slyD: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 |
slyD |
|---|---|
| Gene Synonym(s) |
ECK3336, b3349, JW3311[1], JW3311 |
| Product Desc. |
FKBP-type rotamase, peptidyl prolyl cis-trans isomerase[2]; FKBP-type peptidyl prolyl cis-trans isomerase[3]; Component of FKBP-type peptidyl prolyl cis-trans isomerase[3] FKBP-type peptidyl-prolyl cis-trans isomerase; metal ion regulated; overexpression causes filamentation; required to stabilize E lysis protein of bacteriophage phiX174[4] |
| Product Synonyms(s) |
FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)[1], B3349[2][1], SlyD[2][1], WHP[2][1] , ECK3336, JW3311, b3349 |
| Function from GO |
<GO_nr /> |
| Knock-Out Phenotype | |
| Regulation/Expression | |
| Regulation/Activity | |
| Quick Links | |
| edit table |
See Help:Quickview for help with entering information in the Quickview table.
Notes
HypB requires binding of SlyD for hydrogenase activity as SlyD helps facilitate nickel insertion. Binds TrxA (Kumar, 2004). SlyD has a histidine-rich, nickel-binding region, so it is a common contaminant in protein purification of His-tagged proteins (Parsy, 2007). SlyD is a a heat-shock protein that facilitates folding and enhances the solubilty of aggregation-prone proteins (Han, 2007).[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
slyD |
|---|---|
| Mnemonic |
Sensitivity to lysis |
| Synonyms |
ECK3336, b3349, JW3311[1], JW3311 |
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Notes
Location(s) and DNA Sequence
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 |
74.92 minutes, 74.92 minutes |
MG1655: 3476519..3475929 |
||
|
NC_012967: 3406402..3405812 |
||||
|
NC_012759: 3363086..3363676 |
||||
|
W3110 |
|
W3110: 4161919..4162509 |
||
|
DH10B: 3574264..3573674 |
||||
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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) |
3475929 |
Edman degradation |
PMID:8300624 |
| |
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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 |
|---|---|---|---|---|---|---|---|
|
ΔslyD (Keio:JW3311) |
deletion |
deletion |
PMID:16738554 |
||||
|
ΔslyD738::kan |
PMID:16738554 |
| |||||
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Notes
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
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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 |
|---|---|---|---|
|
JW3311 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCAAAGTAGCAAAAGACCTGGT Primer 2:CCGTGGCAACCGCAACCGCCGTT | |
|
Kohara Phage |
PMID:3038334 | ||
|
Kohara Phage |
PMID:3038334 | ||
|
Linked marker |
est. P1 cotransduction: 12% [6] | ||
|
Linked marker |
est. P1 cotransduction: 36% [6] | ||
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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:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001606 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EchoBASE:EB1614 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010946 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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Product(s)
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Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| Standard name |
SlyD |
|---|---|
| Synonyms |
FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)[1], B3349[2][1], SlyD[2][1], WHP[2][1] , ECK3336, JW3311, b3349 |
| Product description |
FKBP-type rotamase, peptidyl prolyl cis-trans isomerase[2]; FKBP-type peptidyl prolyl cis-trans isomerase[3]; Component of FKBP-type peptidyl prolyl cis-trans isomerase[3] FKBP-type peptidyl-prolyl cis-trans isomerase; metal ion regulated; overexpression causes filamentation; required to stabilize E lysis protein of bacteriophage phiX174[4] |
| EC number (for enzymes) | |
| edit table |
Notes
Function
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:0003755 |
peptidyl-prolyl cis-trans isomerase activity |
GOA:spec |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003755 |
peptidyl-prolyl cis-trans isomerase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005507 |
copper ion binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005737 |
cytoplasm |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005737 |
cytoplasm |
IEA: Inferred from Electronic Annotation |
SP_SL:SL-0086 |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0008270 |
zinc ion binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0008270 |
zinc ion binding |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0016151 |
nickel ion binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0016151 |
nickel ion binding |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0016151 |
nickel ion binding |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0050897 |
cobalt ion binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0051082 |
unfolded protein binding |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0005515 |
protein binding |
IPI: Inferred from Physical Interaction |
F |
complete | ||||
| GO:0051604 |
protein maturation |
IMP: Inferred from Mutant Phenotype |
P |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0022417 |
protein maturation by protein folding |
IMP: Inferred from Mutant Phenotype |
P |
complete | ||||
| GO:0016151 |
nickel ion binding |
IDA: Inferred from Direct Assay |
F |
complete | ||||
| GO:0009408 |
response to heat |
IEP: Inferred from Expression Pattern |
P |
complete | ||||
| GO:0050821 |
protein stabilization |
IMP: Inferred from Mutant Phenotype |
P |
complete | ||||
| GO:0003755 |
peptidyl-prolyl cis-trans isomerase activity |
IMP: Inferred from Mutant Phenotype |
F |
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 |
Subunits of FKBP-type peptidyl prolyl cis-trans isomerase |
could be indirect |
||
|
Protein |
gltL |
Experiment(s):EBI-893588 | ||
|
Protein |
hupA |
Experiment(s):EBI-893588 | ||
|
Protein |
hupB |
Experiment(s):EBI-893588 | ||
|
Protein |
hypB |
Experiment(s):EBI-893588 | ||
|
Protein |
sapD |
Experiment(s):EBI-893588 | ||
|
Protein |
serS |
Experiment(s):EBI-893588 | ||
|
Protein |
ulaF |
Experiment(s):EBI-893588 | ||
|
Protein |
ydeI |
Experiment(s):EBI-893588 | ||
|
Protein |
nudL |
Experiment(s):EBI-893588 | ||
|
Protein |
grcA |
Experiment(s):EBI-893588 | ||
|
Protein |
yhjQ |
Experiment(s):EBI-893588 | ||
|
Protein |
ycgX |
Experiment(s):EBI-1145639 | ||
|
Protein |
rplE |
Experiment(s):EBI-1145639 | ||
|
Protein |
insA7 |
Experiment(s):EBI-1145639 | ||
|
Protein |
betA |
Experiment(s):EBI-1145639 | ||
|
Protein |
rpmA |
Experiment(s):EBI-1145639 | ||
|
Protein |
rplW |
Experiment(s):EBI-1145639 | ||
|
Protein |
rplO |
Experiment(s):EBI-1145639 | ||
|
Protein |
rplF |
Experiment(s):EBI-1145639 | ||
|
Protein |
fliC |
Experiment(s):EBI-1145639 | ||
|
Protein |
rplN |
Experiment(s):EBI-1145639 | ||
|
Protein |
rpsI |
Experiment(s):EBI-1145639 | ||
|
Protein |
lacI |
Experiment(s):EBI-1145639 | ||
|
Protein |
rpsD |
Experiment(s):EBI-1145639 | ||
|
Protein |
yhdZ |
Experiment(s):EBI-1145639 | ||
|
Protein |
rpsE |
Experiment(s):EBI-1145639 | ||
|
Protein |
nusG |
Experiment(s):EBI-1145639 | ||
|
Protein |
yfiD |
LCMS(ID Probability):99.0 MALDI(Z-score):3.263244 | ||
|
Protein |
ampH |
LCMS(ID Probability):99.6 | ||
|
Protein |
HypB (GTPase & hydrogenase accessory protein) |
HypB was shown to directly interact with SlyD & a slyD- strain has reduced hydrogenase activity & accumulates an immature (unprocessed) form of the hydrogenase (HycE), which can be complemented by the addition of nickel to the growth medium or complemented with plasmid-borne expression of SlyD. See PMID:15569666[10] |
| |
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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 |
|---|---|---|---|---|
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Notes
Structure and Physical Properties
Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG GEGCCGGKGN GGCGCH |
| Length |
196 |
| Mol. Wt |
20.85 kDa |
| pI |
4.8 (calculated) |
| Extinction coefficient |
5,960 - 6,710 (calc based on 4 Y, 0 W, and 6 C residues) |
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Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
|
Structure figures
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 |
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-0010946 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120001606 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1614 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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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 |
5.85E+03 |
molecules/cell |
|
emPAI |
PMID:18304323 | |
|
Protein |
Ecoli K-12 |
482.605+/-4.428 |
Molecules/cell |
|
Single Molecule Fluorescence |
PMID:20671182 | |
|
mRNA |
Ecoli K-12 |
0.23487+/-0.01604 |
Molecules/cell |
|
by FISH |
PMID:20671182 | |
|
mRNA |
Ecoli K-12 |
1.038135593 |
Molecules/cell |
|
by RNA_Seq |
PMID:20671182 | |
|
Protein |
E. coli K-12 MG1655 |
38169 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
7302 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
20452 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
| edit table |
Notes
Transcription and Transcriptional Regulation
|
See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
|
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
<gbrowseImage> name=NC_000913:3476499..3476539 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.
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
Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.
| Allele Name | Mutation | Phenotype | Reference |
|---|---|---|---|
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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 slyD | |
|
microarray |
Summary of data for slyD from multiple microarray studies | |
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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 (3476053..3476465) fused to gfpmut2. |
GFP fusion described in Zaslaver, et al. | ||
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<protect>
Notes
Accessions Related to slyD Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1614 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001606 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010946 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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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 |
|---|---|---|
|
Xenopus tropicalis |
|
From Inparanoid:20070104 |
|
Shigella flexneri |
SLYD |
From SHIGELLACYC |
|
E. coli O157 |
SLYD |
From ECOO157CYC |
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Do-It-Yourself Web Tools
Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11663 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001606 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1614 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010946 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 3.0 3.1 3.2 3.3 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).
- ↑ 7.0 7.1 Wülfing, C et al. (1994) An Escherichia coli protein consisting of a domain homologous to FK506-binding proteins (FKBP) and a new metal binding motif. J. Biol. Chem. 269 2895-901 PubMed
- ↑ Kaluarachchi, H et al. (2009) The Ni(II)-binding properties of the metallochaperone SlyD. J. Am. Chem. Soc. 131 18489-500 PubMed
- ↑ Weininger, U et al. (2009) NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function. J. Mol. Biol. 387 295-305 PubMed
- ↑ 10.0 10.1 10.2 Zhang, JW et al. (2005) A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway. J. Biol. Chem. 280 4360-6 PubMed
- ↑ Leach, MR et al. (2007) The role of complex formation between the Escherichia coli hydrogenase accessory factors HypB and SlyD. J. Biol. Chem. 282 16177-86 PubMed
- ↑ Martino, L et al. (2009) The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity. FEBS J. 276 4529-44 PubMed
- ↑ 13.0 13.1 Han, KY et al. (2007) Solubilization of aggregation-prone heterologous proteins by covalent fusion of stress-responsive Escherichia coli protein, SlyD. Protein Eng. Des. Sel. 20 543-9 PubMed
- ↑ Zhang, JW et al. (2007) The peptidyl-prolyl isomerase activity of SlyD is not required for maturation of Escherichia coli hydrogenase. J. Bacteriol. 189 7942-4 PubMed
- ↑ 15.00 15.01 15.02 15.03 15.04 15.05 15.06 15.07 15.08 15.09 15.10 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ 16.00 16.01 16.02 16.03 16.04 16.05 16.06 16.07 16.08 16.09 16.10 16.11 16.12 16.13 16.14 16.15 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
- ↑ 17.0 17.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
- ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
- ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed
Categories
- GO:0003755 ! peptidyl-prolyl cis-trans isomerase activity
- GO:0005507 ! copper ion binding
- GO:0005737 ! cytoplasm
- GO:0008270 ! zinc ion binding
- GO:0016151 ! nickel cation binding
- GO:0050897 ! cobalt ion binding
- GO:0051082 ! unfolded protein binding
- GO:0005515 ! protein binding
- GO:0051604 ! protein maturation
- GO:0022417 ! protein maturation by protein folding
- GO:0009408 ! response to heat
- GO:0050821 ! protein stabilization
- Genes in OpenBioSystems with Promoter Fusions
- Genes with homologs in Xenopus tropicalis
- Genes with homologs in Shigella flexneri
- Genes with homologs in E. coli O157



