1KQ1,3HSB,3GIB,3SB2,3HFN


Conserved Protein Domain Family
Hfq

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cd01716: Hfq 
Click on image for an interactive view with Cn3D
bacterial Hfq-like
Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotropic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Statistics
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PSSM-Id: 212463
Aligned: 38 rows
Threshold Bit Score: 71.0207
Created: 10-May-2012
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Structure:3GIB; Escherichia coli Hfq with bound Poly(A), contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                           #   #####            #         #       ## # 
1KQ1_A         6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNsq---gKQHLIYKHAISTYTV 65  Staphylococcus aureus
AAV88971      87 LLQDVFLSAIMQQQEPVTMFLINGVMLQGEIAAFDLFCVLLTrn---dDAQLVYKHAVSTVQP 146 Zymomonas mobilis subsp. mobilis...
3GIB_A         5 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKn----tVSQMVYKHAISTVVP 63  Escherichia coli K12
3HFN_A        10 LPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTCVCIAde--nsRQTTIWKQAIAYLQP 70  Nostoc sp. PCC 7120
ADO77181       6 NYQDHILKHVHEKQIEVIVYFVNGYQLKGKITAYDNFTVILRsd---eRDQMIYKHAISTIAP 65  Halanaerobium praevalens DSM 2228
YP_002728942   3 SVQDEILNEYRREGKEVTVYLVRGTRIVGKILDADQFTILLDvn---gQQQLIYKHAISTIVV 62  Sulfurihydrogenibium azorense Az...
YP_002121893   4 NLQDKILEDAKEKGIEVVIYLTRGNRMVGKVLDQDKYTVLLKsd---sGTNLIYKHAISTIVI 63  Hydrogenobaculum sp. Y04AAS1
YP_003192393  19 SVQNKILVQLKEQQASIIVYLINGYRLGGKLKDFDTFTVILEek---eTQYIVYKHAISTIIP 78  Desulfotomaculum acetoxidans DSM...
YP_002300003   6 ALQSKVLDVLRTGGTEVTVFLVTGVRLVGRIVAHDAYSLALTgh--ggGLQLIYKHAVTTLVP 66  Rhodospirillum centenum SW
ZP_09622769   14 NLQHLQLSTHSASRNPVVVHLSNGIRLHGVIVAADNYMVLLAesaqdpMPQIVYKHSIAVITP 76  Cupriavidus basilensis OR16

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