Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 12-July-2021 from the annotated genome of Novosphingobium sediminicola DSM 27057, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [Caspi19]. 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_JACIDX010000001527512152551,608RefSeq:NZ_JACIDX010000001
NZ_JACIDX01000000231831804407,231RefSeq:NZ_JACIDX010000002
NZ_JACIDX01000000332532502389,032RefSeq:NZ_JACIDX010000003
NZ_JACIDX010000004274262122303,830RefSeq:NZ_JACIDX010000004
NZ_JACIDX010000005282272103283,009RefSeq:NZ_JACIDX010000005
NZ_JACIDX01000000624123831276,743RefSeq:NZ_JACIDX010000006
NZ_JACIDX01000000723823620274,954RefSeq:NZ_JACIDX010000007
NZ_JACIDX01000000822622426273,203RefSeq:NZ_JACIDX010000008
NZ_JACIDX01000000922422401270,906RefSeq:NZ_JACIDX010000009
NZ_JACIDX01000001017717612201,116RefSeq:NZ_JACIDX010000010
NZ_JACIDX01000001117617511192,032RefSeq:NZ_JACIDX010000011
NZ_JACIDX01000001217316852186,055RefSeq:NZ_JACIDX010000012
NZ_JACIDX01000001316716611178,569RefSeq:NZ_JACIDX010000013
NZ_JACIDX01000001413313211140,682RefSeq:NZ_JACIDX010000014
NZ_JACIDX01000001512512503139,528RefSeq:NZ_JACIDX010000015
NZ_JACIDX01000001611711613127,756RefSeq:NZ_JACIDX010000016
NZ_JACIDX01000001712612060118,452RefSeq:NZ_JACIDX010000017
NZ_JACIDX010000018898813108,886RefSeq:NZ_JACIDX010000018
NZ_JACIDX010000019868607104,321RefSeq:NZ_JACIDX010000019
NZ_JACIDX01000002084840296,318RefSeq:NZ_JACIDX010000020
NZ_JACIDX01000002177770390,055RefSeq:NZ_JACIDX010000021
NZ_JACIDX01000002251510176,327RefSeq:NZ_JACIDX010000022
NZ_JACIDX01000002346460168,937RefSeq:NZ_JACIDX010000023
NZ_JACIDX01000002447470168,715RefSeq:NZ_JACIDX010000024
NZ_JACIDX01000002538380152,307RefSeq:NZ_JACIDX010000025
NZ_JACIDX01000002644440151,612RefSeq:NZ_JACIDX010000026
NZ_JACIDX01000002736360142,759RefSeq:NZ_JACIDX010000027
NZ_JACIDX01000002827270336,894RefSeq:NZ_JACIDX010000028
NZ_JACIDX01000002931301031,746RefSeq:NZ_JACIDX010000029
NZ_JACIDX01000003020200030,618RefSeq:NZ_JACIDX010000030
NZ_JACIDX01000003123230428,560RefSeq:NZ_JACIDX010000031
NZ_JACIDX01000003215150220,756RefSeq:NZ_JACIDX010000032
NZ_JACIDX01000003315150018,704RefSeq:NZ_JACIDX010000033
NZ_JACIDX01000003412120214,076RefSeq:NZ_JACIDX010000034
NZ_JACIDX01000003511110213,604RefSeq:NZ_JACIDX010000035
NZ_JACIDX01000003712120312,898RefSeq:NZ_JACIDX010000037
NZ_JACIDX0100000421111016,653RefSeq:NZ_JACIDX010000042
18 Undisplayed Contigs/Replicons575701583,249
Total:4,7684,61962875,372,701
Ortholog data available?No
Database Contents
Genes4,681
Pathways277
Enzymatic Reactions1,406
Transport Reactions72
Polypeptides4,643
Protein Complexes41
Enzymes910
Transporters395
Compounds1,053
Transcription Units2,960
tRNAs56
Protein Features5,892
Database Version29.6
Sequence SourceGCF_014196525.1
Synonyms Novosphingobium sp. HU1-AH51
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae
Novosphingobium
Novosphingobium sediminicola
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN13173222
NCBI BioProjectPRJNA224116
NCBI-Taxonomy563162
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi19: 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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