Escherichia coli K-12 MG1655
Working With: Genome: Escherichia coli K-12 MG1655 Version: v3

ABE-0011646 (xylF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0011646 showshow history
Names
xylF JW3538 ECK3555 xylT b3566
Product
periplasmic-binding component of an ABC superfamily D-xylose transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3731131 3732123 993 331
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR013456 (IPR013456 D-xylose ABC transporter, substrate-binding protein) Apr 2008
Automated Process Approved IPR001761 (IPR001761 Periplasmic binding protein/LacI sugar binding domain) Apr 2008
Automated Process Approved IPR025997 (IPR025997 Periplasmic binding protein) Jul 2018
Automated Process Approved IPR028082 (IPR028082 Periplasmic binding protein-like I) Jul 2018
Automated Process Approved PF13407 (PF13407 Periplasmic binding protein domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0015753 D-xylose transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013456
Reference: Escherichia coli K-12 MG1655
Jul 2018
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655
Feb 2008
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0048029 monosaccharide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013456
Reference: Escherichia coli K-12 MG1655
Jul 2018
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name xylF Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655
Oct 1998
Person Approved synonym xylT Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym ECK3555 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW3538 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b3566 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product periplasmic-binding component of an ABC superfamily D-xylose transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12
Mar 2008
Automated Process Approved alternate product name D-xylose transporter subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Person Approved alternate product name xylose binding protein transport system Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655
Jan 2006
Person Uncurated alternate product name D-xylose transport protein (ABC superfamily, peri_bind) Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR001761 Periplasmic binding protein/LacI sugar binding domain Protein Sequence Similarity - InterPro Domain: IPR001761
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family IPR013456 D-xylose ABC transporter, substrate-binding protein Protein Sequence Similarity - InterPro Domain: IPR013456
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family IPR028082 Periplasmic binding protein-like I Protein Sequence Similarity - InterPro Domain: IPR028082
Reference: Escherichia coli K-12 MG1655
Jul 2018
Automated Process Approved protein family IPR025997 Periplasmic binding protein Protein Sequence Similarity - InterPro Domain: IPR025997
Reference: Escherichia coli K-12 MG1655
Jul 2018
Automated Process Approved protein family PF13407 Periplasmic binding protein domain Protein Sequence Similarity - PFAM Model Name: PF13407
Reference: Escherichia coli K-12 MG1655
Jul 2018
Other
Person Approved EC number 3.6.3.17 Published Annotation - Swiss-Prot Accession Number: P37387 Feb 2006
Person Uncurated MultiFun 7.2 (location of gene products; periplasmic space) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.S.50 (transport; substrate; D-xylose) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.3.A.1.p (transport; Primary Active Transporters; Pyrophosphate Bond (ATP, GTP, P2) Hydrolysis-driven Active Transporters; The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases; ABC superfamily, periplasmic binding component) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Automated Process Approved codon start 1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P37387 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved db xref GI:1789990 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved db xref GeneID:948090 Published Annotation - Entrez Gene Database ID: 948090
Reference: Escherichia coli K-12 MG1655
Jun 2009
Automated Process Approved db xref ASAP:ABE-0011646 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Person Approved db xref UniProtKB:P37387 Published Annotation - Swiss-Prot Accession Number: P37387 Jan 2005
Automated Process Approved db xref EcoGene:EG20252 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Person Approved function transport; Transport of small molecules: Carbohydrates, organic acids, alcohols Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655
Oct 1998
Automated Process Approved note xylose binding protein transport system; periplasmic-binding component of ABC superfamily; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0016052 - carbohydrate catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved protein id AAC76590.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Uncurated subcellular localization Periplasmic Predicted by PSORTb - PSORTb Final_Score: 9.76
Reference: Escherichia coli K-12 MG1655
Feb 2008
Person Uncurated subsystem component of in silico model iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655
Mar 2009
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655
Feb 2009
Person Uncurated subsystem component of in silico model iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655
Jan 2009
Automated Process Approved transl table 11 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Gene Ontology
Automated Process Uncurated GO biological process GO:0015753 D-xylose transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013456
Reference: Escherichia coli K-12 MG1655
Jul 2018
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655
Feb 2008
Automated Process Uncurated GO molecular function GO:0048029 monosaccharide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013456
Reference: Escherichia coli K-12 MG1655
Jul 2018
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0002084 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002605 xylF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002568 xylF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003733 xylF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002772 xylF CDS
Ortholog
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0001073 CDS
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0004210 xylF CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0004222 xylF CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000202 xylF CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0004452 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0016101 xylF CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0004177 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0000467 xylF CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004737 xylF CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003708 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007505 xylF CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003627 xylF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0000609 xylF CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0005486 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006970 xylF CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005286 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080563 xylF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004075 xylF CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0005066 xylF CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006894 xylF CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005153 xylF CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004062 xylF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008495 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004891 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008273 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006788 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006335 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005091 xylF CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009776 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005173 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007588 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005373 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005438 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005280 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005167 xylF CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005766 xylF CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028636 xylF CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005382 xylF CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008458 xylF CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0004293 xylF CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003322 xylF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003799 xylF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004224 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004220 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004043 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004097 xylF CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178242 xylF CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003913 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003886 xylF CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134522 xylF CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002814 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004116 xylF CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003978 xylF CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0002585 xylF CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0004447 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0003144 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0003333 xylF CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0003280 xylF CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0000712 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0000041 xylF CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0000051 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0007819 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0003483 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0287096 xylF pseudogene
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0007033 xylF CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0060299 xylF CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0000064 xylF CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0001236 xylF CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0000207 xylF CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0009463 CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0003052 xylF CDS
Person Approved Go view Shigella boydii 227 ADV-0003901 xylF CDS
Automated Process Uncurated Go view Shigella boydii BS512 ADJ-0009377 xylF CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003168 xylF CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0075444 xylF CDS
Person Approved Go view Shigella flexneri 301 ABT-0256132 xylF CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0004225 xylF CDS
Person Uncurated Go view Trabulsiella guamensis ATCC 49490 [T] APH-0003402 xylF CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0000165 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0011883 CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0002362 xylF_1 CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0002642 xylF CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0000687 CDS
Person Uncurated Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0242484 xylF CDS
Automated Process Uncurated Go view Yersinia pestis Antiqua (biovar Antiqua) BAE-0004919 CDS
Automated Process Uncurated Go view Yersinia pestis B42003004 (biovar Antiqua) BAL-0007262 xylF CDS
Automated Process Uncurated Go view Yersinia pestis CA88-4125 (biovar Orientalis) BAF-0003364 CDS
Person Uncurated Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0128935 CDS
Automated Process Uncurated Go view Yersinia pestis E1979001 (biovar Antiqua) BAM-0005826 xylF CDS
Automated Process Uncurated Go view Yersinia pestis F1991016 (biovar Orientalis) BAQ-0007199 xylF CDS
Automated Process Uncurated Go view Yersinia pestis FV-1 (biovar Orientalis) BAK-0002045 CDS
Automated Process Uncurated Go view Yersinia pestis IP275 (biovar Orientalis) BAC-0006149 xylF CDS
Automated Process Uncurated Go view Yersinia pestis K1973002 (biovar Mediaevalis) BAO-0006934 xylF CDS
Person Uncurated Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0033855 xylF CDS
Automated Process Uncurated Go view Yersinia pestis MG05-1020 (biovar Orientalis) BAP-0006719 xylF CDS
Automated Process Uncurated Go view Yersinia pestis Nepal516 (biovar Antiqua) BAD-0004426 CDS
Automated Process Uncurated Go view Yersinia pestis Pestoides F (biovar Pestoides) BAI-0004539 CDS
Automated Process Uncurated Go view Yersinia pestis UG05-0454 (biovar Antiqua) BAN-0007868 xylF CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0008140 xylF CDS
Person Uncurated Go view Yersinia pseudotuberculosis IP32953 ACZ-0004010 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0004882 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0000070 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0004641 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0001150 xylF CDS
Experimental to toptop
SelectSetNameSetDetailsNotes
stringent responsetranscriptional profile of the stringent responseNone
Recombinant heat-shock dataexpression data for recombinant strain under heat shockThese data are from the Harcum laboratory. (Jeremy Glasner)
Suppressor tRNA expressionexperiment comparing transcript levels in cells with and without suppressor tRNA expressionThese data were reported in the paper: Herring and Blattner. 2004. Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR. J. Bacteriol. 186(20):6714-20. Link to Abstract (Jeremy Glasner)
Recombinant E. coli expressionexperiment comparing expression of wild-type E. coli with the same strain harboring a plasmid that expresses protein when induced with IPTG These data were reported in the paper: F. T. Haddadin, S. W. Harcum (2005) Transcriptome profiles for high-cell-density recombinant and wild-type Escherichia coli, Biotechnology and Bioengineering, 90:127-153. Link to Abstract (Jeremy Glasner)
Aerobic shiftAerobic shiftThese data were reported in the paper: Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 6;429(6987):92-6. Link to Abstract (Jeremy Glasner)
CalibratorCalibrated microarray experiments (50 hybridizations)This data was used in the paper: Allen et al., J. Bacteriol. 185(21):6392-9 (Jeremy Glasner)
AffyData1Affymetrix Experiments (data from 41 chip hybridizations)This data was used in the paper: Allen et al., J. Bacteriol. 185(21):6392-9 (Jeremy Glasner)

Strains to toptop

Strains with mutations in this feature.

Strain NameStrain TypeStrain InformationStrain RequestFeatureIDNameMutation DetailsExperiments Using StrainSubmitter
FB21290mutantTn5 InsertionRequest the StrainABE-0011646xylFxylF::Tn5KAN-I-SceI at position 202 in Plus orientation ,+ pKD460Blattner Laboratory
FB21291mutantTn5 InsertionRequest the StrainABE-0011646xylFxylF::Tn5KAN-I-SceI at position 202 in Plus orientation ,- pKD465Blattner Laboratory
Context Table to toptop

Listed below are features that lie nearby this feature. Features encoded in multiple intervals may appear more than once in the table. Features that span the origin will have a left endpoint greater than the right endpoint.

Features overlapping the region 3726131 to 3737123
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0011630wecHCDSforward37258873726882Upstream
ABE-0011632yiaACDScomplement37269243727361Upstream
ABE-0011634yiaBCDScomplement37274073727748Upstream
ABE-0011637xylBCDScomplement37279173729371Upstream
ABE-0285848xylZncRNAcomplement37293863729545Upstream
ABE-0011639xylACDScomplement37294433730765Upstream
ABE-0011646xylFCDSforward37311313732123Matches
ABE-0011648xylGCDSforward37322013733742Downstream
ABE-0011650xylHCDSforward37337203734901Downstream
ABE-0011652xylRCDSforward37349793736157Downstream
ABE-0285620repeat_regionforward37361543736324Downstream
ABE-0011655baxCDScomplement37363533737177Downstream
Release Notes to toptop
All MG1655 annotations and sequence data are publicly available, and investigators can use these data in publications without contacting the genome curators. This version of the sequence was the source of GenBank record U00096.3. Ongoing annotation updates to that GenBank record are being generated from a collaboration that includes ASAP, EcoGene, the Coli Genetic Stock Center, EcoliHub, EcoCyc, RegulonDB and UniProtKB/Swiss-Prot.