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_909-05, 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_AMIA01000061	108	104	1	3	125,724	RefSeq:NZ_AMIA01000061
NZ_AMIA01000113	127	123	1	3	124,366	RefSeq:NZ_AMIA01000113
NZ_AMIA01000075	122	118	1	3	115,796	RefSeq:NZ_AMIA01000075
NZ_AMIA01000013	123	118	4	1	115,360	RefSeq:NZ_AMIA01000013
NZ_AMIA01000110	109	102	2	5	109,293	RefSeq:NZ_AMIA01000110
NZ_AMIA01000074	88	86	0	2	105,299	RefSeq:NZ_AMIA01000074
NZ_AMIA01000162	98	97	0	1	103,731	RefSeq:NZ_AMIA01000162
NZ_AMIA01000157	85	83	0	2	89,619	RefSeq:NZ_AMIA01000157
NZ_AMIA01000119	84	80	1	3	87,384	RefSeq:NZ_AMIA01000119
NZ_AMIA01000039	78	74	3	1	84,158	RefSeq:NZ_AMIA01000039
NZ_AMIA01000096	83	80	1	2	83,852	RefSeq:NZ_AMIA01000096
NZ_AMIA01000123	77	75	0	2	82,249	RefSeq:NZ_AMIA01000123
NZ_AMIA01000148	81	72	7	2	74,195	RefSeq:NZ_AMIA01000148
NZ_AMIA01000101	71	69	0	2	72,075	RefSeq:NZ_AMIA01000101
NZ_AMIA01000021	62	57	2	3	71,242	RefSeq:NZ_AMIA01000021
NZ_AMIA01000142	66	64	0	2	68,714	RefSeq:NZ_AMIA01000142
NZ_AMIA01000020	57	55	0	2	68,060	RefSeq:NZ_AMIA01000020
NZ_AMIA01000053	67	65	0	2	65,826	RefSeq:NZ_AMIA01000053
NZ_AMIA01000155	64	61	2	1	63,781	RefSeq:NZ_AMIA01000155
NZ_AMIA01000008	42	38	3	1	57,747	RefSeq:NZ_AMIA01000008
NZ_AMIA01000091	51	49	0	2	57,524	RefSeq:NZ_AMIA01000091
NZ_AMIA01000012	64	63	0	1	57,110	RefSeq:NZ_AMIA01000012
NZ_AMIA01000128	49	48	0	1	55,945	RefSeq:NZ_AMIA01000128
NZ_AMIA01000057	67	65	0	2	55,203	RefSeq:NZ_AMIA01000057
NZ_AMIA01000063	49	48	0	1	54,820	RefSeq:NZ_AMIA01000063
NZ_AMIA01000086	43	41	2	0	52,469	RefSeq:NZ_AMIA01000086
NZ_AMIA01000181	47	47	0	0	52,028	RefSeq:NZ_AMIA01000181
NZ_AMIA01000040	49	46	0	3	51,717	RefSeq:NZ_AMIA01000040
NZ_AMIA01000104	55	51	4	0	49,942	RefSeq:NZ_AMIA01000104
NZ_AMIA01000138	46	45	0	1	47,868	RefSeq:NZ_AMIA01000138
NZ_AMIA01000069	41	39	0	2	46,637	RefSeq:NZ_AMIA01000069
NZ_AMIA01000134	39	38	0	1	44,890	RefSeq:NZ_AMIA01000134
NZ_AMIA01000159	49	46	0	3	43,990	RefSeq:NZ_AMIA01000159
NZ_AMIA01000078	39	39	0	0	42,702	RefSeq:NZ_AMIA01000078
NZ_AMIA01000083	42	39	0	3	42,250	RefSeq:NZ_AMIA01000083
NZ_AMIA01000124	41	39	0	2	41,486	RefSeq:NZ_AMIA01000124
NZ_AMIA01000114	35	34	0	1	40,337	RefSeq:NZ_AMIA01000114
NZ_AMIA01000105	51	47	1	3	40,217	RefSeq:NZ_AMIA01000105
NZ_AMIA01000153	39	38	0	1	38,622	RefSeq:NZ_AMIA01000153
NZ_AMIA01000010	35	33	0	2	37,652	RefSeq:NZ_AMIA01000010
NZ_AMIA01000131	35	33	0	2	37,260	RefSeq:NZ_AMIA01000131
NZ_AMIA01000122	34	33	0	1	36,081	RefSeq:NZ_AMIA01000122
NZ_AMIA01000118	43	43	0	0	35,526	RefSeq:NZ_AMIA01000118
NZ_AMIA01000093	27	26	0	1	35,116	RefSeq:NZ_AMIA01000093
NZ_AMIA01000125	32	30	1	1	34,997	RefSeq:NZ_AMIA01000125
NZ_AMIA01000136	35	33	0	2	34,619	RefSeq:NZ_AMIA01000136
NZ_AMIA01000156	34	31	1	2	34,318	RefSeq:NZ_AMIA01000156
NZ_AMIA01000002	34	29	4	1	32,983	RefSeq:NZ_AMIA01000002
NZ_AMIA01000051	31	30	0	1	32,678	RefSeq:NZ_AMIA01000051
NZ_AMIA01000143	30	30	0	0	32,269	RefSeq:NZ_AMIA01000143
NZ_AMIA01000179	30	28	0	2	31,958	RefSeq:NZ_AMIA01000179
NZ_AMIA01000151	31	30	0	1	30,530	RefSeq:NZ_AMIA01000151
NZ_AMIA01000068	23	23	0	0	27,962	RefSeq:NZ_AMIA01000068
NZ_AMIA01000006	25	24	0	1	27,574	RefSeq:NZ_AMIA01000006
NZ_AMIA01000115	23	22	0	1	26,626	RefSeq:NZ_AMIA01000115
NZ_AMIA01000111	21	18	2	1	26,013	RefSeq:NZ_AMIA01000111
NZ_AMIA01000139	24	23	0	1	25,796	RefSeq:NZ_AMIA01000139
NZ_AMIA01000160	23	22	0	1	25,155	RefSeq:NZ_AMIA01000160
NZ_AMIA01000027	17	17	0	0	23,101	RefSeq:NZ_AMIA01000027
NZ_AMIA01000149	24	23	0	1	22,966	RefSeq:NZ_AMIA01000149
NZ_AMIA01000178	19	18	0	1	20,654	RefSeq:NZ_AMIA01000178
NZ_AMIA01000170	19	19	0	0	19,485	RefSeq:NZ_AMIA01000170
NZ_AMIA01000005	19	18	0	1	18,049	RefSeq:NZ_AMIA01000005
NZ_AMIA01000152	17	13	1	3	17,415	RefSeq:NZ_AMIA01000152
NZ_AMIA01000117	16	16	0	0	16,502	RefSeq:NZ_AMIA01000117
NZ_AMIA01000132	20	18	1	1	16,428	RefSeq:NZ_AMIA01000132
NZ_AMIA01000007	18	16	0	2	16,257	RefSeq:NZ_AMIA01000007
NZ_AMIA01000137	19	19	0	0	16,139	RefSeq:NZ_AMIA01000137
NZ_AMIA01000146	17	16	0	1	14,815	RefSeq:NZ_AMIA01000146
NZ_AMIA01000172	15	14	0	1	14,317	RefSeq:NZ_AMIA01000172
NZ_AMIA01000163	12	11	0	1	14,116	RefSeq:NZ_AMIA01000163
NZ_AMIA01000016	12	11	0	1	14,052	RefSeq:NZ_AMIA01000016
NZ_AMIA01000133	17	13	3	1	14,010	RefSeq:NZ_AMIA01000133
NZ_AMIA01000141	11	11	0	0	13,962	RefSeq:NZ_AMIA01000141
NZ_AMIA01000144	11	10	1	0	13,820	RefSeq:NZ_AMIA01000144
NZ_AMIA01000129	14	13	0	1	13,803	RefSeq:NZ_AMIA01000129
NZ_AMIA01000099	15	15	0	0	13,354	RefSeq:NZ_AMIA01000099
NZ_AMIA01000112	14	11	2	1	13,079	RefSeq:NZ_AMIA01000112
NZ_AMIA01000108	14	13	0	1	13,014	RefSeq:NZ_AMIA01000108
NZ_AMIA01000130	13	12	0	1	12,839	RefSeq:NZ_AMIA01000130
NZ_AMIA01000029	19	17	0	2	12,605	RefSeq:NZ_AMIA01000029
NZ_AMIA01000009	15	15	0	0	12,243	RefSeq:NZ_AMIA01000009
NZ_AMIA01000135	17	16	0	1	11,472	RefSeq:NZ_AMIA01000135
NZ_AMIA01000047	12	12	0	0	11,400	RefSeq:NZ_AMIA01000047
NZ_AMIA01000103	18	17	0	1	11,049	RefSeq:NZ_AMIA01000103
NZ_AMIA01000025	14	8	4	2	9,213	RefSeq:NZ_AMIA01000025
NZ_AMIA01000167	16	16	0	0	8,945	RefSeq:NZ_AMIA01000167
NZ_AMIA01000161	16	15	0	1	8,507	RefSeq:NZ_AMIA01000161
NZ_AMIA01000126	12	12	0	0	6,255	RefSeq:NZ_AMIA01000126
92 Undisplayed Contigs/Replicons	246	241	7	68	312,394

Total:	3,966	3,720	62	184	4,045,601

Ortholog data available?	Yes

Database Contents

Genes	3,964
Pathways	258
Enzymatic Reactions	1,297
Transport Reactions	112
Polypeptides	3,791
Protein Complexes	53
Enzymes	802
Transporters	359
Compounds	1,057
Transcription Units	2,811
tRNAs	55
GO Terms	2,349

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Moraxellales Moraxellaceae Acinetobacter Acinetobacter calcoaceticus/baumannii complex Acinetobacter baumannii Acinetobacter baumannii AB_909-05
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02471227
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1221271
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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