Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinobacillus minor NM305, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_ACQL0100005515314913152,035RefSeq:NZ_ACQL01000055
NZ_ACQL0100010613012802144,753RefSeq:NZ_ACQL01000106
NZ_ACQL0100008515014811144,430RefSeq:NZ_ACQL01000085
NZ_ACQL0100006813212822138,650RefSeq:NZ_ACQL01000068
NZ_ACQL0100006915414383137,320RefSeq:NZ_ACQL01000069
NZ_ACQL01000097959302112,941RefSeq:NZ_ACQL01000097
NZ_ACQL0100010110710601112,667RefSeq:NZ_ACQL01000101
NZ_ACQL0100008760590171,424RefSeq:NZ_ACQL01000087
NZ_ACQL0100010976760071,294RefSeq:NZ_ACQL01000109
NZ_ACQL0100010063612068,076RefSeq:NZ_ACQL01000100
NZ_ACQL0100009861601067,819RefSeq:NZ_ACQL01000098
NZ_ACQL0100003168661165,890RefSeq:NZ_ACQL01000031
NZ_ACQL0100015447460153,131RefSeq:NZ_ACQL01000154
NZ_ACQL0100000150462248,813RefSeq:NZ_ACQL01000001
NZ_ACQL0100009455520348,209RefSeq:NZ_ACQL01000094
NZ_ACQL0100009031300142,991RefSeq:NZ_ACQL01000090
NZ_ACQL0100006554511242,610RefSeq:NZ_ACQL01000065
NZ_ACQL0100009935330238,619RefSeq:NZ_ACQL01000099
NZ_ACQL0100009330300036,772RefSeq:NZ_ACQL01000093
NZ_ACQL0100016631300135,471RefSeq:NZ_ACQL01000166
NZ_ACQL0100017139326134,753RefSeq:NZ_ACQL01000171
NZ_ACQL0100011223221031,810RefSeq:NZ_ACQL01000112
NZ_ACQL0100015345421231,116RefSeq:NZ_ACQL01000153
NZ_ACQL0100002328270130,431RefSeq:NZ_ACQL01000023
NZ_ACQL0100012026223124,598RefSeq:NZ_ACQL01000120
NZ_ACQL0100013329290024,521RefSeq:NZ_ACQL01000133
NZ_ACQL0100003828280022,472RefSeq:NZ_ACQL01000038
NZ_ACQL0100006322210122,147RefSeq:NZ_ACQL01000063
NZ_ACQL0100011522183121,678RefSeq:NZ_ACQL01000115
NZ_ACQL0100010217160121,678RefSeq:NZ_ACQL01000102
NZ_ACQL0100019025250021,473RefSeq:NZ_ACQL01000190
NZ_ACQL0100017214140019,882RefSeq:NZ_ACQL01000172
NZ_ACQL0100012221183019,027RefSeq:NZ_ACQL01000122
NZ_ACQL0100011812101118,904RefSeq:NZ_ACQL01000118
NZ_ACQL0100001422210118,040RefSeq:NZ_ACQL01000014
NZ_ACQL0100000717160117,520RefSeq:NZ_ACQL01000007
NZ_ACQL0100002422220015,973RefSeq:NZ_ACQL01000024
NZ_ACQL0100012516140215,391RefSeq:NZ_ACQL01000125
NZ_ACQL0100013516160012,915RefSeq:NZ_ACQL01000135
NZ_ACQL0100016215150012,883RefSeq:NZ_ACQL01000162
NZ_ACQL0100011612120012,757RefSeq:NZ_ACQL01000116
NZ_ACQL0100006616150112,458RefSeq:NZ_ACQL01000066
NZ_ACQL0100013913111111,023RefSeq:NZ_ACQL01000139
NZ_ACQL0100001513120110,157RefSeq:NZ_ACQL01000015
NZ_ACQL010001171410409,668RefSeq:NZ_ACQL01000117
152 Undisplayed Contigs/Replicons2021921422298,074
Total:2,3372,21556662,425,264
Ortholog data available?Yes
Database Contents
Genes2,333
Pathways244
Enzymatic Reactions1,258
Transport Reactions90
Polypeptides2,268
Protein Complexes72
Enzymes640
Transporters241
Compounds895
Transcription Units1,532
tRNAs47
Protein Features3,004
GO Terms223
Database Version29.0
Sequence SourceGCF_000175195.1
Synonyms Actinobacillus minor strain NM305
Actinobacillus minor str. NM305
Actinobacillus minor NM305
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
Actinobacillus
Actinobacillus minor
Actinobacillus minor NM305
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02470284
NCBI BioProjectPRJNA224116
NCBI-Taxonomy637911
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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