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_TG2023, 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_AMIG01000079	166	157	5	4	172,974	RefSeq:NZ_AMIG01000079
NZ_AMIG01000108	173	169	1	3	162,736	RefSeq:NZ_AMIG01000108
NZ_AMIG01000081	121	115	5	1	122,227	RefSeq:NZ_AMIG01000081
NZ_AMIG01000104	101	98	0	3	107,348	RefSeq:NZ_AMIG01000104
NZ_AMIG01000023	110	108	0	2	107,018	RefSeq:NZ_AMIG01000023
NZ_AMIG01000042	85	82	0	3	97,706	RefSeq:NZ_AMIG01000042
NZ_AMIG01000151	105	102	1	2	90,099	RefSeq:NZ_AMIG01000151
NZ_AMIG01000096	74	72	0	2	81,578	RefSeq:NZ_AMIG01000096
NZ_AMIG01000093	66	65	0	1	76,341	RefSeq:NZ_AMIG01000093
NZ_AMIG01000142	63	61	1	1	75,932	RefSeq:NZ_AMIG01000142
NZ_AMIG01000102	85	83	1	1	75,208	RefSeq:NZ_AMIG01000102
NZ_AMIG01000097	70	70	0	0	70,572	RefSeq:NZ_AMIG01000097
NZ_AMIG01000161	72	71	0	1	67,613	RefSeq:NZ_AMIG01000161
NZ_AMIG01000164	65	61	0	4	67,298	RefSeq:NZ_AMIG01000164
NZ_AMIG01000146	63	59	4	0	66,544	RefSeq:NZ_AMIG01000146
NZ_AMIG01000116	55	55	0	0	63,291	RefSeq:NZ_AMIG01000116
NZ_AMIG01000123	60	58	0	2	61,911	RefSeq:NZ_AMIG01000123
NZ_AMIG01000084	59	56	2	1	60,657	RefSeq:NZ_AMIG01000084
NZ_AMIG01000119	59	58	0	1	60,616	RefSeq:NZ_AMIG01000119
NZ_AMIG01000024	46	41	4	1	59,775	RefSeq:NZ_AMIG01000024
NZ_AMIG01000015	58	54	4	0	56,915	RefSeq:NZ_AMIG01000015
NZ_AMIG01000105	50	48	0	2	55,295	RefSeq:NZ_AMIG01000105
NZ_AMIG01000072	49	47	0	2	52,296	RefSeq:NZ_AMIG01000072
NZ_AMIG01000125	52	50	0	2	49,710	RefSeq:NZ_AMIG01000125
NZ_AMIG01000073	42	41	1	0	49,451	RefSeq:NZ_AMIG01000073
NZ_AMIG01000077	72	71	0	1	49,333	RefSeq:NZ_AMIG01000077
NZ_AMIG01000144	58	57	0	1	49,247	RefSeq:NZ_AMIG01000144
NZ_AMIG01000115	50	48	0	2	48,662	RefSeq:NZ_AMIG01000115
NZ_AMIG01000134	45	43	0	2	47,593	RefSeq:NZ_AMIG01000134
NZ_AMIG01000126	50	43	5	2	44,460	RefSeq:NZ_AMIG01000126
NZ_AMIG01000133	40	39	0	1	43,358	RefSeq:NZ_AMIG01000133
NZ_AMIG01000010	41	40	0	1	42,617	RefSeq:NZ_AMIG01000010
NZ_AMIG01000091	41	40	0	1	40,418	RefSeq:NZ_AMIG01000091
NZ_AMIG01000052	30	28	0	2	38,122	RefSeq:NZ_AMIG01000052
NZ_AMIG01000120	34	33	0	1	38,025	RefSeq:NZ_AMIG01000120
NZ_AMIG01000087	35	31	3	1	37,087	RefSeq:NZ_AMIG01000087
NZ_AMIG01000035	34	34	0	0	36,965	RefSeq:NZ_AMIG01000035
NZ_AMIG01000111	30	30	0	0	35,345	RefSeq:NZ_AMIG01000111
NZ_AMIG01000095	34	33	1	0	34,800	RefSeq:NZ_AMIG01000095
NZ_AMIG01000127	30	30	0	0	34,786	RefSeq:NZ_AMIG01000127
NZ_AMIG01000092	24	24	0	0	34,456	RefSeq:NZ_AMIG01000092
NZ_AMIG01000086	32	31	0	1	33,642	RefSeq:NZ_AMIG01000086
NZ_AMIG01000085	27	26	0	1	33,628	RefSeq:NZ_AMIG01000085
NZ_AMIG01000148	32	30	0	2	31,685	RefSeq:NZ_AMIG01000148
NZ_AMIG01000129	27	25	2	0	30,532	RefSeq:NZ_AMIG01000129
NZ_AMIG01000166	29	27	0	2	30,164	RefSeq:NZ_AMIG01000166
NZ_AMIG01000099	26	25	0	1	28,731	RefSeq:NZ_AMIG01000099
NZ_AMIG01000143	24	23	0	1	28,359	RefSeq:NZ_AMIG01000143
NZ_AMIG01000136	31	31	0	0	28,358	RefSeq:NZ_AMIG01000136
NZ_AMIG01000011	27	25	1	1	27,741	RefSeq:NZ_AMIG01000011
NZ_AMIG01000054	26	26	0	0	27,378	RefSeq:NZ_AMIG01000054
NZ_AMIG01000117	24	23	0	1	27,158	RefSeq:NZ_AMIG01000117
NZ_AMIG01000103	24	24	0	0	27,083	RefSeq:NZ_AMIG01000103
NZ_AMIG01000088	24	24	0	0	26,440	RefSeq:NZ_AMIG01000088
NZ_AMIG01000004	23	23	0	0	26,307	RefSeq:NZ_AMIG01000004
NZ_AMIG01000118	29	28	0	1	25,700	RefSeq:NZ_AMIG01000118
NZ_AMIG01000145	27	26	0	1	25,580	RefSeq:NZ_AMIG01000145
NZ_AMIG01000113	23	22	0	1	25,156	RefSeq:NZ_AMIG01000113
NZ_AMIG01000109	17	17	0	0	24,212	RefSeq:NZ_AMIG01000109
NZ_AMIG01000158	24	23	0	1	24,205	RefSeq:NZ_AMIG01000158
NZ_AMIG01000021	22	20	1	1	23,096	RefSeq:NZ_AMIG01000021
NZ_AMIG01000059	27	24	1	2	23,077	RefSeq:NZ_AMIG01000059
NZ_AMIG01000173	24	24	0	0	22,974	RefSeq:NZ_AMIG01000173
NZ_AMIG01000107	19	18	0	1	21,367	RefSeq:NZ_AMIG01000107
NZ_AMIG01000128	23	22	0	1	20,911	RefSeq:NZ_AMIG01000128
NZ_AMIG01000132	19	18	0	1	20,651	RefSeq:NZ_AMIG01000132
NZ_AMIG01000131	28	26	1	1	20,538	RefSeq:NZ_AMIG01000131
NZ_AMIG01000175	18	16	0	2	20,264	RefSeq:NZ_AMIG01000175
NZ_AMIG01000153	21	20	0	1	20,241	RefSeq:NZ_AMIG01000153
NZ_AMIG01000121	15	15	0	0	20,143	RefSeq:NZ_AMIG01000121
NZ_AMIG01000012	19	16	0	3	19,796	RefSeq:NZ_AMIG01000012
NZ_AMIG01000061	17	13	4	0	19,110	RefSeq:NZ_AMIG01000061
NZ_AMIG01000101	17	15	2	0	18,269	RefSeq:NZ_AMIG01000101
NZ_AMIG01000008	16	15	0	1	16,090	RefSeq:NZ_AMIG01000008
NZ_AMIG01000094	15	15	0	0	16,078	RefSeq:NZ_AMIG01000094
NZ_AMIG01000006	13	10	2	1	15,228	RefSeq:NZ_AMIG01000006
NZ_AMIG01000122	12	12	0	0	14,723	RefSeq:NZ_AMIG01000122
NZ_AMIG01000156	12	11	0	1	14,349	RefSeq:NZ_AMIG01000156
NZ_AMIG01000074	12	10	1	1	13,869	RefSeq:NZ_AMIG01000074
NZ_AMIG01000110	14	14	0	0	13,052	RefSeq:NZ_AMIG01000110
NZ_AMIG01000155	11	10	0	1	12,817	RefSeq:NZ_AMIG01000155
NZ_AMIG01000137	12	12	0	0	12,416	RefSeq:NZ_AMIG01000137
NZ_AMIG01000013	13	12	0	1	11,637	RefSeq:NZ_AMIG01000013
92 Undisplayed Contigs/Replicons	266	253	13	60	335,142

Total:	3,818	3,605	66	147	3,944,282

Ortholog data available?	Yes

Database Contents

Genes	3,818
Pathways	256
Enzymatic Reactions	1,283
Transport Reactions	110
Polypeptides	3,666
Protein Complexes	51
Enzymes	798
Transporters	357
Compounds	1,040
Transcription Units	2,692
tRNAs	59
GO Terms	2,206

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Moraxellales Moraxellaceae Acinetobacter Acinetobacter calcoaceticus/baumannii complex Acinetobacter baumannii Acinetobacter baumannii AB_TG2023
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02471239
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1221276
Environment	blood
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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