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_515-8, 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_AMHU01000215	129	121	5	3	139,311	RefSeq:NZ_AMHU01000215
NZ_AMHU01000003	114	108	3	3	118,219	RefSeq:NZ_AMHU01000003
NZ_AMHU01000151	111	108	0	3	110,986	RefSeq:NZ_AMHU01000151
NZ_AMHU01000160	98	96	1	1	100,721	RefSeq:NZ_AMHU01000160
NZ_AMHU01000172	86	85	0	1	92,707	RefSeq:NZ_AMHU01000172
NZ_AMHU01000189	91	91	0	0	88,284	RefSeq:NZ_AMHU01000189
NZ_AMHU01000121	75	74	0	1	81,854	RefSeq:NZ_AMHU01000121
NZ_AMHU01000167	72	71	0	1	79,928	RefSeq:NZ_AMHU01000167
NZ_AMHU01000118	83	79	2	2	79,147	RefSeq:NZ_AMHU01000118
NZ_AMHU01000165	77	73	1	3	76,593	RefSeq:NZ_AMHU01000165
NZ_AMHU01000032	69	67	0	2	74,376	RefSeq:NZ_AMHU01000032
NZ_AMHU01000096	67	66	0	1	70,564	RefSeq:NZ_AMHU01000096
NZ_AMHU01000161	61	59	0	2	69,844	RefSeq:NZ_AMHU01000161
NZ_AMHU01000142	60	58	0	2	69,632	RefSeq:NZ_AMHU01000142
NZ_AMHU01000009	70	66	3	1	68,735	RefSeq:NZ_AMHU01000009
NZ_AMHU01000106	57	57	0	0	63,091	RefSeq:NZ_AMHU01000106
NZ_AMHU01000171	49	47	0	2	62,093	RefSeq:NZ_AMHU01000171
NZ_AMHU01000158	56	55	0	1	59,615	RefSeq:NZ_AMHU01000158
NZ_AMHU01000163	55	55	0	0	58,485	RefSeq:NZ_AMHU01000163
NZ_AMHU01000018	69	68	0	1	58,354	RefSeq:NZ_AMHU01000018
NZ_AMHU01000045	56	49	7	0	54,432	RefSeq:NZ_AMHU01000045
NZ_AMHU01000170	55	52	2	1	48,356	RefSeq:NZ_AMHU01000170
NZ_AMHU01000184	38	37	1	0	47,191	RefSeq:NZ_AMHU01000184
NZ_AMHU01000220	51	49	0	2	47,165	RefSeq:NZ_AMHU01000220
NZ_AMHU01000166	52	52	0	0	44,103	RefSeq:NZ_AMHU01000166
NZ_AMHU01000178	46	45	0	1	44,068	RefSeq:NZ_AMHU01000178
NZ_AMHU01000198	38	37	0	1	43,733	RefSeq:NZ_AMHU01000198
NZ_AMHU01000214	31	28	1	2	43,624	RefSeq:NZ_AMHU01000214
NZ_AMHU01000195	41	41	0	0	43,491	RefSeq:NZ_AMHU01000195
NZ_AMHU01000141	41	41	0	0	42,260	RefSeq:NZ_AMHU01000141
NZ_AMHU01000153	42	42	0	0	41,493	RefSeq:NZ_AMHU01000153
NZ_AMHU01000135	36	34	0	2	41,399	RefSeq:NZ_AMHU01000135
NZ_AMHU01000024	36	31	4	1	41,349	RefSeq:NZ_AMHU01000024
NZ_AMHU01000222	37	37	0	0	41,269	RefSeq:NZ_AMHU01000222
NZ_AMHU01000180	36	35	0	1	40,618	RefSeq:NZ_AMHU01000180
NZ_AMHU01000082	36	33	3	0	38,945	RefSeq:NZ_AMHU01000082
NZ_AMHU01000057	55	55	0	0	38,160	RefSeq:NZ_AMHU01000057
NZ_AMHU01000212	34	34	0	0	37,833	RefSeq:NZ_AMHU01000212
NZ_AMHU01000131	37	35	0	2	37,383	RefSeq:NZ_AMHU01000131
NZ_AMHU01000102	33	31	0	2	36,733	RefSeq:NZ_AMHU01000102
NZ_AMHU01000164	35	35	0	0	36,249	RefSeq:NZ_AMHU01000164
NZ_AMHU01000006	36	35	1	0	35,800	RefSeq:NZ_AMHU01000006
NZ_AMHU01000185	31	31	0	0	33,648	RefSeq:NZ_AMHU01000185
NZ_AMHU01000203	34	32	0	2	33,451	RefSeq:NZ_AMHU01000203
NZ_AMHU01000030	33	32	0	1	32,999	RefSeq:NZ_AMHU01000030
NZ_AMHU01000159	28	27	0	1	32,792	RefSeq:NZ_AMHU01000159
NZ_AMHU01000145	27	26	0	1	32,030	RefSeq:NZ_AMHU01000145
NZ_AMHU01000201	29	29	0	0	31,814	RefSeq:NZ_AMHU01000201
NZ_AMHU01000148	27	26	0	1	31,682	RefSeq:NZ_AMHU01000148
NZ_AMHU01000007	32	31	0	1	30,354	RefSeq:NZ_AMHU01000007
NZ_AMHU01000196	29	25	4	0	30,021	RefSeq:NZ_AMHU01000196
NZ_AMHU01000206	23	23	0	0	28,572	RefSeq:NZ_AMHU01000206
NZ_AMHU01000155	20	20	0	0	28,219	RefSeq:NZ_AMHU01000155
NZ_AMHU01000140	23	22	0	1	26,933	RefSeq:NZ_AMHU01000140
NZ_AMHU01000209	28	28	0	0	26,659	RefSeq:NZ_AMHU01000209
NZ_AMHU01000154	25	24	0	1	26,625	RefSeq:NZ_AMHU01000154
NZ_AMHU01000210	24	23	0	1	26,305	RefSeq:NZ_AMHU01000210
NZ_AMHU01000054	25	24	0	1	25,373	RefSeq:NZ_AMHU01000054
NZ_AMHU01000174	20	20	0	0	25,024	RefSeq:NZ_AMHU01000174
NZ_AMHU01000029	23	23	0	0	24,073	RefSeq:NZ_AMHU01000029
NZ_AMHU01000207	19	18	0	1	23,441	RefSeq:NZ_AMHU01000207
NZ_AMHU01000095	26	26	0	0	23,160	RefSeq:NZ_AMHU01000095
NZ_AMHU01000117	25	23	1	1	23,114	RefSeq:NZ_AMHU01000117
NZ_AMHU01000088	21	20	0	1	22,091	RefSeq:NZ_AMHU01000088
NZ_AMHU01000022	25	24	1	0	21,854	RefSeq:NZ_AMHU01000022
NZ_AMHU01000020	27	24	0	3	21,656	RefSeq:NZ_AMHU01000020
NZ_AMHU01000098	18	17	0	1	21,105	RefSeq:NZ_AMHU01000098
NZ_AMHU01000046	17	16	0	1	20,716	RefSeq:NZ_AMHU01000046
NZ_AMHU01000199	25	23	1	1	20,603	RefSeq:NZ_AMHU01000199
NZ_AMHU01000060	11	10	0	1	20,561	RefSeq:NZ_AMHU01000060
NZ_AMHU01000213	23	22	0	1	20,440	RefSeq:NZ_AMHU01000213
NZ_AMHU01000211	21	19	1	1	20,232	RefSeq:NZ_AMHU01000211
NZ_AMHU01000069	19	18	1	0	19,989	RefSeq:NZ_AMHU01000069
NZ_AMHU01000004	25	24	0	1	19,746	RefSeq:NZ_AMHU01000004
NZ_AMHU01000039	16	15	0	1	19,341	RefSeq:NZ_AMHU01000039
NZ_AMHU01000204	18	17	0	1	18,807	RefSeq:NZ_AMHU01000204
NZ_AMHU01000200	35	35	0	0	18,675	RefSeq:NZ_AMHU01000200
NZ_AMHU01000042	20	20	0	0	18,484	RefSeq:NZ_AMHU01000042
NZ_AMHU01000050	16	15	1	0	18,411	RefSeq:NZ_AMHU01000050
NZ_AMHU01000181	16	14	1	1	18,197	RefSeq:NZ_AMHU01000181
NZ_AMHU01000130	17	16	0	1	15,955	RefSeq:NZ_AMHU01000130
NZ_AMHU01000083	16	12	3	1	15,644	RefSeq:NZ_AMHU01000083
NZ_AMHU01000176	13	10	2	1	14,903	RefSeq:NZ_AMHU01000176
NZ_AMHU01000202	16	16	0	0	14,507	RefSeq:NZ_AMHU01000202
NZ_AMHU01000219	15	13	0	2	14,386	RefSeq:NZ_AMHU01000219
NZ_AMHU01000002	17	15	0	2	14,210	RefSeq:NZ_AMHU01000002
NZ_AMHU01000010	12	12	0	0	14,000	RefSeq:NZ_AMHU01000010
NZ_AMHU01000217	22	22	0	0	13,850	RefSeq:NZ_AMHU01000217
NZ_AMHU01000026	12	12	0	0	13,291	RefSeq:NZ_AMHU01000026
NZ_AMHU01000001	12	11	0	1	12,839	RefSeq:NZ_AMHU01000001
NZ_AMHU01000025	12	12	0	0	12,455	RefSeq:NZ_AMHU01000025
NZ_AMHU01000169	14	14	0	0	12,288	RefSeq:NZ_AMHU01000169
NZ_AMHU01000085	10	10	0	0	11,881	RefSeq:NZ_AMHU01000085
NZ_AMHU01000193	16	16	0	0	11,765	RefSeq:NZ_AMHU01000193
NZ_AMHU01000188	12	12	0	0	6,965	RefSeq:NZ_AMHU01000188
127 Undisplayed Contigs/Replicons	325	315	12	85	393,151

Total:	3,983	3,756	62	165	4,077,480

Ortholog data available?	Yes

Database Contents

Genes	3,980
Pathways	261
Enzymatic Reactions	1,300
Transport Reactions	111
Polypeptides	3,833
Protein Complexes	53
Enzymes	809
Transporters	364
Compounds	1,055
Transcription Units	2,820
tRNAs	54
GO Terms	2,340

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Moraxellales Moraxellaceae Acinetobacter Acinetobacter calcoaceticus/baumannii complex Acinetobacter baumannii Acinetobacter baumannii AB_515-8
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02471262
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1221265
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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