Conserved Protein Domain Family
homeodomain

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cd00086: homeodomain 
Click on image for an interactive view with Cn3D
Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Statistics
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PSSM-Id: 238039
View PSSM: cd00086
Aligned: 317 rows
Threshold Bit Score: 31.4449
Threshold Setting Gi: 7510366
Created: 1-Nov-2000
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
specific DNADNA binding
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:specific DNA base contacts [nucleic acid binding site]
Evidence:
  • Comment:sequence specific interactions with major and minor groove nucleotides
  • Comment:position of residues interacting with minor groove (helix1) are shifted in subgroups
  • Citation:PMID 9154919
  • Structure:1AKH; MATalpha1
    View structure with Cn3D
  • Citation:PMID 7569974

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          #  #                                                  #  ##  #      
1AKH_B         3 PYRGHRFTKENVRILESWFAkni---enPYLDTKGLENLMKNTS-----LSRIQIKNWVSNRRRKEKTIT 64
gi 4138131   731 KRKRTIMNDEQVMLIERALLde----pdMQRNAASLQSWADKLSlhgsdVTPSQIKNWLNNRKARLARTA 796
gi 7510366   460 PKPKSQYSKFEDETMEKAYMrtvkmnpsSYESRDLLESISISLR-----MSLIKVHEWFNNRKFVDSVSI 524
gi 19424344    3 AQTGSGPTEDQVEILEYNFNkv-----nKHPDPTTLCLIAAEAG-----LTEEQTQKWFKQRLAEWRRSE 62
gi 3025752   240 EQKRSTFTPDQLEALEQAFNrg-----hYPTDPFNRDNMSNKVD-----LSQTRVQDVKPSISCSTTSVA 299
gi 544148    582 LSPGQPPLKNLLSLLKAYYAl------nAQPSAEELSKIADSVN-----LPLDVVKKWFEKMQAGQISVQ 640
gi 7503266   318 EKNWSSFSYDAIHFLEQEYRk------tKYISSTDCQKISEKIH-----LDEELIEKWFRARRATSKREA 376
gi 13124503  645 MTSPINPYKDHMSVLKAYYAm------nMEPNSDELLKISIAVG-----LPQEFVKEWFEQRKVYQYSNS 703
gi 7503437   464 ERKRTSNLDYASRILEQKFAn------rANLLPSDLVDLEKTIG-----WTLDEISEWFETREKLQERRE 522
gi 15239002  283 WSAQKRVKKAHIETLEKVYRr------sKRPTNAVVSSIVQVTN-----LPRKRVLKWFEDKRAEDGVPD 341

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