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 Moraxella sp. HMSC061H09 HMSC061H09, 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_KV79683427926928330,692RefSeq:NZ_KV796834
NZ_KV79685629528726325,717RefSeq:NZ_KV796856
NZ_KV796849284264713316,938RefSeq:NZ_KV796849
NZ_KV79685316415851166,478RefSeq:NZ_KV796853
NZ_KV79686013612871138,424RefSeq:NZ_KV796860
NZ_KV79683812611871134,146RefSeq:NZ_KV796838
NZ_KV796840969402106,257RefSeq:NZ_KV796840
NZ_KV79683977731385,785RefSeq:NZ_KV796839
NZ_KV79684573710282,930RefSeq:NZ_KV796845
NZ_KV79685860581162,418RefSeq:NZ_KV796858
NZ_KV79684431241633,792RefSeq:NZ_KV796844
NZ_KV79681923194017,668RefSeq:NZ_KV796819
NZ_KV79683520160415,962RefSeq:NZ_KV796835
NZ_KV79681812100212,308RefSeq:NZ_KV796818
NZ_KV79683112110111,132RefSeq:NZ_KV796831
31 Undisplayed Contigs/Replicons61549859,265
Total:1,7591,65446591,899,912
Ortholog data available?No
Database Contents
Genes1,757
Pathways199
Enzymatic Reactions1,065
Transport Reactions44
Polypeptides1,698
Protein Complexes49
Enzymes520
Transporters138
Compounds747
Transcription Units1,253
tRNAs38
Protein Features2,143
GO Terms738
Database Version29.0
Sequence SourceGCF_001809255.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Moraxella
unclassified Moraxella
Moraxella sp. HMSC061H09
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04495798
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1715217
Environmentsputum
HostHomo sapiens
Human Microbiome Body Siteoral
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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