Summary of Acinetobacter baumannii AB

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Peter Midford, Ingrid Keseler¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter baumannii AB_1583-8, 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

Contig	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
NZ_AMHC01000214	107	101	2	4	115,943	RefSeq:NZ_AMHC01000214
NZ_AMHC01000156	62	61	0	1	72,776	RefSeq:NZ_AMHC01000156
NZ_AMHC01000002	76	70	3	3	72,303	RefSeq:NZ_AMHC01000002
NZ_AMHC01000300	60	57	0	3	71,400	RefSeq:NZ_AMHC01000300
NZ_AMHC01000318	71	69	0	2	68,911	RefSeq:NZ_AMHC01000318
NZ_AMHC01000252	61	57	0	4	68,054	RefSeq:NZ_AMHC01000252
NZ_AMHC01000185	58	55	0	3	62,012	RefSeq:NZ_AMHC01000185
NZ_AMHC01000316	70	68	0	2	61,572	RefSeq:NZ_AMHC01000316
NZ_AMHC01000022	52	52	0	0	57,633	RefSeq:NZ_AMHC01000022
NZ_AMHC01000291	49	48	1	0	57,028	RefSeq:NZ_AMHC01000291
NZ_AMHC01000096	62	60	0	2	57,021	RefSeq:NZ_AMHC01000096
NZ_AMHC01000127	50	48	0	2	54,202	RefSeq:NZ_AMHC01000127
NZ_AMHC01000200	48	48	0	0	53,497	RefSeq:NZ_AMHC01000200
NZ_AMHC01000094	60	58	2	0	52,446	RefSeq:NZ_AMHC01000094
NZ_AMHC01000016	46	45	0	1	52,114	RefSeq:NZ_AMHC01000016
NZ_AMHC01000034	52	49	0	3	51,410	RefSeq:NZ_AMHC01000034
NZ_AMHC01000145	48	47	1	0	46,353	RefSeq:NZ_AMHC01000145
NZ_AMHC01000303	54	52	1	1	45,433	RefSeq:NZ_AMHC01000303
NZ_AMHC01000055	45	45	0	0	43,854	RefSeq:NZ_AMHC01000055
NZ_AMHC01000228	38	38	0	0	40,834	RefSeq:NZ_AMHC01000228
NZ_AMHC01000193	37	35	0	2	40,725	RefSeq:NZ_AMHC01000193
NZ_AMHC01000009	38	36	0	2	40,432	RefSeq:NZ_AMHC01000009
NZ_AMHC01000005	47	43	3	1	39,246	RefSeq:NZ_AMHC01000005
NZ_AMHC01000024	51	50	0	1	36,904	RefSeq:NZ_AMHC01000024
NZ_AMHC01000194	35	35	0	0	36,265	RefSeq:NZ_AMHC01000194
NZ_AMHC01000315	37	34	0	3	36,046	RefSeq:NZ_AMHC01000315
NZ_AMHC01000177	27	27	0	0	35,623	RefSeq:NZ_AMHC01000177
NZ_AMHC01000296	28	28	0	0	35,300	RefSeq:NZ_AMHC01000296
NZ_AMHC01000006	32	28	2	2	34,823	RefSeq:NZ_AMHC01000006
NZ_AMHC01000056	31	31	0	0	34,252	RefSeq:NZ_AMHC01000056
NZ_AMHC01000051	29	29	0	0	33,990	RefSeq:NZ_AMHC01000051
NZ_AMHC01000251	44	41	1	2	33,939	RefSeq:NZ_AMHC01000251
NZ_AMHC01000098	23	22	1	0	33,932	RefSeq:NZ_AMHC01000098
NZ_AMHC01000287	30	29	0	1	33,062	RefSeq:NZ_AMHC01000287
NZ_AMHC01000280	26	26	0	0	32,351	RefSeq:NZ_AMHC01000280
NZ_AMHC01000282	29	29	0	0	31,094	RefSeq:NZ_AMHC01000282
NZ_AMHC01000290	30	29	0	1	30,984	RefSeq:NZ_AMHC01000290
NZ_AMHC01000003	29	28	0	1	30,815	RefSeq:NZ_AMHC01000003
NZ_AMHC01000033	31	31	0	0	30,767	RefSeq:NZ_AMHC01000033
NZ_AMHC01000294	25	22	2	1	30,501	RefSeq:NZ_AMHC01000294
NZ_AMHC01000072	26	25	0	1	29,703	RefSeq:NZ_AMHC01000072
NZ_AMHC01000029	29	27	1	1	29,456	RefSeq:NZ_AMHC01000029
NZ_AMHC01000293	33	32	0	1	29,208	RefSeq:NZ_AMHC01000293
NZ_AMHC01000226	33	32	0	1	29,179	RefSeq:NZ_AMHC01000226
NZ_AMHC01000048	27	27	0	0	28,345	RefSeq:NZ_AMHC01000048
NZ_AMHC01000260	25	21	4	0	28,304	RefSeq:NZ_AMHC01000260
NZ_AMHC01000281	29	29	0	0	28,181	RefSeq:NZ_AMHC01000281
NZ_AMHC01000220	27	26	0	1	27,754	RefSeq:NZ_AMHC01000220
NZ_AMHC01000086	23	22	0	1	26,754	RefSeq:NZ_AMHC01000086
NZ_AMHC01000049	29	28	0	1	26,495	RefSeq:NZ_AMHC01000049
NZ_AMHC01000301	24	24	0	0	26,236	RefSeq:NZ_AMHC01000301
NZ_AMHC01000011	24	24	0	0	26,145	RefSeq:NZ_AMHC01000011
NZ_AMHC01000023	24	21	0	3	26,122	RefSeq:NZ_AMHC01000023
NZ_AMHC01000286	30	30	0	0	25,817	RefSeq:NZ_AMHC01000286
NZ_AMHC01000295	28	28	0	0	25,070	RefSeq:NZ_AMHC01000295
NZ_AMHC01000087	40	40	0	0	25,055	RefSeq:NZ_AMHC01000087
NZ_AMHC01000314	28	27	1	0	24,970	RefSeq:NZ_AMHC01000314
NZ_AMHC01000309	20	20	0	0	24,030	RefSeq:NZ_AMHC01000309
NZ_AMHC01000014	22	20	0	2	23,560	RefSeq:NZ_AMHC01000014
NZ_AMHC01000313	18	17	0	1	22,731	RefSeq:NZ_AMHC01000313
NZ_AMHC01000102	20	19	0	1	22,662	RefSeq:NZ_AMHC01000102
NZ_AMHC01000321	18	17	0	1	22,556	RefSeq:NZ_AMHC01000321
NZ_AMHC01000083	18	18	0	0	21,365	RefSeq:NZ_AMHC01000083
NZ_AMHC01000077	21	18	0	3	21,338	RefSeq:NZ_AMHC01000077
NZ_AMHC01000057	25	21	2	2	21,217	RefSeq:NZ_AMHC01000057
NZ_AMHC01000035	18	17	0	1	21,105	RefSeq:NZ_AMHC01000035
NZ_AMHC01000320	23	23	0	0	20,426	RefSeq:NZ_AMHC01000320
NZ_AMHC01000219	17	16	0	1	19,830	RefSeq:NZ_AMHC01000219
NZ_AMHC01000043	17	17	0	0	19,752	RefSeq:NZ_AMHC01000043
NZ_AMHC01000044	14	14	0	0	19,717	RefSeq:NZ_AMHC01000044
NZ_AMHC01000283	19	18	0	1	19,656	RefSeq:NZ_AMHC01000283
NZ_AMHC01000305	14	14	0	0	19,286	RefSeq:NZ_AMHC01000305
NZ_AMHC01000037	17	16	0	1	19,138	RefSeq:NZ_AMHC01000037
NZ_AMHC01000306	16	16	0	0	19,008	RefSeq:NZ_AMHC01000306
NZ_AMHC01000078	21	21	0	0	18,561	RefSeq:NZ_AMHC01000078
NZ_AMHC01000207	16	15	0	1	18,083	RefSeq:NZ_AMHC01000207
NZ_AMHC01000122	20	19	0	1	17,985	RefSeq:NZ_AMHC01000122
NZ_AMHC01000105	28	27	0	1	17,876	RefSeq:NZ_AMHC01000105
NZ_AMHC01000075	13	12	1	0	17,348	RefSeq:NZ_AMHC01000075
NZ_AMHC01000031	18	17	1	0	16,217	RefSeq:NZ_AMHC01000031
NZ_AMHC01000053	17	16	0	1	15,977	RefSeq:NZ_AMHC01000053
NZ_AMHC01000138	14	13	0	1	15,964	RefSeq:NZ_AMHC01000138
NZ_AMHC01000264	27	26	0	1	15,269	RefSeq:NZ_AMHC01000264
NZ_AMHC01000115	15	14	0	1	15,207	RefSeq:NZ_AMHC01000115
NZ_AMHC01000018	12	11	0	1	15,032	RefSeq:NZ_AMHC01000018
NZ_AMHC01000079	15	14	0	1	14,995	RefSeq:NZ_AMHC01000079
NZ_AMHC01000032	17	17	0	0	14,598	RefSeq:NZ_AMHC01000032
NZ_AMHC01000289	12	12	0	0	14,313	RefSeq:NZ_AMHC01000289
NZ_AMHC01000310	14	13	1	0	14,271	RefSeq:NZ_AMHC01000310
NZ_AMHC01000046	16	15	0	1	14,168	RefSeq:NZ_AMHC01000046
NZ_AMHC01000135	14	12	1	1	14,167	RefSeq:NZ_AMHC01000135
NZ_AMHC01000040	12	11	0	1	13,985	RefSeq:NZ_AMHC01000040
NZ_AMHC01000019	13	12	0	1	13,618	RefSeq:NZ_AMHC01000019
NZ_AMHC01000110	12	11	0	1	13,288	RefSeq:NZ_AMHC01000110
NZ_AMHC01000013	12	11	1	0	13,170	RefSeq:NZ_AMHC01000013
NZ_AMHC01000020	12	12	0	0	13,095	RefSeq:NZ_AMHC01000020
NZ_AMHC01000062	16	16	0	0	12,933	RefSeq:NZ_AMHC01000062
NZ_AMHC01000143	12	12	0	0	12,794	RefSeq:NZ_AMHC01000143
NZ_AMHC01000120	14	13	0	1	12,296	RefSeq:NZ_AMHC01000120
NZ_AMHC01000106	16	14	0	2	12,034	RefSeq:NZ_AMHC01000106
NZ_AMHC01000304	11	11	0	0	11,202	RefSeq:NZ_AMHC01000304
NZ_AMHC01000249	15	14	0	1	10,620	RefSeq:NZ_AMHC01000249
NZ_AMHC01000007	10	6	4	0	10,116	RefSeq:NZ_AMHC01000007
NZ_AMHC01000164	13	10	1	2	9,592	RefSeq:NZ_AMHC01000164
NZ_AMHC01000080	13	12	0	1	6,551	RefSeq:NZ_AMHC01000080
NZ_AMHC01000217	12	10	0	2	5,588	RefSeq:NZ_AMHC01000217
216 Undisplayed Contigs/Replicons	591	578	15	129	732,682

Total:	3,828	3,552	52	224	3,889,613

Ortholog data available?	Yes

Database Contents

Genes	3,826
Pathways	252
Enzymatic Reactions	1,270
Transport Reactions	98
Polypeptides	3,662
Protein Complexes	51
Enzymes	765
Transporters	328
Compounds	1,037
Transcription Units	2,685
tRNAs	44
GO Terms	1,910

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Moraxellales Moraxellaceae Acinetobacter Acinetobacter calcoaceticus/baumannii complex Acinetobacter baumannii Acinetobacter baumannii AB_1583-8
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02471247
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1221246
Annotation Provider	NCBI
Annotation Date	2017-11-23
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version	4.3
Annotation Comment	Best-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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