Conserved Protein Domain Family
homeodomain

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cd00086: homeodomain 
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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:
Hierarchy
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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

cd00086 is part of a hierarchy of related CD models.
Use the graphical representation to navigate this hierarchy.
cd00086 is a member of the superfamily cl00084.
cd00086:homeodomain1AKH B1064363857715101B72 B1756726119074756165528291907475719074324391576424952951723892200662444510417135199933272711346387580226019920444198637004566516492786272999258546011479428766028515953892563848898675043607497647479300630439585458213336727072702LFB  1043775017507563106436425771503127409750960416549929749561275103661233347290931755616413627184136270991362710113627102749929974977954177471748848174462827446282117043413467911170410134679075106451FJL A683167661749181079133590276360936331170306424967727650736093787312261224952734174252842721151821466854807335704451962539142767507779366146735502756226633270239721027287510164391561619262987750001510089067496254359950514764782185957803901364462280133863761285659266795131B72 A260069771147628348920399914643480613220017296522765012458580675732652582183156938171134422092007297491232604625611147624790882114762617090797500391170811860161081352398142861391353159302346746434017083493287858573133717082312809211403340812329417384021213520475104772014134119171513841324285150324952971NK2 P2506524750520323312191233927503588302395563204660162133023967318452160162877497211375782460943067302366302532875002451343132910242117082545476607496100423872174401763999112980868763590976571801167986532687473007506094307123239302397228332561234651706313750610654765873006661756628412845697123322458580417483177813454824354042315591820251058693718202510145745111708827170882982479307500095586936182025921838993518389931183899291BW5  66347721002661747207514350381748848114350381019860011359845273177617490024174884811907418119074174113224931723488249528713011627072686502544632065917308807322531820251019074300191732191907403919173020191730212147484250652523885745668786174329481969734120197728386883742180041168548426218515239522117016837859731OCP  24953092149211CQT A3915629123408477331117030724953023024410302463475103663336980667763976623427243284175370077503437979855675034407500110750343766776392052102972432847662342333698076623426677639205210296677639766234275106457497254194243425441481312450315239002150778411460312718602337128455407504641185860231756664841381314107113194243447503266317019617433134302575220197596225358239550217508489751093272913997291399751093275062126752990766234675062471AKH B1064363857715101B72 B1756726119074756165528291907475719074324391576424952951723892200662444510417135199933272711346387580226019920444198637004566516492786272999258546011479428766028515953892563848898675043607497647479300630439585458213336727072702LFB  1043775017507563106436425771503127409750960416549929749561275103661233347290931755616413627184136270991362710113627102749929974977954177471748848174462827446282117043413467911170410134679075106451FJL A683167661749181079133590276360936331170306424967727650736093787312261224952734174252842721151821466854807335704451962539142767507779366146735502756226633270239721027287510164391561619262987750001510089067496254359950514764782185957803901364462280133863761285659266795131B72 A260069771147628348920399914643480613220017296522765012458580675732652582183156938171134422092007297491232604625611147624790882114762617090797500391170811860161081352398142861391353159302346746434017083493287858573133717082312809211403340812329417384021213520475104772014134119171513841324285150324952971NK2 P2506524750520323312191233927503588302395563204660162133023967318452160162877497211375782460943067302366302532875002451343132910242117082545476607496100423872174401763999112980868763590976571801167986532687473007506094307123239302397228332561234651706313750610654765873006661756628412845697123322458580417483177813454824354042315591820251058693718202510145745111708827170882982479307500095586936182025921838993518389931183899291BW5  66347721002661747207514350381748848114350381019860011359845273177617490024174884811907418119074174113224931723488249528713011627072686502544632065917308807322531820251019074300191732191907403919173020191730212147484250652523885745668786174329481969734120197728386883742180041168548426218515239522117016837859731OCP  24953092149211CQT A391562912340847733111703072495302302441030246347510366333698066776397662342724328417537007750343797985567503440750011075034376677639205210297243284766234233369807662342667763920521029667763976623427510645749725419424342544148131245031523900215077841146031271860233712845540750464118586023175666484138131410711319424344750326631701961743313430257522019759622535823955021750848975109327291399729139975109327506212675299076623467506247
cd00086 Sequence Cluster
cd00086 Sequence Cluster
Sub-family Hierarchy
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CD Hierarchy
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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Conserved site includes 6 residues -Click on image for an interactive view with Cn3D