Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Tim Holland1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp02, Dale10, Karp11, Caspi12] using Pathway Tools software version 18.5 and MetaCyc version 18.5 on 10-Aug-2014 18:43:19 from the annotated genome of Enhydrobacter aerosaccus SK60 as obtained from RefSeq downloaded on 21-May-2014.

This BioCyc Tier 3 PGDB was computationally generated. It has not undergone any manual curation nor manual review, and thus may contain errors. Development of this PGDB was supported by grant GM080746 from the NIH.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Enhydrobacter aerosaccus SK60 contig00004, whole genome shotgun sequence.28728700308,473RefSeq:NZ_ACYI01000062
Enhydrobacter aerosaccus SK60 contig00039, whole genome shotgun sequence.15214840155,776RefSeq:NZ_ACYI01000007
Enhydrobacter aerosaccus SK60 contig00016, whole genome shotgun sequence.11511230125,808RefSeq:NZ_ACYI01000068
Enhydrobacter aerosaccus SK60 contig00046, whole genome shotgun sequence.11111100125,082RefSeq:NZ_ACYI01000019
Enhydrobacter aerosaccus SK60 contig00029, whole genome shotgun sequence.12311850119,517RefSeq:NZ_ACYI01000041
Enhydrobacter aerosaccus SK60 contig00024, whole genome shotgun sequence.12411860115,598RefSeq:NZ_ACYI01000046
Enhydrobacter aerosaccus SK60 contig00032, whole genome shotgun sequence.1009460110,788RefSeq:NZ_ACYI01000049
Enhydrobacter aerosaccus SK60 contig00022, whole genome shotgun sequence.11311210103,273RefSeq:NZ_ACYI01000023
Enhydrobacter aerosaccus SK60 contig00043, whole genome shotgun sequence.93903095,453RefSeq:NZ_ACYI01000002
Enhydrobacter aerosaccus SK60 contig00066, whole genome shotgun sequence.76742091,841RefSeq:NZ_ACYI01000035
Enhydrobacter aerosaccus SK60 contig00005, whole genome shotgun sequence.71701079,074RefSeq:NZ_ACYI01000059
Enhydrobacter aerosaccus SK60 contig00058, whole genome shotgun sequence.68680076,603RefSeq:NZ_ACYI01000080
Enhydrobacter aerosaccus SK60 contig00063, whole genome shotgun sequence.67661071,724RefSeq:NZ_ACYI01000027
Enhydrobacter aerosaccus SK60 contig00038, whole genome shotgun sequence.71692062,255RefSeq:NZ_ACYI01000071
Enhydrobacter aerosaccus SK60 contig00045, whole genome shotgun sequence.64631062,164RefSeq:NZ_ACYI01000021
Enhydrobacter aerosaccus SK60 contig00009, whole genome shotgun sequence.63621060,865RefSeq:NZ_ACYI01000034
Enhydrobacter aerosaccus SK60 contig00064, whole genome shotgun sequence.68671058,829RefSeq:NZ_ACYI01000067
Enhydrobacter aerosaccus SK60 contig00018, whole genome shotgun sequence.51501050,938RefSeq:NZ_ACYI01000043
Enhydrobacter aerosaccus SK60 contig00008, whole genome shotgun sequence.39390047,430RefSeq:NZ_ACYI01000020
Enhydrobacter aerosaccus SK60 contig00011, whole genome shotgun sequence.39372044,912RefSeq:NZ_ACYI01000016
Enhydrobacter aerosaccus SK60 contig00025, whole genome shotgun sequence.43430040,913RefSeq:NZ_ACYI01000039
Enhydrobacter aerosaccus SK60 contig00061, whole genome shotgun sequence.42420039,264RefSeq:NZ_ACYI01000040
Enhydrobacter aerosaccus SK60 contig00065, whole genome shotgun sequence.34340038,753RefSeq:NZ_ACYI01000024
Enhydrobacter aerosaccus SK60 contig00017, whole genome shotgun sequence.39390038,446RefSeq:NZ_ACYI01000069
Enhydrobacter aerosaccus SK60 contig00086, whole genome shotgun sequence.35350037,054RefSeq:NZ_ACYI01000031
Enhydrobacter aerosaccus SK60 contig00073, whole genome shotgun sequence.30300035,152RefSeq:NZ_ACYI01000052
Enhydrobacter aerosaccus SK60 contig00013, whole genome shotgun sequence.23230029,866RefSeq:NZ_ACYI01000001
Enhydrobacter aerosaccus SK60 contig00036, whole genome shotgun sequence.25250029,253RefSeq:NZ_ACYI01000064
Enhydrobacter aerosaccus SK60 contig00082, whole genome shotgun sequence.26260027,057RefSeq:NZ_ACYI01000053
Enhydrobacter aerosaccus SK60 contig00021, whole genome shotgun sequence.25250026,880RefSeq:NZ_ACYI01000078
Enhydrobacter aerosaccus SK60 contig00003, whole genome shotgun sequence.27270026,162RefSeq:NZ_ACYI01000065
Enhydrobacter aerosaccus SK60 contig00035, whole genome shotgun sequence.29290026,135RefSeq:NZ_ACYI01000011
Enhydrobacter aerosaccus SK60 contig00026, whole genome shotgun sequence.26242026,112RefSeq:NZ_ACYI01000037
Enhydrobacter aerosaccus SK60 contig00080, whole genome shotgun sequence.23230025,246RefSeq:NZ_ACYI01000009
Enhydrobacter aerosaccus SK60 contig00020, whole genome shotgun sequence.20200021,113RefSeq:NZ_ACYI01000030
Enhydrobacter aerosaccus SK60 contig00012, whole genome shotgun sequence.19190019,965RefSeq:NZ_ACYI01000010
Enhydrobacter aerosaccus SK60 contig00014, whole genome shotgun sequence.12120019,086RefSeq:NZ_ACYI01000054
Enhydrobacter aerosaccus SK60 contig00083, whole genome shotgun sequence.18180018,504RefSeq:NZ_ACYI01000088
Enhydrobacter aerosaccus SK60 contig00079, whole genome shotgun sequence.15150018,094RefSeq:NZ_ACYI01000003
Enhydrobacter aerosaccus SK60 contig00067, whole genome shotgun sequence.20200016,476RefSeq:NZ_ACYI01000026
48 Undisplayed Contigs/Replicons15515230176,692
Total:2,5812,5364502,702,626
Ortholog data available?Yes
Database Contents
Genes2,576
Pathways300
Enzymatic Reactions1,370
Transport Reactions81
Polypeptides2,574
Protein Complexes5
Enzymes753
Transporters179
Compounds995
Transcription Units1,974
tRNAs39
Protein Features2,939
GO Terms3,796
Database Version29.0
Synonyms Enhydrobacter aerosaccus str. SK60
Enhydrobacter aerosaccus strain SK60
Enhydrobacter aerosaccus SK60
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Enhydrobacter
Enhydrobacter aerosaccus
Enhydrobacter aerosaccus SK60
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0004124
NCBI-Taxonomy553217
Environmentterrestrial biome [ENVO:00000446]
HostHomo sapiens
Human Microbiome Body Siteskin

References

Caspi12: Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 40(Database issue);D742-53. PMID: 22102576

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Karp02: Karp PD, Paley S, Romero P (2002). "The Pathway Tools software." Bioinformatics 18 Suppl 1;S225-32. PMID: 12169551

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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