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Homo sapiens Reactions Class: Small-Molecule Reactions

Summary:
Reactions in which all participants are small molecules.

Parent Classes:
Reactions Classified By Substrate

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 Enterococcus faecium R501 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.

Taxonomic lineage: cellular organisms , Bacteria , Firmicutes , Bacilli , Lactobacillales , Enterococcaceae , Enterococcus , Enterococcus faecium , Enterococcus faecium R501

Unification Links: GOLD:0013796 , NCBI BioProject:PRJNA82067 , NCBI BioProject:PRJNA181833 , NCBI-Taxonomy:1134839

Organism or Sample Properties
Environmentterrestrial biome [ENVO:00000446]
human-associated habitat [ENVO:00009003]
biological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified

RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JH807121 scaffold12112010109,181NCBI-RefSeq:NZ_JH807121
NZ_JH807310 scaffold10910810103,106NCBI-RefSeq:NZ_JH807310
NZ_JH807232 scaffold11511500102,160NCBI-RefSeq:NZ_JH807232
NZ_JH807157 scaffold1061060099,286NCBI-RefSeq:NZ_JH807157
NZ_JH807296 scaffold98962094,055NCBI-RefSeq:NZ_JH807296
NZ_JH807277 scaffold1071061091,945NCBI-RefSeq:NZ_JH807277
NZ_JH807253 scaffold97952090,926NCBI-RefSeq:NZ_JH807253
NZ_JH807173 scaffold83830083,070NCBI-RefSeq:NZ_JH807173
NZ_JH807115 scaffold82802077,676NCBI-RefSeq:NZ_JH807115
NZ_JH807113 scaffold63621068,269NCBI-RefSeq:NZ_JH807113
NZ_JH807112 scaffold89863068,252NCBI-RefSeq:NZ_JH807112
NZ_JH807093 scaffold54531056,416NCBI-RefSeq:NZ_JH807093
NZ_JH807315 scaffold51510052,907NCBI-RefSeq:NZ_JH807315
NZ_JH807184 scaffold55550052,651NCBI-RefSeq:NZ_JH807184
NZ_JH807111 scaffold51510051,771NCBI-RefSeq:NZ_JH807111
NZ_JH807304 scaffold71701048,901NCBI-RefSeq:NZ_JH807304
NZ_JH807075 scaffold44440048,772NCBI-RefSeq:NZ_JH807075
NZ_JH807082 scaffold48480047,508NCBI-RefSeq:NZ_JH807082
NZ_JH807255 scaffold44431043,663NCBI-RefSeq:NZ_JH807255
NZ_JH807263 scaffold40400042,734NCBI-RefSeq:NZ_JH807263
NZ_JH807171 scaffold47461038,711NCBI-RefSeq:NZ_JH807171
NZ_JH807229 scaffold29290037,877NCBI-RefSeq:NZ_JH807229
NZ_JH807251 scaffold32320037,211NCBI-RefSeq:NZ_JH807251
NZ_JH807250 scaffold40400036,515NCBI-RefSeq:NZ_JH807250
NZ_JH807259 scaffold32320035,617NCBI-RefSeq:NZ_JH807259
NZ_JH807160 scaffold33330034,565NCBI-RefSeq:NZ_JH807160
NZ_JH807074 scaffold30300032,460NCBI-RefSeq:NZ_JH807074
NZ_JH807176 scaffold30300031,775NCBI-RefSeq:NZ_JH807176
NZ_JH807140 scaffold33330031,149NCBI-RefSeq:NZ_JH807140
NZ_JH807185 scaffold35350030,926NCBI-RefSeq:NZ_JH807185
NZ_JH807303 scaffold27270030,640NCBI-RefSeq:NZ_JH807303
NZ_JH807220 scaffold31310030,417NCBI-RefSeq:NZ_JH807220
NZ_JH807080 scaffold33330029,177NCBI-RefSeq:NZ_JH807080
NZ_JH807104 scaffold35350028,701NCBI-RefSeq:NZ_JH807104
NZ_JH807139 scaffold26260028,512NCBI-RefSeq:NZ_JH807139
NZ_JH807299 scaffold30300028,211NCBI-RefSeq:NZ_JH807299
NZ_JH807227 scaffold27270027,035NCBI-RefSeq:NZ_JH807227
NZ_JH807204 scaffold17170026,692NCBI-RefSeq:NZ_JH807204
NZ_JH807076 scaffold29290026,434NCBI-RefSeq:NZ_JH807076
NZ_JH807083 scaffold22220025,565NCBI-RefSeq:NZ_JH807083
NZ_JH807143 scaffold28280023,889NCBI-RefSeq:NZ_JH807143
NZ_JH807246 scaffold23230023,641NCBI-RefSeq:NZ_JH807246
NZ_JH807089 scaffold26260021,963NCBI-RefSeq:NZ_JH807089
NZ_JH807165 scaffold28280020,996NCBI-RefSeq:NZ_JH807165
NZ_JH807148 scaffold19190020,878NCBI-RefSeq:NZ_JH807148
NZ_JH807230 scaffold21210020,247NCBI-RefSeq:NZ_JH807230
NZ_JH807301 scaffold25223019,669NCBI-RefSeq:NZ_JH807301
NZ_JH807187 scaffold17170018,895NCBI-RefSeq:NZ_JH807187
NZ_JH807178 scaffold17170017,570NCBI-RefSeq:NZ_JH807178
NZ_JH807108 scaffold14140017,248NCBI-RefSeq:NZ_JH807108
NZ_JH807128 scaffold23230016,931NCBI-RefSeq:NZ_JH807128
NZ_JH807161 scaffold21210016,839NCBI-RefSeq:NZ_JH807161
NZ_JH807257 scaffold14140016,718NCBI-RefSeq:NZ_JH807257
NZ_JH807191 scaffold19190016,216NCBI-RefSeq:NZ_JH807191
NZ_JH807100 scaffold15150016,170NCBI-RefSeq:NZ_JH807100
NZ_JH807228 scaffold16160016,033NCBI-RefSeq:NZ_JH807228
NZ_JH807316 scaffold15150016,017NCBI-RefSeq:NZ_JH807316
NZ_JH807073 scaffold17170015,930NCBI-RefSeq:NZ_JH807073
NZ_JH807096 scaffold14140015,645NCBI-RefSeq:NZ_JH807096
NZ_JH807124 scaffold15150014,930NCBI-RefSeq:NZ_JH807124
NZ_JH807193 scaffold12120014,174NCBI-RefSeq:NZ_JH807193
NZ_JH807086 scaffold14140013,877NCBI-RefSeq:NZ_JH807086
NZ_JH807268 scaffold15150013,470NCBI-RefSeq:NZ_JH807268
NZ_JH807078 scaffold12120012,085NCBI-RefSeq:NZ_JH807078
NZ_JH807294 scaffold12120011,527NCBI-RefSeq:NZ_JH807294
NZ_JH807211 scaffold11110011,207NCBI-RefSeq:NZ_JH807211
NZ_JH807151 scaffold14140010,729NCBI-RefSeq:NZ_JH807151
NZ_JH807136 scaffold12120010,598NCBI-RefSeq:NZ_JH807136
NZ_JH807085 scaffold1313008,817NCBI-RefSeq:NZ_JH807085
NZ_JH807243 scaffold1716108,367NCBI-RefSeq:NZ_JH807243
178 Undisplayed Contigs/Replicons450430210466,679
Total:331530744203,009,394

Pathways:190
Enzymatic Reactions:1004
Transport Reactions:6
Polypeptides:3279
Protein Complexes:0
Enzymes:617
Transporters:28
Compounds:761
Transcription Units:2053
tRNAs:33

Genetic Code Number:
11 -- Bacterial and Plant Plastid (same as Standard, except for alternate initiation codons)

PGDB Unique ID: 10WG


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(D1);D742-D753. 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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of HumanCyc: Genome Biology 6(1):1-17 2004
Page generated by SRI International Pathway Tools version 18.5 on Fri Feb 27, 2015, biocyc11.