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Protein

Uncharacterized HTH-type transcriptional regulator YddM

Gene

yddM

Organism
Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi24 – 43H-T-H motifPROSITE-ProRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciECOL199310:C1909-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Uncharacterized HTH-type transcriptional regulator YddM
Gene namesi
Name:yddM
Ordered Locus Names:c1909
OrganismiEscherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
Taxonomic identifieri199310 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000001410 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001497601 – 94Uncharacterized HTH-type transcriptional regulator YddMAdd BLAST94

Proteomic databases

PRIDEiP67700.

Interactioni

Protein-protein interaction databases

STRINGi199310.c1909.

Structurei

Secondary structure

194
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 20Combined sources12
Helixi24 – 31Combined sources8
Helixi35 – 42Combined sources8
Helixi50 – 59Combined sources10
Helixi64 – 80Combined sources17
Helixi85 – 87Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ICPX-ray1.88A1-94[»]
2ICTX-ray1.63A1-94[»]
ProteinModelPortaliP67700.
SMRiP67700.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67700.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini13 – 67HTH cro/C1-typePROSITE-ProRule annotationAdd BLAST55

Sequence similaritiesi

Belongs to the VapA/VapI family.Curated
Contains 1 HTH cro/C1-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG41084S7. Bacteria.
COG3093. LUCA.
HOGENOMiHOG000265974.
OMAiCRFLAKQ.

Family and domain databases

Gene3Di1.10.260.40. 1 hit.
InterProiIPR001387. Cro/C1-type_HTH.
IPR010982. Lambda_DNA-bd_dom.
IPR013430. Toxin_antidote_HigA.
[Graphical view]
PfamiPF01381. HTH_3. 1 hit.
[Graphical view]
SMARTiSM00530. HTH_XRE. 1 hit.
[Graphical view]
SUPFAMiSSF47413. SSF47413. 1 hit.
TIGRFAMsiTIGR02607. antidote_HigA. 1 hit.
PROSITEiPS50943. HTH_CROC1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P67700-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMANHPRPG DIIQESLDEL NVSLREFARA MEIAPSTASR LLTGKAALTP
60 70 80 90
EMAIKLSVVI GSSPQMWLNL QNAWSLAEAE KTVDVSRLRR LVTQ
Length:94
Mass (Da):10,401
Last modified:October 11, 2004 - v1
Checksum:iE330280EDA2AEC1B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014075 Genomic DNA. Translation: AAN80368.1.
RefSeqiWP_000781370.1. NC_004431.1.

Genome annotation databases

EnsemblBacteriaiAAN80368; AAN80368; c1909.
KEGGiecc:c1909.
PATRICi18281717. VBIEscCol75197_1777.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014075 Genomic DNA. Translation: AAN80368.1.
RefSeqiWP_000781370.1. NC_004431.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ICPX-ray1.88A1-94[»]
2ICTX-ray1.63A1-94[»]
ProteinModelPortaliP67700.
SMRiP67700.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi199310.c1909.

Proteomic databases

PRIDEiP67700.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN80368; AAN80368; c1909.
KEGGiecc:c1909.
PATRICi18281717. VBIEscCol75197_1777.

Phylogenomic databases

eggNOGiENOG41084S7. Bacteria.
COG3093. LUCA.
HOGENOMiHOG000265974.
OMAiCRFLAKQ.

Enzyme and pathway databases

BioCyciECOL199310:C1909-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP67700.

Family and domain databases

Gene3Di1.10.260.40. 1 hit.
InterProiIPR001387. Cro/C1-type_HTH.
IPR010982. Lambda_DNA-bd_dom.
IPR013430. Toxin_antidote_HigA.
[Graphical view]
PfamiPF01381. HTH_3. 1 hit.
[Graphical view]
SMARTiSM00530. HTH_XRE. 1 hit.
[Graphical view]
SUPFAMiSSF47413. SSF47413. 1 hit.
TIGRFAMsiTIGR02607. antidote_HigA. 1 hit.
PROSITEiPS50943. HTH_CROC1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYDDM_ECOL6
AccessioniPrimary (citable) accession number: P67700
Secondary accession number(s): P76125
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: November 2, 2016
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The crystal structure has erroneously been identified as HigA, the sequence submitted is in fact that of YddM.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.