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_1595-8, 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_AMHE01000066	123	119	4	0	130,322	RefSeq:NZ_AMHE01000066
NZ_AMHE01000033	118	110	5	3	127,655	RefSeq:NZ_AMHE01000033
NZ_AMHE01000122	111	108	0	3	111,069	RefSeq:NZ_AMHE01000122
NZ_AMHE01000121	95	92	1	2	102,615	RefSeq:NZ_AMHE01000121
NZ_AMHE01000135	99	98	0	1	101,073	RefSeq:NZ_AMHE01000135
NZ_AMHE01000085	98	96	1	1	100,715	RefSeq:NZ_AMHE01000085
NZ_AMHE01000146	77	75	0	2	90,119	RefSeq:NZ_AMHE01000146
NZ_AMHE01000163	91	91	0	0	88,283	RefSeq:NZ_AMHE01000163
NZ_AMHE01000195	85	81	4	0	87,266	RefSeq:NZ_AMHE01000195
NZ_AMHE01000155	72	71	0	1	79,917	RefSeq:NZ_AMHE01000155
NZ_AMHE01000004	83	79	2	2	79,147	RefSeq:NZ_AMHE01000004
NZ_AMHE01000100	74	71	0	3	77,254	RefSeq:NZ_AMHE01000100
NZ_AMHE01000164	73	72	0	1	75,609	RefSeq:NZ_AMHE01000164
NZ_AMHE01000149	65	62	1	2	69,746	RefSeq:NZ_AMHE01000149
NZ_AMHE01000081	55	49	4	2	69,738	RefSeq:NZ_AMHE01000081
NZ_AMHE01000166	60	58	0	2	69,631	RefSeq:NZ_AMHE01000166
NZ_AMHE01000022	60	58	0	2	69,226	RefSeq:NZ_AMHE01000022
NZ_AMHE01000171	49	47	0	2	62,074	RefSeq:NZ_AMHE01000171
NZ_AMHE01000145	55	55	0	0	58,485	RefSeq:NZ_AMHE01000145
NZ_AMHE01000147	55	52	1	2	52,527	RefSeq:NZ_AMHE01000147
NZ_AMHE01000150	58	58	0	0	49,052	RefSeq:NZ_AMHE01000150
NZ_AMHE01000173	55	52	2	1	48,356	RefSeq:NZ_AMHE01000173
NZ_AMHE01000178	40	39	1	0	47,349	RefSeq:NZ_AMHE01000178
NZ_AMHE01000152	46	45	0	1	47,237	RefSeq:NZ_AMHE01000152
NZ_AMHE01000154	38	37	1	0	47,188	RefSeq:NZ_AMHE01000154
NZ_AMHE01000113	50	48	0	2	46,630	RefSeq:NZ_AMHE01000113
NZ_AMHE01000144	43	41	0	2	45,387	RefSeq:NZ_AMHE01000144
NZ_AMHE01000181	37	33	2	2	44,166	RefSeq:NZ_AMHE01000181
NZ_AMHE01000131	52	52	0	0	44,103	RefSeq:NZ_AMHE01000131
NZ_AMHE01000201	45	44	0	1	43,977	RefSeq:NZ_AMHE01000201
NZ_AMHE01000138	36	36	0	0	42,985	RefSeq:NZ_AMHE01000138
NZ_AMHE01000015	39	39	0	0	42,702	RefSeq:NZ_AMHE01000015
NZ_AMHE01000126	40	40	0	0	42,269	RefSeq:NZ_AMHE01000126
NZ_AMHE01000130	32	32	0	0	41,494	RefSeq:NZ_AMHE01000130
NZ_AMHE01000114	46	42	4	0	40,242	RefSeq:NZ_AMHE01000114
NZ_AMHE01000019	35	30	4	1	39,534	RefSeq:NZ_AMHE01000019
NZ_AMHE01000172	35	35	0	0	38,714	RefSeq:NZ_AMHE01000172
NZ_AMHE01000106	54	54	0	0	37,782	RefSeq:NZ_AMHE01000106
NZ_AMHE01000011	39	35	4	0	36,972	RefSeq:NZ_AMHE01000011
NZ_AMHE01000115	34	33	0	1	36,963	RefSeq:NZ_AMHE01000115
NZ_AMHE01000137	29	28	0	1	35,797	RefSeq:NZ_AMHE01000137
NZ_AMHE01000049	35	34	1	0	34,784	RefSeq:NZ_AMHE01000049
NZ_AMHE01000191	30	30	0	0	33,461	RefSeq:NZ_AMHE01000191
NZ_AMHE01000160	32	32	0	0	33,118	RefSeq:NZ_AMHE01000160
NZ_AMHE01000003	29	29	0	0	31,814	RefSeq:NZ_AMHE01000003
NZ_AMHE01000187	31	30	0	1	30,901	RefSeq:NZ_AMHE01000187
NZ_AMHE01000056	31	29	0	2	30,733	RefSeq:NZ_AMHE01000056
NZ_AMHE01000157	32	31	0	1	30,298	RefSeq:NZ_AMHE01000157
NZ_AMHE01000024	34	32	0	2	29,522	RefSeq:NZ_AMHE01000024
NZ_AMHE01000117	20	20	0	0	29,236	RefSeq:NZ_AMHE01000117
NZ_AMHE01000159	24	23	0	1	27,375	RefSeq:NZ_AMHE01000159
NZ_AMHE01000029	23	22	0	1	26,933	RefSeq:NZ_AMHE01000029
NZ_AMHE01000002	28	28	0	0	26,659	RefSeq:NZ_AMHE01000002
NZ_AMHE01000179	24	23	0	1	26,298	RefSeq:NZ_AMHE01000179
NZ_AMHE01000095	26	24	0	2	25,915	RefSeq:NZ_AMHE01000095
NZ_AMHE01000180	34	31	2	1	25,611	RefSeq:NZ_AMHE01000180
NZ_AMHE01000039	24	24	0	0	25,511	RefSeq:NZ_AMHE01000039
NZ_AMHE01000194	20	20	0	0	25,002	RefSeq:NZ_AMHE01000194
NZ_AMHE01000108	27	25	1	1	24,727	RefSeq:NZ_AMHE01000108
NZ_AMHE01000184	19	17	1	1	24,227	RefSeq:NZ_AMHE01000184
NZ_AMHE01000177	23	23	0	0	24,074	RefSeq:NZ_AMHE01000177
NZ_AMHE01000027	19	18	0	1	23,442	RefSeq:NZ_AMHE01000027
NZ_AMHE01000205	27	26	0	1	23,433	RefSeq:NZ_AMHE01000205
NZ_AMHE01000188	21	20	0	1	23,343	RefSeq:NZ_AMHE01000188
NZ_AMHE01000008	21	21	0	0	23,287	RefSeq:NZ_AMHE01000008
NZ_AMHE01000162	23	23	0	0	21,657	RefSeq:NZ_AMHE01000162
NZ_AMHE01000007	21	20	0	1	21,344	RefSeq:NZ_AMHE01000007
NZ_AMHE01000165	17	17	0	0	21,060	RefSeq:NZ_AMHE01000165
NZ_AMHE01000018	17	17	0	0	20,392	RefSeq:NZ_AMHE01000018
NZ_AMHE01000034	21	19	1	1	20,142	RefSeq:NZ_AMHE01000034
NZ_AMHE01000196	15	14	0	1	20,103	RefSeq:NZ_AMHE01000196
NZ_AMHE01000153	21	21	0	0	19,282	RefSeq:NZ_AMHE01000153
NZ_AMHE01000151	18	17	0	1	18,807	RefSeq:NZ_AMHE01000151
NZ_AMHE01000129	35	35	0	0	18,563	RefSeq:NZ_AMHE01000129
NZ_AMHE01000001	21	21	0	0	18,547	RefSeq:NZ_AMHE01000001
NZ_AMHE01000203	16	15	1	0	18,410	RefSeq:NZ_AMHE01000203
NZ_AMHE01000170	21	19	1	1	18,218	RefSeq:NZ_AMHE01000170
NZ_AMHE01000156	18	18	0	0	17,187	RefSeq:NZ_AMHE01000156
NZ_AMHE01000078	15	12	3	0	16,098	RefSeq:NZ_AMHE01000078
NZ_AMHE01000197	15	13	0	2	16,039	RefSeq:NZ_AMHE01000197
NZ_AMHE01000158	17	16	0	1	15,956	RefSeq:NZ_AMHE01000158
NZ_AMHE01000071	18	17	0	1	15,876	RefSeq:NZ_AMHE01000071
NZ_AMHE01000037	16	16	0	0	14,526	RefSeq:NZ_AMHE01000037
NZ_AMHE01000020	12	12	0	0	14,287	RefSeq:NZ_AMHE01000020
NZ_AMHE01000006	11	11	0	0	14,180	RefSeq:NZ_AMHE01000006
NZ_AMHE01000014	17	15	0	2	14,138	RefSeq:NZ_AMHE01000014
NZ_AMHE01000116	12	12	0	0	13,982	RefSeq:NZ_AMHE01000116
NZ_AMHE01000012	20	20	0	0	13,404	RefSeq:NZ_AMHE01000012
NZ_AMHE01000124	12	12	0	0	13,392	RefSeq:NZ_AMHE01000124
NZ_AMHE01000183	12	12	0	0	13,287	RefSeq:NZ_AMHE01000183
NZ_AMHE01000142	12	12	0	0	13,273	RefSeq:NZ_AMHE01000142
NZ_AMHE01000021	12	12	0	0	12,433	RefSeq:NZ_AMHE01000021
NZ_AMHE01000168	16	16	0	0	11,765	RefSeq:NZ_AMHE01000168
NZ_AMHE01000061	13	10	0	3	9,482	RefSeq:NZ_AMHE01000061
NZ_AMHE01000193	12	12	0	0	7,046	RefSeq:NZ_AMHE01000193
NZ_AMHE01000050	13	12	0	1	6,480	RefSeq:NZ_AMHE01000050
109 Undisplayed Contigs/Replicons	262	256	8	68	319,824

Total:	3,966	3,763	60	143	4,070,254

Ortholog data available?	Yes

Database Contents

Genes	3,963
Pathways	261
Enzymatic Reactions	1,300
Transport Reactions	111
Polypeptides	3,829
Protein Complexes	53
Enzymes	809
Transporters	363
Compounds	1,059
Transcription Units	2,798
tRNAs	52
GO Terms	2,332

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Moraxellales Moraxellaceae Acinetobacter Acinetobacter calcoaceticus/baumannii complex Acinetobacter baumannii Acinetobacter baumannii AB_1595-8
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02471270
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1221248
Environment	urine
Host	Homo sapiens
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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