01000001
NZ_AMHD0100020720200011,332RefSeq:NZ_AMHD01000207
NZ_AMHD0100015919190011,030RefSeq:NZ_AMHD01000159
NZ_AMHD0100012712101110,417RefSeq:NZ_AMHD01000127
NZ_AMHD0100000517170010,349RefSeq:NZ_AMHD01000005
NZ_AMHD01000081138058,585RefSeq:NZ_AMHD01000081
NZ_AMHD010000301919008,059RefSeq:NZ_AMHD01000030
NZ_AMHD010000721414008,056RefSeq:NZ_AMHD01000072
NZ_AMHD010000831412025,416RefSeq:NZ_AMHD01000083
119 Undisplayed Contigs/Replicons3703591174456,342
Total:3,8543,615551843,973,074
Ortholog data available?Yes
Database Contents
Genes3,854
Pathways266
Enzymatic Reactions1,303
Transport Reactions102
Polypeptides3,684
Protein Complexes52
Enzymes770
Transporters349
Compounds1,064
Transcription Units2,743
tRNAs48
GO Terms1,276
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_1594-8
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471258
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221247
Environmentsputum
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-23
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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