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_1582-8, 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_AMHB01000123	122	119	0	3	137,922	RefSeq:NZ_AMHB01000123
NZ_AMHB01000144	121	119	1	1	111,015	RefSeq:NZ_AMHB01000144
NZ_AMHB01000043	98	96	1	1	100,430	RefSeq:NZ_AMHB01000043
NZ_AMHB01000072	83	83	0	0	91,001	RefSeq:NZ_AMHB01000072
NZ_AMHB01000221	79	77	0	2	88,239	RefSeq:NZ_AMHB01000221
NZ_AMHB01000201	91	88	1	2	83,277	RefSeq:NZ_AMHB01000201
NZ_AMHB01000229	69	68	0	1	78,837	RefSeq:NZ_AMHB01000229
NZ_AMHB01000188	79	76	2	1	78,541	RefSeq:NZ_AMHB01000188
NZ_AMHB01000227	70	70	0	0	78,265	RefSeq:NZ_AMHB01000227
NZ_AMHB01000202	65	61	0	4	71,479	RefSeq:NZ_AMHB01000202
NZ_AMHB01000198	62	62	0	0	70,919	RefSeq:NZ_AMHB01000198
NZ_AMHB01000179	67	66	0	1	70,547	RefSeq:NZ_AMHB01000179
NZ_AMHB01000071	56	55	0	1	68,159	RefSeq:NZ_AMHB01000071
NZ_AMHB01000159	63	58	2	3	64,668	RefSeq:NZ_AMHB01000159
NZ_AMHB01000244	54	54	0	0	56,681	RefSeq:NZ_AMHB01000244
NZ_AMHB01000208	55	54	0	1	56,003	RefSeq:NZ_AMHB01000208
NZ_AMHB01000226	49	48	0	1	55,840	RefSeq:NZ_AMHB01000226
NZ_AMHB01000213	50	47	0	3	54,788	RefSeq:NZ_AMHB01000213
NZ_AMHB01000204	49	48	1	0	53,027	RefSeq:NZ_AMHB01000204
NZ_AMHB01000192	53	51	1	1	50,661	RefSeq:NZ_AMHB01000192
NZ_AMHB01000225	58	58	0	0	49,129	RefSeq:NZ_AMHB01000225
NZ_AMHB01000228	55	52	2	1	48,416	RefSeq:NZ_AMHB01000228
NZ_AMHB01000222	55	51	2	2	46,632	RefSeq:NZ_AMHB01000222
NZ_AMHB01000156	38	36	0	2	46,264	RefSeq:NZ_AMHB01000156
NZ_AMHB01000205	46	42	3	1	46,208	RefSeq:NZ_AMHB01000205
NZ_AMHB01000233	45	44	0	1	45,448	RefSeq:NZ_AMHB01000233
NZ_AMHB01000178	46	45	0	1	44,068	RefSeq:NZ_AMHB01000178
NZ_AMHB01000114	38	36	1	1	43,787	RefSeq:NZ_AMHB01000114
NZ_AMHB01000212	47	45	0	2	43,756	RefSeq:NZ_AMHB01000212
NZ_AMHB01000220	32	29	1	2	43,610	RefSeq:NZ_AMHB01000220
NZ_AMHB01000195	34	32	0	2	42,992	RefSeq:NZ_AMHB01000195
NZ_AMHB01000251	38	38	0	0	41,921	RefSeq:NZ_AMHB01000251
NZ_AMHB01000166	37	32	4	1	41,414	RefSeq:NZ_AMHB01000166
NZ_AMHB01000099	46	42	4	0	40,272	RefSeq:NZ_AMHB01000099
NZ_AMHB01000243	36	33	3	0	39,582	RefSeq:NZ_AMHB01000243
NZ_AMHB01000241	40	40	0	0	39,465	RefSeq:NZ_AMHB01000241
NZ_AMHB01000004	37	36	0	1	39,330	RefSeq:NZ_AMHB01000004
NZ_AMHB01000023	36	35	0	1	38,968	RefSeq:NZ_AMHB01000023
NZ_AMHB01000021	34	34	0	0	38,362	RefSeq:NZ_AMHB01000021
NZ_AMHB01000031	41	39	1	1	37,950	RefSeq:NZ_AMHB01000031
NZ_AMHB01000193	35	35	0	0	37,733	RefSeq:NZ_AMHB01000193
NZ_AMHB01000234	35	34	0	1	35,113	RefSeq:NZ_AMHB01000234
NZ_AMHB01000026	31	31	0	0	33,408	RefSeq:NZ_AMHB01000026
NZ_AMHB01000253	29	29	0	0	31,813	RefSeq:NZ_AMHB01000253
NZ_AMHB01000211	31	31	0	0	31,459	RefSeq:NZ_AMHB01000211
NZ_AMHB01000080	41	37	3	1	30,620	RefSeq:NZ_AMHB01000080
NZ_AMHB01000051	32	31	0	1	30,383	RefSeq:NZ_AMHB01000051
NZ_AMHB01000194	29	25	4	0	30,061	RefSeq:NZ_AMHB01000194
NZ_AMHB01000207	30	28	0	2	29,946	RefSeq:NZ_AMHB01000207
NZ_AMHB01000005	24	23	0	1	28,777	RefSeq:NZ_AMHB01000005
NZ_AMHB01000010	25	25	0	0	28,111	RefSeq:NZ_AMHB01000010
NZ_AMHB01000160	29	28	0	1	26,713	RefSeq:NZ_AMHB01000160
NZ_AMHB01000216	28	28	0	0	26,659	RefSeq:NZ_AMHB01000216
NZ_AMHB01000129	33	33	0	0	25,891	RefSeq:NZ_AMHB01000129
NZ_AMHB01000217	21	20	0	1	25,753	RefSeq:NZ_AMHB01000217
NZ_AMHB01000183	24	23	0	1	25,374	RefSeq:NZ_AMHB01000183
NZ_AMHB01000173	20	20	0	0	25,030	RefSeq:NZ_AMHB01000173
NZ_AMHB01000232	21	19	1	1	24,435	RefSeq:NZ_AMHB01000232
NZ_AMHB01000100	23	23	0	0	23,770	RefSeq:NZ_AMHB01000100
NZ_AMHB01000148	21	19	0	2	23,289	RefSeq:NZ_AMHB01000148
NZ_AMHB01000250	23	22	0	1	23,095	RefSeq:NZ_AMHB01000250
NZ_AMHB01000078	25	23	1	1	22,815	RefSeq:NZ_AMHB01000078
NZ_AMHB01000136	22	22	0	0	22,564	RefSeq:NZ_AMHB01000136
NZ_AMHB01000218	18	18	0	0	21,442	RefSeq:NZ_AMHB01000218
NZ_AMHB01000189	19	19	0	0	21,061	RefSeq:NZ_AMHB01000189
NZ_AMHB01000239	17	17	0	0	21,060	RefSeq:NZ_AMHB01000239
NZ_AMHB01000089	19	19	0	0	20,436	RefSeq:NZ_AMHB01000089
NZ_AMHB01000235	20	20	0	0	20,076	RefSeq:NZ_AMHB01000235
NZ_AMHB01000086	21	21	0	0	18,548	RefSeq:NZ_AMHB01000086
NZ_AMHB01000238	16	15	1	0	18,412	RefSeq:NZ_AMHB01000238
NZ_AMHB01000107	29	28	0	1	17,173	RefSeq:NZ_AMHB01000107
NZ_AMHB01000076	12	12	0	0	17,028	RefSeq:NZ_AMHB01000076
NZ_AMHB01000012	15	15	0	0	16,796	RefSeq:NZ_AMHB01000012
NZ_AMHB01000245	13	13	0	0	16,165	RefSeq:NZ_AMHB01000245
NZ_AMHB01000030	15	12	3	0	16,152	RefSeq:NZ_AMHB01000030
NZ_AMHB01000134	17	16	0	1	15,746	RefSeq:NZ_AMHB01000134
NZ_AMHB01000034	23	21	0	2	15,125	RefSeq:NZ_AMHB01000034
NZ_AMHB01000128	15	15	0	0	15,058	RefSeq:NZ_AMHB01000128
NZ_AMHB01000019	16	16	0	0	14,749	RefSeq:NZ_AMHB01000019
NZ_AMHB01000170	17	17	0	0	14,607	RefSeq:NZ_AMHB01000170
NZ_AMHB01000027	16	14	0	2	14,583	RefSeq:NZ_AMHB01000027
NZ_AMHB01000118	16	14	0	2	13,407	RefSeq:NZ_AMHB01000118
NZ_AMHB01000001	12	12	0	0	13,261	RefSeq:NZ_AMHB01000001
NZ_AMHB01000215	13	13	0	0	13,216	RefSeq:NZ_AMHB01000215
NZ_AMHB01000084	12	11	1	0	13,179	RefSeq:NZ_AMHB01000084
NZ_AMHB01000121	13	12	0	1	12,592	RefSeq:NZ_AMHB01000121
NZ_AMHB01000008	12	12	0	0	12,422	RefSeq:NZ_AMHB01000008
NZ_AMHB01000055	14	13	0	1	11,911	RefSeq:NZ_AMHB01000055
NZ_AMHB01000025	13	12	1	0	11,565	RefSeq:NZ_AMHB01000025
NZ_AMHB01000103	11	9	0	2	11,295	RefSeq:NZ_AMHB01000103
NZ_AMHB01000057	15	12	0	3	10,948	RefSeq:NZ_AMHB01000057
NZ_AMHB01000150	12	10	0	2	10,893	RefSeq:NZ_AMHB01000150
NZ_AMHB01000199	15	15	0	0	10,885	RefSeq:NZ_AMHB01000199
160 Undisplayed Contigs/Replicons	467	452	19	107	574,361

Total:	3,960	3,713	64	183	4,054,837

Ortholog data available?	Yes

Database Contents

Genes	3,956
Pathways	263
Enzymatic Reactions	1,315
Transport Reactions	110
Polypeptides	3,804
Protein Complexes	54
Enzymes	808
Transporters	365
Compounds	1,075
Transcription Units	2,831
tRNAs	55
GO Terms	2,334

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Moraxellales Moraxellaceae Acinetobacter Acinetobacter calcoaceticus/baumannii complex Acinetobacter baumannii Acinetobacter baumannii AB_1582-8
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02471275
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1221245
Environment	sputum
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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