rapA:On One Page
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| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| Quickview | | Gene | | Product(s) | | Expression| | Evolution | | References | |
Quickview
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| Standard Name |
rapA |
|---|---|
| Gene Synonym(s) |
ECK0060, b0059, JW0058, rapA, yabA, hepA[1], hepA, yabA |
| Product Desc. |
RNA Polymerase (RNAP)-binding ATPase and RNAP recycling factor[2][3] RNA polymerase binding protein; mutants are UV-S; mutant biofilms have less polysaccharide and are antibiotic sensitive; ATPase and putative helicase[4] |
| Product Synonyms(s) |
RNA polymerase-associated helicase protein (ATPase and RNA polymerase recycling factor)[1], B0059[2][1], YabA[2][1], RapA[2][1], RapA[2][1] , ECK0060, hepA, JW0058, yabA, b0059 |
| Function from GO |
<GO_nr /> |
| Knock-Out Phenotype | |
| Regulation/Expression | |
| Regulation/Activity | |
| Quick Links |
|
| edit table |
</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>
Notes
HepA has sequence similarity to SWI2/SNF2 helicases. hepA is downstream of polB, but is not under lexA control. The mutant phentypes may be indirect since other genes, e.g. yeeZ and aaeA(yhcQ), are downregulated in hepA(rapA) mutants (Lynch, 2007).[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
rapA |
|---|---|
| Mnemonic | |
| Synonyms |
ECK0060, b0059, JW0058, rapA, yabA, hepA[1], hepA, yabA |
| edit table |
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Notes
Location(s) and DNA Sequence
<protect>
See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
| Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
|---|---|---|---|---|
|
MG1655 |
1.3 minutes |
MG1655: 63264..60358 |
||
|
NC_012967: 66068..63162 |
||||
|
NC_012759: 60358..63264 |
||||
|
W3110 |
|
W3110: 63264..60358 |
||
|
DH10B: 62378..60358 |
||||
| edit table |
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Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
|
Coding Start (SO:0000323) |
60361 |
Edman degradation |
PMID:9614128 |
| |
| edit table |
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Notes
Alleles and Phenotypes
See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.
| Allele | Nt change(s) | AA change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|---|
|
hepA(del) (Keio:JW0058) |
deletion |
deletion |
PMID:16738554 |
||||
|
rapAK183A |
K183A |
Loss of function. Still interacts with RNAP |
seeded from UniProt:P60240 | ||||
|
rapADE280AA |
DE280AA |
Loss of function. Still interacts with RNAP |
seeded from UniProt:P60240 | ||||
|
hepA769(del)::kan |
PMID:16738554 |
| |||||
| edit table |
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Notes
HepA has a plausible function and reasonable map location to be the gene affected by the psu-1 mutation.
Genetic Interactions
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| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW0058 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCCCTTTTACACTTGGTCAACG Primer 2:CCCTGATGCGTTACAACGATCAA | |
|
Kohara Phage |
PMID:3038334 | ||
|
Kohara Phage |
PMID:3038334 | ||
|
Linked marker |
est. P1 cotransduction: 34% [6] | ||
|
leuO3051::Tn10 |
Linked marker |
est. P1 cotransduction: 42% [6] | |
| edit table |
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1075 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0000198 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120001071 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Product(s)
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Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| Standard name |
RapA |
|---|---|
| Synonyms |
RNA polymerase-associated helicase protein (ATPase and RNA polymerase recycling factor)[1], B0059[2][1], YabA[2][1], RapA[2][1], RapA[2][1] , ECK0060, hepA, JW0058, yabA, b0059 |
| Product description |
RNA Polymerase (RNAP)-binding ATPase and RNAP recycling factor[2][3] RNA polymerase binding protein; mutants are UV-S; mutant biofilms have less polysaccharide and are antibiotic sensitive; ATPase and putative helicase[4] |
| EC number (for enzymes) | |
| edit table |
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Notes
Function
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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.
| Qualifier | GO ID | GO term name | Reference | Evidence Code | with/from | Aspect | Notes | Status |
|---|---|---|---|---|---|---|---|---|
|
GO:0005737 |
cytoplasm |
C |
Seeded from Riley et al 2006 [1]. |
Missing: evidence, reference | ||||
|
GO:0009451 |
RNA modification |
P |
Seeded from Riley et al 2006 [1]. |
Missing: evidence, reference | ||||
|
GO:0000166 |
nucleotide binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0547 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001650 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0003677 |
DNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR000330 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0003677 |
DNA binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0238 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0004386 |
helicase activity |
GOA:hamap |
IEA: Inferred from Electronic Annotation |
HAMAP:MF_01821 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0004386 |
helicase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001650 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0004386 |
helicase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0347 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0005524 |
ATP binding |
GOA:hamap |
IEA: Inferred from Electronic Annotation |
HAMAP:MF_01821 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR000330 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001650 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0005524 |
ATP binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0067 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006350 |
transcription |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0804 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006355 |
regulation of transcription, DNA-dependent |
GOA:hamap |
IEA: Inferred from Electronic Annotation |
HAMAP:MF_01821 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0016787 |
hydrolase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0378 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
| edit table |
Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.
| Partner Type | Partner | Notes | References | Evidence |
|---|---|---|---|---|
|
Protein |
yfaS |
PMID:15690043 |
Experiment(s):EBI-886894 | |
|
Protein |
nusA |
PMID:15690043 |
Experiment(s):EBI-886894 | |
|
Protein |
rplC |
PMID:15690043 |
Experiment(s):EBI-886894 | |
|
Protein |
rpoA |
PMID:15690043 |
Experiment(s):EBI-886894, EBI-879354, EBI-883271 | |
|
Protein |
rpoB |
PMID:15690043 |
Experiment(s):EBI-886894, EBI-879304 | |
|
Protein |
rpoC |
PMID:15690043 |
Experiment(s):EBI-886894, EBI-879261, EBI-883046, EBI-893152 | |
|
Protein |
rpsE |
PMID:15690043 |
Experiment(s):EBI-886894 | |
|
Protein |
fhiA |
PMID:15690043 |
Experiment(s):EBI-893152 | |
|
Protein |
yfcU |
PMID:15690043 |
Experiment(s):EBI-893152 | |
|
Protein |
nusA |
PMID:19402753 |
MALDI(Z-score):25.829542 | |
|
Protein |
rpoC |
PMID:19402753 |
LCMS(ID Probability):99.6 MALDI(Z-score):17.170700 | |
| edit table |
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Notes
Localization
See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
| Compartment | Description | Evidence | Reference/Source | Notes |
|---|---|---|---|---|
| edit table |
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Notes
Structure and Physical Properties
<protect>
Physical Properties
See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT ITSHDGWQMQ VEEVKEENGL LTYIGTRLDT EESGVALREV FLDSKLVFSK PQDRLFAGQI DRMDRFALRY RARKYSSEQF RMPYSGLRGQ RTSLIPHQLN IAHDVGRRHA PRVLLADEVG LGKTIEAGMI LHQQLLSGAA ERVLIIVPET LQHQWLVEML RRFNLRFALF DDERYAEAQH DAYNPFDTEQ LVICSLDFAR RSKQRLEHLC EAEWDLLVVD EAHHLVWSED APSREYQAIE QLAEHVPGVL LLTATPEQLG MESHFARLRL LDPNRFHDFA QFVEEQKNYR PVADAVAMLL AGNKLSNDEL NMLGEMIGEQ DIEPLLQAAN SDSEDAQSAR QELVSMLMDR HGTSRVLFRN TRNGVKGFPK RELHTIKLPL PTQYQTAIKV SGIMGARKSA EDRARDMLYP ERIYQEFEGD NATWWNFDPR VEWLMGYLTS HRSQKVLVIC AKAATALQLE QVLREREGIR AAVFHEGMSI IERDRAAAWF AEEDTGAQVL LCSEIGSEGR NFQFASHMVM FDLPFNPDLL EQRIGRLDRI GQAHDIQIHV PYLEKTAQSV LVRWYHEGLD AFEHTCPTGR TIYDSVYNDL INYLASPDQT EGFDDLIKNC REQHEALKAQ LEQGRDRLLE IHSNGGEKAQ ALAESIEEQD DDTNLIAFAM NLFDIIGINQ DDRGDNMIVL TPSDHMLVPD FPGLSEDGIT ITFDREVALA REDAQFITWE HPLIRNGLDL ILSGDTGSST ISLLKNKALP VGTLLVELIY VVEAQAPKQL QLNRFLPPTP VRMLLDKNGN NLAAQVEFET FNRQLNAVNR HTGSKLVNAV QQDVHAILQL GEAQIEKSAR ALIDAARNEA DEKLSAELSR LEALRAVNPN IRDDELTAIE SNRQQVMESL DQAGWRLDAL RLIVVTHQ |
| Length |
968 |
| Mol. Wt |
109.77 kDa |
| pI |
4.9 (calculated) |
| Extinction coefficient |
94,310 - 95,060 (calc based on 19 Y, 12 W, and 6 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
| </protect>
Structure figures<protect> | ||||||
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| edit table |
<protect></protect>
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
ASAP:ABE-0000198 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120001071 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1075 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Expression
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Overview
This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.
Cellular Levels
| Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
|---|---|---|---|---|---|---|---|
|
Protein |
E. coli K-12 MC4100 |
4.21E+02 |
molecules/cell |
|
emPAI |
PMID:18304323 | |
|
Protein |
Ecoli K-12 |
25.95+/-0.112 |
Molecules/cell |
|
Single Molecule Fluorescence |
PMID:20671182 | |
|
mRNA |
Ecoli K-12 |
0.028389539 |
Molecules/cell |
|
by RNA_Seq |
PMID:20671182 | |
|
Protein |
E. coli K-12 MG1655 |
5109 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
347 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
1139 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
| edit table |
Notes
Transcription and Transcriptional Regulation
<protect>
|
See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
|
 Figure courtesy of RegulonDB |
</protect>
Notes
This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.
Translation and Regulation of Translation
<protect><gbrowseImage>
name=NC_000913:63244..63284
source=MG1655
flip=1
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
This picture shows the sequence around the N-terminus.
</protect>
Notes
This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.
Turnover and Regulation of Turnover
</protect>
Notes
This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.
Experimental
<protect>
Mutations Affecting Expression
See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.
| Allele Name | Mutation | Phenotype | Reference |
|---|---|---|---|
| edit table |
Expression Studies
See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.
| Type | Reference | Notes |
|---|---|---|
|
microarray |
NCBI GEO profiles for hepA | |
|
microarray |
Summary of data for hepA from multiple microarray studies | |
| edit table |
Expression Resources
See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.
| Resource Name | Resource Type | Description | Source | Notes |
|---|---|---|---|---|
|
GFP Fusion |
Intergenic region (63194..63506) fused to gfpmut2. |
GFP fusion described in Zaslaver, et al. | ||
| edit table |
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Notes
Accessions Related to rapA Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1075 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001071 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0000198 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
| Organism | Homologs (Statistics) | Comments |
|---|---|---|
|
Anopheles gambiae |
|
From Inparanoid:20070104 |
|
Arabidopsis thaliana |
|
From Inparanoid:20070104 |
|
Bos taurus |
|
From Inparanoid:20070104 |
|
Canis familiaris |
|
From Inparanoid:20070104 |
|
Ciona intestinalis |
|
From Inparanoid:20070104 |
|
Homo sapiens |
|
From Inparanoid:20070104 |
|
Monodelphis domestica |
|
From Inparanoid:20070104 |
|
Oryza gramene |
|
From Inparanoid:20070104 |
|
Pan troglodytes |
|
From Inparanoid:20070104 |
|
Schizosaccharomyces pombe |
|
From Inparanoid:20070104 |
|
Takifugu rubripes |
|
From Inparanoid:20070104 |
|
Tetraodon nigroviridis |
|
From Inparanoid:20070104 |
|
Xenopus tropicalis |
|
From Inparanoid:20070104 |
|
Shigella flexneri |
HEPA |
From SHIGELLACYC |
|
E. coli O157 |
Z0067 |
From ECOO157CYC |
| edit table |
Do-It-Yourself Web Tools
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Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11083 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001071 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1075 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0000198 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
<protect></protect>
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
- ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
- ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed
Categories
- Genes in OpenBioSystems with Promoter Fusions
- Genes with homologs in Anopheles gambiae
- Genes with homologs in Arabidopsis thaliana
- Genes with homologs in Bos taurus
- Genes with homologs in Canis familiaris
- Genes with homologs in Ciona intestinalis
- Genes with homologs in Homo sapiens
- Genes with homologs in Monodelphis domestica
- Genes with homologs in Oryza gramene
- Genes with homologs in Pan troglodytes
- Genes with homologs in Schizosaccharomyces pombe
- Genes with homologs in Takifugu rubripes
- Genes with homologs in Tetraodon nigroviridis
- Genes with homologs in Xenopus tropicalis
- Genes with homologs in Shigella flexneri
- Genes with homologs in E. coli O157
