Citrus Sinensis ID: 004454

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750---
Protein Sequence
MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQSLVPAGEKELAGSELVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQVTLEL
Secondary Structure (PSIPRED)
cccHHHHHHHHHccccccHHcccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHcccccHHHHHHHHHHHHHHHHcHHHHHcccccccccccccccccccccHHHHHHHHHHcccHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccccccccccccHHHcccccHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHccccccccccccEEcccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEccccHHcccHHHHHHHccccccccEcccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHccccHHHHHHHcccccHHHHHHHHHHHcccccHccccccHHccccccccccccccHHEcccccHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTyavesypsEALRAELSAQLGLSDRQLQMWFCHrrlkdrkaptakrqpkdfqslvpagekelagSELVRGGMAVQRYyavpmapmlpfplpqrniVEMRVIAFVESqlgeplredgpilgvefdslppdafgrpigpaamghqkhsvrpleakeyerldvkpfkdmftihpqgatrtvheykflpeqptvrsethekaassypygspadgstarnsslraghpfmhgseqissgygfpgqlpnlnllshqgrhshllpsvsgeyeNILRKNSFISAAMdahvggqpitamdnafissdrrvshdedvsrteKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAAsskglptivsldfetlqnldlfrdrpctfppksvqlkrpfavqpwndsednIGNLLMVWRFLITFADvlglwpftLDEFVQAFhdydprllGEIHVTLLRSVIKDIEDaaktpftglganqnsavnpggahpqiVEGAYAWGFDIRSWQLHLNALTWPEILRQFALsagfgpqlnkrniekmyphdnnegndgenIISNLRNGSAVGNAVAIMHEMGLSNlrrsrhrltpgtvKFAAFHVLSlegsegltiLEVADKIQVTLEL
Flexible Loop (DISEMBL)
meaaseaeekkkkkkpleaevktkrkmktasqleILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRlkdrkaptakrqpkdfqslvpagekelagselVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAfissdrrvshdedvsrtekkrkseeariareveahekrirkelekqdilrrkreeqirkemerqdrerrkeeerllreklreeerylreqrrelerrekflqkesiraekrrqkeelrrvkeaerlkvaneravarrIAKESMALVEDERLELMELAASskglptivSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSlegsegltilevADKIQVTLEL
Low Complexity Region (SEG)
MeaaseaeekkkkkkpleaevktkRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQSLVPAGEKELAGSELVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIrkemerqdrerrkeeerllreklreeerylreqrrelerrekflqkeSIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQVTLEL
Disordered region (IsUnstruct)
***********************************LEKTYAVE*********ELSAQLGLSDRQLQMWFCHRRL*****************************ELVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFD********************************RLDVKPFKDMFTIHPQGATRTVHEYKF************************************************************LNLL********LLPSVSGEYENILRKNSFISAAMDAHVGGQPIT***********************************************************************************************************************************************************LELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGAN****VNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLN*********************I*NLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQV****
Disordered Region (DISOPRED)
********************************LEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWF************************************************************************VESQLGEPLREDGPILGVEFDSLPP*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************QLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDA****************NPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQL**************EGNDGENIISNLRNGSAVGNAVA***************RLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQVTLEL
Disordered Region (DISEMBL)
***************************KTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK*************FQSLVPAGEKELAGSELVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAA*********PLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQP**************************NSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSD**********************IAREVEAHEKRIRKELEKQDILRRKREEQIR**************ERLLREKLREEERYLREQRRELERREKFLQKESIRA***********VKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQVTLEL
Disordered Region (DISPRO)
*************************KMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA*****************************************APMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSE*HEKAASSYPYGSPADGS********************SSGY*FP*QLPNL************LPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREE*******************LLREKL***ERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNI*KMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQVTLEL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQSLVPAGEKELAGSELVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIARExxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQVTLEL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	753	2.2.26 [Sep-21-2011]
Q8IDX6	3130	Reticulocyte-binding prot	yes	no	0.233	0.056	0.293	1e-08
Q54ST3	885	DDT domain-containing pro	no	no	0.108	0.092	0.337	9e-05
Q1MTN9	544	Chromatin assembly factor	yes	no	0.148	0.205	0.343	0.0002

>sp|Q8IDX6|RBP2A_PLAF7 Reticulocyte-binding protein 2 homolog a OS=Plasmodium falciparum (isolate 3D7) GN=PF13_0198 PE=3 SV=1

 Score = 62.4 bits (150), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 56/191 (29%), Positives = 107/191 (56%), Gaps = 15/191 (7%)

Query: 365  AHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEE-ERLLREKLREEERYLREQRR 423
            A +++ ++ L+K++ L  KR+EQ R E E+Q++ +++EE +R  +E+L++EE   R+++ 
Sbjct: 2738 ALKRQEQERLQKEEEL--KRQEQERLEREKQEQLQKEEELKRQEQERLQKEEALKRQEQE 2795

Query: 424  ELERREKFLQKESIRAEKRRQ-----KEELRRVKEAERLKV--ANERAVARRIAK-ESMA 475
             L++ E+  ++E  R E+ +Q     +EEL+R +E ERL+   A +R    R+ K E + 
Sbjct: 2796 RLQKEEELKRQEQERLEREKQEQLQKEEELKR-QEQERLQKEEALKRQEQERLQKEEELK 2854

Query: 476  LVEDERLEL--MELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQP 533
              E ERLE   +ELA   + + + +  D   +   +L +++      K ++L+     Q 
Sbjct: 2855 RQEQERLERKKIELAEREQHIKSKLESDMVKIIKDELTKEKDEIIKNKDIKLRHSLE-QK 2913

Query: 534  WNDSEDNIGNL 544
            W     NI +L
Sbjct: 2914 WLKHLQNILSL 2924

Involved in reticulocyte adhesion.
Plasmodium falciparum (isolate 3D7) (taxid: 36329)

>sp|Q54ST3|Y2237_DICDI DDT domain-containing protein DDB_G0282237 OS=Dictyostelium discoideum GN=DDB_G0282237 PE=3 SV=1

 Score = 49.7 bits (117), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 527 RPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAF-HDYDPRLLGEIHV 585
           RP A   +    +  G+ LMVW FL  F  VL L PF LD+F  A  H  +  +L E H+
Sbjct: 432 RPIASSDFFCLSNTFGDFLMVWHFLNHFEKVLLLSPFPLDDFEMAIQHHTETNILVESHI 491

Query: 586 TLLRSVIKDIEDAAKTPFTGLGA 608
            L++++      ++ TP    G 
Sbjct: 492 RLMKTIFTLPSYSSGTPKKTFGG 514

Dictyostelium discoideum (taxid: 44689)

>sp|Q1MTN9|RLF2_SCHPO Chromatin assembly factor 1 subunit rlf2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rlf2 PE=3 SV=2

 Score = 48.5 bits (114), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/137 (34%), Positives = 80/137 (58%), Gaps = 25/137 (18%)

Query: 367 EKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELE 426
           EK+++K+  +++ +R+K  E++++E ERQ RE+ K        KLRE+E+   ++ +ELE
Sbjct: 77  EKKLQKQRAQEERIRQKEAERLKREKERQQREQEK--------KLREQEKIAAKKMKELE 128

Query: 427 RREK---FLQKESIRAEKR----RQKEELRRV-------KEAERLKVAN--ERAVARRIA 470
           + EK    LQ++  R E+R    R+KEE +R+       KE ++LK+ N   + V +RIA
Sbjct: 129 KLEKERIRLQEQQRRKEERDQKLREKEEAQRLRQEQILNKERQQLKLNNFFTKGVEKRIA 188

Query: 471 KESMALVEDERLELMEL 487
             +   V D+  EL E 
Sbjct: 189 P-NENFVADKTDELNEF 204

Acts as a component of chromatin assembly factor 1 (CAF-1), which assembles histone octamers onto replicating DNA in vitro. It performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. May facilitate the efficient and timely assembly of histones into telomeric chromatin.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	753
225446457	1772	PREDICTED: uncharacterized protein LOC10	0.970	0.412	0.719	0.0
224132876	1746	predicted protein [Populus trichocarpa]	0.968	0.417	0.700	0.0
224095585	1728	predicted protein [Populus trichocarpa]	0.962	0.419	0.688	0.0
255553623	1784	homeobox protein, putative [Ricinus comm	0.953	0.402	0.706	0.0
356515148	1768	PREDICTED: uncharacterized protein LOC10	0.966	0.411	0.631	0.0
297794989	1684	hypothetical protein ARALYDRAFT_494576 [	0.949	0.424	0.594	0.0
334188190	1507	Homeodomain-like transcriptional regulat	0.932	0.465	0.588	0.0
15241428	1694	Homeodomain-like transcriptional regulat	0.932	0.414	0.588	0.0
302143341	1870	unnamed protein product [Vitis vinifera]	0.722	0.290	0.783	0.0
359483496	1729	PREDICTED: uncharacterized protein LOC10	0.942	0.410	0.602	0.0

>gi|225446457|ref|XP_002275272.1| PREDICTED: uncharacterized protein LOC100250601 [Vitis vinifera]

 Score = 1029 bits (2661), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 558/776 (71%), Positives = 616/776 (79%), Gaps = 45/776 (5%)

Query: 1   MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
           ME  +E E    KKK  E E K+KRKMKTASQLEILEKTYAVE+YPSE LRAELSA+LGL
Sbjct: 1   MEGGAEEE----KKKAPEGENKSKRKMKTASQLEILEKTYAVETYPSETLRAELSAKLGL 56

Query: 61  SDRQLQMWFCHRRLKDRKAPTAKRQPKDFQSLV-------PAGEKELAGSE--------- 104
           SDRQLQMWFCHRRLKDRK P  KR  KD    V       P  E+   G+E         
Sbjct: 57  SDRQLQMWFCHRRLKDRKTPPVKRPRKDSPVKVTSSAAGTPVREEMEVGNEHPSGSGSGS 116

Query: 105 ------------LVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLRE 152
                       + R G AV R  A  M PM  +  P + I E+R IAFVE+QLGEPLRE
Sbjct: 117 SPFGHVLESRRVVPRPGTAVARIGA-DMPPMKRYYEPPQPISELRAIAFVEAQLGEPLRE 175

Query: 153 DGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGA 212
           DGPILG+EFD LPPDAFG PI  A +G QK  VRP E K YER D KP K        GA
Sbjct: 176 DGPILGMEFDPLPPDAFGAPI--ATVGQQKQGVRPYETKLYERPDAKPIK--------GA 225

Query: 213 TRTVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSG 272
            R VHEY+FLPEQP+VR++T+E+  S Y YGSPADG +AR +SL  G  FMHG+EQ++SG
Sbjct: 226 GRAVHEYQFLPEQPSVRTDTYERVGSHY-YGSPADGPSAR-ASLSTGRSFMHGNEQVASG 283

Query: 273 YGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAF 332
           YGF GQ+PNLNLLS QGR +H L S SG+Y+ + RKNS  S  MDAH G  PITA+DN F
Sbjct: 284 YGFQGQMPNLNLLSQQGRQNHGLSSTSGDYDTVPRKNSLGSIGMDAHFGSHPITALDNPF 343

Query: 333 ISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEM 392
           ISSDRRV++DEDV R E+KRKSEEARIA+EVEAHEKRIRKELEKQDILRRKREEQ+RKEM
Sbjct: 344 ISSDRRVTNDEDVLRMERKRKSEEARIAKEVEAHEKRIRKELEKQDILRRKREEQMRKEM 403

Query: 393 ERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK 452
           ER DRERRKEEERLLREK REEERY REQRRELERREKFLQKESIRAEK RQKEELRR K
Sbjct: 404 ERHDRERRKEEERLLREKQREEERYQREQRRELERREKFLQKESIRAEKMRQKEELRREK 463

Query: 453 EAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFR 512
           EA R+K AN+RA+ARRIAKESM L+EDERLELMEL A SKGLP+I+SLD ETLQNL+ FR
Sbjct: 464 EAARVKAANDRAIARRIAKESMELIEDERLELMELVALSKGLPSILSLDSETLQNLESFR 523

Query: 513 DRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAF 572
           D    FPPKSVQL+RPF +QPW DSE+NIGNLLMVWRFLITF+DVLGLWPFT+DEFVQAF
Sbjct: 524 DMLTAFPPKSVQLRRPFTIQPWTDSEENIGNLLMVWRFLITFSDVLGLWPFTMDEFVQAF 583

Query: 573 HDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGF 632
           HDYDPRLLGEIHV LLRS+IKDIED A+TP  GLGANQNSA NPGG HPQIVEGAYAWGF
Sbjct: 584 HDYDPRLLGEIHVALLRSIIKDIEDVARTPSIGLGANQNSAANPGGGHPQIVEGAYAWGF 643

Query: 633 DIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNG 692
           DIRSWQ HLN LTWPEILRQFALSAGFGP+L KRN+E+ Y  D+NEGND E+II+NLR+G
Sbjct: 644 DIRSWQRHLNPLTWPEILRQFALSAGFGPKLKKRNVEETYLRDDNEGNDCEDIITNLRSG 703

Query: 693 SAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           +A  NAVAIM E G SN RRSRHRLTPGTVKFAAFHVLSLEGS+GLTILEVADKIQ
Sbjct: 704 AAAENAVAIMQERGFSNPRRSRHRLTPGTVKFAAFHVLSLEGSKGLTILEVADKIQ 759

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132876|ref|XP_002327902.1| predicted protein [Populus trichocarpa] gi|222837311|gb|EEE75690.1| predicted protein [Populus trichocarpa]

 Score = 1022 bits (2643), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 533/761 (70%), Positives = 605/761 (79%), Gaps = 32/761 (4%)

Query: 12  KKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCH 71
           KKK P E E K+KRKMKTASQLEILEKTYA ++YPSEA+RAELS QLGLSDRQLQMWFCH
Sbjct: 18  KKKTPGEGESKSKRKMKTASQLEILEKTYAADTYPSEAVRAELSVQLGLSDRQLQMWFCH 77

Query: 72  RRLKDRKAPTAKRQPKDFQS--LVPAGEKELAGSELVR---------GGMAVQRYYAV-- 118
           RRLKDRKAP  KR  K+  S   +P G +   G+E+            G+ V    AV  
Sbjct: 78  RRLKDRKAPLVKRPHKESPSPAGMPGGVEMGVGTEVGNEHGSGSASLSGLGVDSRRAVGR 137

Query: 119 PMAPMLP-----------FPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPD 167
           P    +P           +  PQ+++ E+R IAFVE+QLGEPLREDGPILG+EFD LPPD
Sbjct: 138 PTGVAVPRISADVQAMKRYYEPQQSVAELRAIAFVEAQLGEPLREDGPILGIEFDPLPPD 197

Query: 168 AFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPT 227
           AFG PIG A +G QK  VR  E   YER D+KP K        G TRT+HEY+FLP+QPT
Sbjct: 198 AFGAPIGSATLGQQKQPVRIFETNLYERPDIKPIK--------GTTRTLHEYQFLPQQPT 249

Query: 228 VRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSH 287
           V++E +E+AA S+ YGSPADG   +  SL A   FMH +EQ+SSGYGF  Q+P+L L+  
Sbjct: 250 VKAEAYERAAPSFQYGSPADGHNTKTGSLSATRSFMHANEQVSSGYGFSSQVPSLTLMPQ 309

Query: 288 QGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSR 347
           +GR  HLLPS +GEYEN  +K  F +  MD  +G  PITA+DN F+SSD+RV+HDE+  R
Sbjct: 310 EGRQGHLLPSATGEYENTSQKIPFTNVGMDVQIGAHPITALDNPFMSSDQRVTHDENALR 369

Query: 348 TEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLL 407
            E+KRKSEEARIAREVEAHEKRIRKELEKQDIL RKREEQIRKEMER DRERRKEEERLL
Sbjct: 370 MERKRKSEEARIAREVEAHEKRIRKELEKQDILNRKREEQIRKEMERHDRERRKEEERLL 429

Query: 408 REKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVAR 467
           REK RE ER+ REQRRELERREKFLQKESIR EK RQKEELRR +EA R K A+ERA+AR
Sbjct: 430 REKQREVERHQREQRRELERREKFLQKESIRVEKMRQKEELRRQREAARQKAASERAIAR 489

Query: 468 RIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKR 527
           R+AKES+ LVEDERLELMELAASSKGLP+I+ LDFETLQNLDLFRD+   FPPKSV LKR
Sbjct: 490 RMAKESLELVEDERLELMELAASSKGLPSIIPLDFETLQNLDLFRDKLTKFPPKSVLLKR 549

Query: 528 PFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTL 587
           PF +QPWN SE+NIGNLLMVWRFLITF DVLG+WPFTLDEFVQAFHDY+PRLLGEIH++L
Sbjct: 550 PFLIQPWNGSEENIGNLLMVWRFLITFVDVLGIWPFTLDEFVQAFHDYEPRLLGEIHISL 609

Query: 588 LRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWP 647
           L+S+IKDIED A+TP T LG NQNSA NPGG HPQIVEGAYAWGFDIRSWQ HLN LTWP
Sbjct: 610 LKSIIKDIEDVARTPATSLGPNQNSAANPGGGHPQIVEGAYAWGFDIRSWQRHLNPLTWP 669

Query: 648 EILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGL 707
           EILRQF LSAGFGPQL KRN+E+ Y  D+NEGNDGE++I+NLRNG+AV NA AIM E G 
Sbjct: 670 EILRQFGLSAGFGPQLKKRNVEQAYLCDDNEGNDGEDVITNLRNGAAVENAFAIMQERGF 729

Query: 708 SNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           SN RRSRHRLTPGTVKFA+FHVLSLEGS+GLTILEVADKIQ
Sbjct: 730 SNPRRSRHRLTPGTVKFASFHVLSLEGSKGLTILEVADKIQ 770

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224095585|ref|XP_002310414.1| predicted protein [Populus trichocarpa] gi|222853317|gb|EEE90864.1| predicted protein [Populus trichocarpa]

 Score = 1014 bits (2622), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 527/765 (68%), Positives = 601/765 (78%), Gaps = 40/765 (5%)

Query: 10  KKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWF 69
           KKK     E E K+KRKMK+ASQLEILEKTY+V++YPSEA RAELS QLGLSDRQLQMWF
Sbjct: 2   KKKTPGEGEGESKSKRKMKSASQLEILEKTYSVDTYPSEAARAELSVQLGLSDRQLQMWF 61

Query: 70  CHRRLKDRKAPTAKRQPKDFQSLVPAG---------------EKELAGSELVRG------ 108
           CHRRLKDRKAP  KR  K+  S  PAG               E     S  V G      
Sbjct: 62  CHRRLKDRKAPLVKRPRKESPS--PAGMPGGGEMGVVAEVGNEHGSGSSPFVLGVDPRRA 119

Query: 109 -----GMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDS 163
                G+AV R  A   A M  +  PQ++I E+R +AFVE+QLGEPLREDGPILG+EFD 
Sbjct: 120 VGRPTGVAVPRISADVQA-MKRYYEPQQSIAELRAVAFVEAQLGEPLREDGPILGMEFDP 178

Query: 164 LPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLP 223
           LPPDAFG PI  A  G QK SVR +EA  YER DVKP K          TRT+HEY+FLP
Sbjct: 179 LPPDAFGAPI--ATTGQQKQSVR-IEANLYERPDVKPIK--------STTRTLHEYQFLP 227

Query: 224 EQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLN 283
           +QPTVR+E +E+AA S  YGSPAD    +  S+ A  PFMH ++Q+SSGY    Q+P+L+
Sbjct: 228 QQPTVRAEAYERAAPSCQYGSPADVHNVKTESISATLPFMHANKQVSSGYDLSNQVPSLS 287

Query: 284 LLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDE 343
           L+  + R  HLLPS +GEYE +++K SF +  MDA  G   +TA+DN ++SSDRRV+HDE
Sbjct: 288 LMPQESRQGHLLPSTTGEYETVIQKCSFTNIGMDAQSGAHLVTALDNPYMSSDRRVTHDE 347

Query: 344 DVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEE 403
           D  R ++KRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQ+RKEME+ DRERRKEE
Sbjct: 348 DALRMQRKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQMRKEMEKHDRERRKEE 407

Query: 404 ERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANER 463
           ERLLREK RE ERY REQ+RELERREKFLQKESIR EK RQKEELRR KEA R K A ER
Sbjct: 408 ERLLREKQREVERYQREQKRELERREKFLQKESIRVEKMRQKEELRREKEAARQKAATER 467

Query: 464 AVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSV 523
           A+ARR+AKESM L++DERLELME+AASSKGLP+I+ LDFETLQNLDLFRD+   FPPKSV
Sbjct: 468 AIARRMAKESMELIDDERLELMEMAASSKGLPSIIPLDFETLQNLDLFRDKLTEFPPKSV 527

Query: 524 QLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEI 583
            LKRPF +QPWNDSE+N+GNLLMVWRFLITFADVLG+WPFTLDEFVQAFHDYD RLL E+
Sbjct: 528 LLKRPFLIQPWNDSEENVGNLLMVWRFLITFADVLGIWPFTLDEFVQAFHDYDSRLLSEV 587

Query: 584 HVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNA 643
           HV LL+S+IKDIED A+TP TGLG NQN A NPGG HPQIVEGAYAWGFD+RSWQ HLN 
Sbjct: 588 HVALLKSIIKDIEDVARTPATGLGPNQNGAANPGGGHPQIVEGAYAWGFDLRSWQRHLNP 647

Query: 644 LTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMH 703
           LTWPEILRQF LSAGFGPQ+ KRN+++ Y  D+NEGNDGE++I+NLRNG+AV NAV+IM 
Sbjct: 648 LTWPEILRQFGLSAGFGPQMKKRNVDQAYLRDDNEGNDGEDVITNLRNGAAVENAVSIMQ 707

Query: 704 EMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           E G SN RRSRHRLTPGTVKFAAFHVLSLEGS+GLTILEVADKIQ
Sbjct: 708 ERGFSNPRRSRHRLTPGTVKFAAFHVLSLEGSKGLTILEVADKIQ 752

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553623|ref|XP_002517852.1| homeobox protein, putative [Ricinus communis] gi|223542834|gb|EEF44370.1| homeobox protein, putative [Ricinus communis]

 Score = 1012 bits (2616), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 538/761 (70%), Positives = 605/761 (79%), Gaps = 43/761 (5%)

Query: 16  PLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK 75
           P E EVK+KRKMKTASQLEILEKTYAVE+YPSE LRAELSAQLGL+DRQLQMWFCHRRLK
Sbjct: 18  PPEGEVKSKRKMKTASQLEILEKTYAVETYPSEELRAELSAQLGLTDRQLQMWFCHRRLK 77

Query: 76  DRKAPTAKRQPKDFQ---SLVPAGE---------KEL-----AGSELVRGGMAVQRYYA- 117
           DRK P  KRQ KD     S+VP GE          EL     AGS     GM  +R  A 
Sbjct: 78  DRKGPPVKRQRKDESPAPSVVPGGEVTGVAAEVRNELLPMPAAGSSPFGHGMDSRRVVAR 137

Query: 118 VP----------MAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPD 167
            P          M+ +  +  PQ+ I E+R IAFVE+QLGEPLREDGPILG+EFD LPPD
Sbjct: 138 TPGVAVARISSEMSAIKRYYEPQQAIAELRAIAFVEAQLGEPLREDGPILGMEFDPLPPD 197

Query: 168 AFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPT 227
           AFG PI  A +G QK   RP EA  YER DVK  K          TR VHEY+FLP+QPT
Sbjct: 198 AFGAPI--ATVGQQKQPGRPYEANLYERPDVKTIK---------GTRPVHEYQFLPQQPT 246

Query: 228 VRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSH 287
           VR++ +E+  ++Y YGSPAD    + ++L    PF+H +EQ+SSGY FP QLP+LNL+  
Sbjct: 247 VRADAYERVTTNYHYGSPADSHNTKTAALSTARPFVHANEQVSSGYSFPSQLPSLNLMPQ 306

Query: 288 QGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSR 347
           +GR  HLL S +GEY+ +LRK+S  +  MDAH    PI A+DN F+ SD+RV+ DEDV R
Sbjct: 307 EGRQGHLLSSATGEYDTVLRKSSLTNIGMDAH----PINALDNPFMPSDKRVAPDEDVLR 362

Query: 348 TEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLL 407
            E+KRK EEARIAREVEAHEKRIRKELEKQD+LRRKREEQI+KEMER DRERRKEEERLL
Sbjct: 363 IERKRKIEEARIAREVEAHEKRIRKELEKQDVLRRKREEQIKKEMERHDRERRKEEERLL 422

Query: 408 REKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVAR 467
           REK REEERY REQRRELERRE++LQKE IRAEK RQKEELRR KEA R K A ERA+AR
Sbjct: 423 REKQREEERYQREQRRELERRERYLQKEFIRAEKMRQKEELRREKEAARQKAATERAIAR 482

Query: 468 RIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKR 527
           RIAKESM LV+DERLELMELAASSKGLP++ SLDFETLQNLD FRD+   FPPKSV LK+
Sbjct: 483 RIAKESMELVDDERLELMELAASSKGLPSVASLDFETLQNLDTFRDKLAVFPPKSVLLKK 542

Query: 528 PFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTL 587
           PF++QPWNDSE+N+GNLLMVWRFLITFADVLG+WPFTLDEFVQAFHD+DPRLLGE+HV L
Sbjct: 543 PFSIQPWNDSEENVGNLLMVWRFLITFADVLGMWPFTLDEFVQAFHDFDPRLLGEMHVAL 602

Query: 588 LRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWP 647
           LR++IKDIED A+TP TGLGANQNSA NPGG HPQIVEGAYAWGFDI SWQ HLN LTWP
Sbjct: 603 LRTIIKDIEDVARTPATGLGANQNSAANPGGGHPQIVEGAYAWGFDICSWQRHLNPLTWP 662

Query: 648 EILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGL 707
           EILRQFALSAGFGPQL KRN+E+ Y  D NEGNDGE++I+NLRNGSAV NAVAIM E G 
Sbjct: 663 EILRQFALSAGFGPQLKKRNVEQAYHRDENEGNDGEDVITNLRNGSAVENAVAIMQERGF 722

Query: 708 SNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           SN RRSRHRLTPGTVKFAAFHVLSLEGS+GLTILEVA+KIQ
Sbjct: 723 SNPRRSRHRLTPGTVKFAAFHVLSLEGSKGLTILEVAEKIQ 763

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356515148|ref|XP_003526263.1| PREDICTED: uncharacterized protein LOC100797480 [Glycine max]

 Score =  887 bits (2292), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 489/774 (63%), Positives = 587/774 (75%), Gaps = 46/774 (5%)

Query: 1   MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
           ME  SE E   KKK+P+E E K+KRKMKTASQLE+LEK YA E+YPSEALRAELS +L L
Sbjct: 1   MEGVSEGE---KKKEPVEGENKSKRKMKTASQLEVLEKAYAAEAYPSEALRAELSVKLSL 57

Query: 61  SDRQLQMWFCHRRLKDRKAPTAKRQPKDFQSLVPA----GEKELAGSELVR-GGMA---- 111
           SDRQLQMWFCHRRLKDR A   K Q     +  PA    G +++ G+++ R  G+A    
Sbjct: 58  SDRQLQMWFCHRRLKDRNAK--KLQNDSSLAGAPAVGEEGVEQVTGADVGRDCGLASGPF 115

Query: 112 --VQRYYAVPMAPMLPFPL---------------PQRNIVEMRVIAFVESQLGEPLREDG 154
             +     VP   M  FP                P +N+  ++V+AFVE QLGEP+REDG
Sbjct: 116 DHLDSRKIVPRPGMTAFPSMGAGLPAVVGSSYYEPPQNMDVLQVVAFVERQLGEPIREDG 175

Query: 155 PILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATR 214
           PILG+EFDSLPPDAFG PI    MG  +    P EAK YE+LD    KD+        +R
Sbjct: 176 PILGMEFDSLPPDAFGAPI--VTMGQHRQCGGPFEAKIYEQLD----KDV--------SR 221

Query: 215 TVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYG 274
           T+HEY+F+PE+P+VR+ET+E+ A S  Y S  DG     + L +G  F++G+E    GYG
Sbjct: 222 TLHEYQFIPEKPSVRNETYERVAPSIHYSS-LDGIPHSRTLLSSGRSFLNGNESAPYGYG 280

Query: 275 FPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFIS 334
             G LP LNLLS QGR +HLLPS SGE + I RKN F+    D H G  PIT +D+  + 
Sbjct: 281 IQGHLPGLNLLSRQGRQNHLLPSASGENDGIPRKNPFVDVTADIHNGAHPITLIDSPLMP 340

Query: 335 SDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMER 394
           SD RV H E++SR ++KRK   ARI +E+EA E++ RKELEKQDILR+KREEQ +KEMER
Sbjct: 341 SDGRVIHVEELSRLQRKRKVSNARIQQELEAQERKNRKELEKQDILRQKREEQTKKEMER 400

Query: 395 QDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEA 454
            +RER+KEEERLLRE+ REEERY REQRRE ERR+KFLQKESIRAEK RQKEELRR KEA
Sbjct: 401 HERERQKEEERLLRERQREEERYQREQRREQERRQKFLQKESIRAEKLRQKEELRREKEA 460

Query: 455 ERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDR 514
            R+K ANERA+ARRIAKES+ L+EDERLELMELAAS K L +I++LD+ET+QNL+ +RD 
Sbjct: 461 ARIKAANERAIARRIAKESIELIEDERLELMELAASKKELSSILALDYETIQNLEFYRDG 520

Query: 515 PCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHD 574
             +FPPKSVQLKR F+++PW+DS++N+GNLLMVWRFLITFADVLG+WPFT+DE +QAFHD
Sbjct: 521 RASFPPKSVQLKRIFSIKPWSDSDENVGNLLMVWRFLITFADVLGIWPFTVDELIQAFHD 580

Query: 575 YDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDI 634
           +DPRLLGEIH+ LL+S+IKDIED A+TP TGLG NQ+S  N GG HPQ+VEGAY WGFDI
Sbjct: 581 HDPRLLGEIHIALLKSIIKDIEDVARTPSTGLGCNQHSVTNSGGGHPQVVEGAYLWGFDI 640

Query: 635 RSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSA 694
           R+WQ HLN LTWPEILRQFALSAGFGPQL K +IE+++P +NNEGNDG +IISNLR+G+A
Sbjct: 641 RNWQRHLNPLTWPEILRQFALSAGFGPQLKKLSIEQVHPCNNNEGNDGRDIISNLRSGAA 700

Query: 695 VGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           V NAVAIM E GLSN RRSRH LTPGTVKFAAFHVLSLEGS+GL ILEVADKIQ
Sbjct: 701 VENAVAIMQEKGLSNPRRSRHCLTPGTVKFAAFHVLSLEGSKGLNILEVADKIQ 754

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297794989|ref|XP_002865379.1| hypothetical protein ARALYDRAFT_494576 [Arabidopsis lyrata subsp. lyrata] gi|297311214|gb|EFH41638.1| hypothetical protein ARALYDRAFT_494576 [Arabidopsis lyrata subsp. lyrata]

 Score =  828 bits (2140), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 451/758 (59%), Positives = 549/758 (72%), Gaps = 43/758 (5%)

Query: 1   MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
           ME  SE      K  P   E K+KRKMKTA+QLE+LE TYA E YPSEA+RA+LS +L L
Sbjct: 1   MEGGSE------KTTPEGGESKSKRKMKTAAQLEVLENTYAAEPYPSEAIRADLSVKLNL 54

Query: 61  SDRQLQMWFCHRRLKDRKAPT-AKRQPKDFQS---------LVPAGEKELAGSELVRGGM 110
           SDRQLQMWFCHRRLKDRK+ T +KR  K+  +          V AG+  +AG+EL     
Sbjct: 55  SDRQLQMWFCHRRLKDRKSTTPSKRHRKELVTPTAVESSKPAVNAGDL-VAGNELDSRRA 113

Query: 111 AVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFG 170
           A     +      +     + +  E+R I +VE+QLGE LR++GPILG+EFD LPP AFG
Sbjct: 114 ARGGGGSGSGGVTVVRRFNEPSSAEVRAIGYVEAQLGERLRDNGPILGMEFDPLPPGAFG 173

Query: 171 RPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRS 230
            PI      H+K   +  E   Y R DVKP KD          R + EY+F+PE P+ R+
Sbjct: 174 MPI--EMPSHRKAPRQAFETNIYVRSDVKPIKDH--------VRPIREYQFIPELPSSRT 223

Query: 231 ETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGR 290
           +  E+ + S+ +G P DGS  R S++ AGH            Y    Q+PNLNL +HQG+
Sbjct: 224 DHSERVSPSHHFGVPLDGSVMRASAVSAGH---------RDDYKISPQIPNLNLATHQGK 274

Query: 291 HSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEK 350
             H+      EY++  +K S++  A  AHV   P    +  F + D     D+D  + E+
Sbjct: 275 PGHVYSPNLAEYDSPYQK-SYVDTA--AHVHEDPFVKSERDFGNED----EDDDALQLER 327

Query: 351 KRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREK 410
           +RK+EEARIAREVEAHEKRIR+ELEKQD+LRRKREEQIRKEMERQDRERRKEEERLLREK
Sbjct: 328 QRKNEEARIAREVEAHEKRIRRELEKQDMLRRKREEQIRKEMERQDRERRKEEERLLREK 387

Query: 411 LREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIA 470
            REEERYL+EQ REL+RREKFL+KE+IRAEK RQKEE+R+ KE  RLK ANERA+AR+IA
Sbjct: 388 QREEERYLKEQMRELQRREKFLKKETIRAEKMRQKEEMRKEKEVARLKAANERAIARKIA 447

Query: 471 KESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFA 530
           KESM L+EDERLELME+AA +KGLP++++LDFETLQNL+ +RD+   FPP SV+LK+PFA
Sbjct: 448 KESMELIEDERLELMEVAALTKGLPSMLALDFETLQNLEEYRDKQVLFPPTSVRLKKPFA 507

Query: 531 VQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRS 590
           V+PWN S++N+ NLLMVWRFLITFADVLGLWPFTLDEF QAFHDYDPRL+GEIH+ LL++
Sbjct: 508 VKPWNGSDENVANLLMVWRFLITFADVLGLWPFTLDEFAQAFHDYDPRLMGEIHIVLLKT 567

Query: 591 VIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEIL 650
           +IKDIE  A+T  TG+GANQN+A NPGG HP +VEGAYAWGFDIRSW+ +LN  TWPEIL
Sbjct: 568 IIKDIEGVARTLLTGVGANQNTASNPGGGHPHVVEGAYAWGFDIRSWRRNLNVFTWPEIL 627

Query: 651 RQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNL 710
           RQ ALSAG GPQL K NI+ +  HD+NE N+ EN+I NLR G A  NA A M E GLSN 
Sbjct: 628 RQLALSAGLGPQLKKMNIKTVSVHDDNEANNSENVIVNLRKGVAAENAFAKMQERGLSNP 687

Query: 711 RRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           RRSRHRLTPGTVKFAAFHVLSLEG +GLTIL+VA+KIQ
Sbjct: 688 RRSRHRLTPGTVKFAAFHVLSLEGEKGLTILDVAEKIQ 725

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334188190|ref|NP_001190470.1| Homeodomain-like transcriptional regulator [Arabidopsis thaliana] gi|332007688|gb|AED95071.1| Homeodomain-like transcriptional regulator [Arabidopsis thaliana]

 Score =  828 bits (2138), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 453/770 (58%), Positives = 553/770 (71%), Gaps = 68/770 (8%)

Query: 1   MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
           ME  SE    K   +    E K+KRKMKTA+QLE+LE TY+ E YPSEA+RA+LS +L L
Sbjct: 1   MEGGSE----KTTPEGCGGESKSKRKMKTAAQLEVLENTYSAEPYPSEAIRADLSVKLNL 56

Query: 61  SDRQLQMWFCHRRLKDRKAPT-AKRQPKD---------FQSLVPAGEKELAGSEL----- 105
           SDRQLQMWFCHRRLK+RK+ T +KRQ K+         ++  V AG+  +AG+EL     
Sbjct: 57  SDRQLQMWFCHRRLKERKSTTPSKRQRKELVTPTAMESWEPPVNAGDL-VAGNELDSRRA 115

Query: 106 VRG----GMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEF 161
            RG    G+ V R +  P +             E+R I +VE+QLGE LR++GP+LG+EF
Sbjct: 116 ARGSGGSGVTVVRRFNEPSS------------AEVRAIGYVEAQLGERLRDNGPVLGMEF 163

Query: 162 DSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKF 221
           D LPP AFG PI      H+K + +  E   Y R DVKP KD          R + EY+F
Sbjct: 164 DPLPPGAFGMPI--EMPSHRKATRQAFETNIYVRSDVKPIKDH--------VRPIREYQF 213

Query: 222 LPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPN 281
           +PE P+ R++  E+ + S+ +G P DGS  R S++ AGH            Y    Q+PN
Sbjct: 214 IPELPSSRTDHSERVSPSHHFGVPLDGSVMRVSAVSAGH---------RDDYKISPQIPN 264

Query: 282 LNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSH 341
           LNL +HQG+  H+      EY++  +K S++  A   H         D+ F+ S+R V +
Sbjct: 265 LNLATHQGKPGHVYSPNLVEYDSPYQK-SYMDTAAQVH---------DDPFVKSEREVGN 314

Query: 342 ---DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRE 398
              D+D  + E+ RK+EEARIAREVEAHEKRIR+ELEKQD+LRRKREEQIRKEMERQDRE
Sbjct: 315 EDEDDDALQLERHRKNEEARIAREVEAHEKRIRRELEKQDMLRRKREEQIRKEMERQDRE 374

Query: 399 RRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
           RRKEEERLLREK REEERYL+EQ REL+RREKFL+KE+IRAEK RQKEE+R+ KE  RLK
Sbjct: 375 RRKEEERLLREKQREEERYLKEQMRELQRREKFLKKETIRAEKMRQKEEMRKEKEVARLK 434

Query: 459 VANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTF 518
            ANERA+AR+IAKESM L+EDERLELME+AA +KGLP++++LDFETLQNLD +RD+   F
Sbjct: 435 AANERAIARKIAKESMELIEDERLELMEVAALTKGLPSMLALDFETLQNLDEYRDKQAIF 494

Query: 519 PPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPR 578
           PP SV+LK+PFAV+PWN S++N+ NLLMVWRFLITFADVLGLWPFTLDEF QAFHDYDPR
Sbjct: 495 PPTSVKLKKPFAVKPWNGSDENVANLLMVWRFLITFADVLGLWPFTLDEFAQAFHDYDPR 554

Query: 579 LLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQ 638
           L+GEIH+ LL+++IKDIE   +T  TG+GANQN A NPGG HP +VEGAYAWGFDIRSW+
Sbjct: 555 LMGEIHIVLLKTIIKDIEGVVRTLSTGVGANQNVAANPGGGHPHVVEGAYAWGFDIRSWR 614

Query: 639 LHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNA 698
            +LN  TWPEILRQ ALSAG GPQL K NI  +  HD+NE N+ EN+I NLR G A  NA
Sbjct: 615 KNLNVFTWPEILRQLALSAGLGPQLKKMNIRTVSVHDDNEANNSENVIFNLRKGVAAENA 674

Query: 699 VAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
            A M E GLSN RRSRHRLTPGTVKFAAFHVLSLEG +GL ILEVA+KIQ
Sbjct: 675 FAKMQERGLSNPRRSRHRLTPGTVKFAAFHVLSLEGEKGLNILEVAEKIQ 724

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15241428|ref|NP_199231.1| Homeodomain-like transcriptional regulator [Arabidopsis thaliana] gi|9759519|dbj|BAB10985.1| unnamed protein product [Arabidopsis thaliana] gi|332007687|gb|AED95070.1| Homeodomain-like transcriptional regulator [Arabidopsis thaliana]

 Score =  827 bits (2135), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 453/770 (58%), Positives = 553/770 (71%), Gaps = 68/770 (8%)

Query: 1   MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
           ME  SE    K   +    E K+KRKMKTA+QLE+LE TY+ E YPSEA+RA+LS +L L
Sbjct: 1   MEGGSE----KTTPEGCGGESKSKRKMKTAAQLEVLENTYSAEPYPSEAIRADLSVKLNL 56

Query: 61  SDRQLQMWFCHRRLKDRKAPT-AKRQPKD---------FQSLVPAGEKELAGSEL----- 105
           SDRQLQMWFCHRRLK+RK+ T +KRQ K+         ++  V AG+  +AG+EL     
Sbjct: 57  SDRQLQMWFCHRRLKERKSTTPSKRQRKELVTPTAMESWEPPVNAGDL-VAGNELDSRRA 115

Query: 106 VRG----GMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEF 161
            RG    G+ V R +  P +             E+R I +VE+QLGE LR++GP+LG+EF
Sbjct: 116 ARGSGGSGVTVVRRFNEPSS------------AEVRAIGYVEAQLGERLRDNGPVLGMEF 163

Query: 162 DSLPPDAFGRPIGPAAMGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKF 221
           D LPP AFG PI      H+K + +  E   Y R DVKP KD          R + EY+F
Sbjct: 164 DPLPPGAFGMPI--EMPSHRKATRQAFETNIYVRSDVKPIKDH--------VRPIREYQF 213

Query: 222 LPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPN 281
           +PE P+ R++  E+ + S+ +G P DGS  R S++ AGH            Y    Q+PN
Sbjct: 214 IPELPSSRTDHSERVSPSHHFGVPLDGSVMRVSAVSAGH---------RDDYKISPQIPN 264

Query: 282 LNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSH 341
           LNL +HQG+  H+      EY++  +K S++  A   H         D+ F+ S+R V +
Sbjct: 265 LNLATHQGKPGHVYSPNLVEYDSPYQK-SYMDTAAQVH---------DDPFVKSEREVGN 314

Query: 342 ---DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRE 398
              D+D  + E+ RK+EEARIAREVEAHEKRIR+ELEKQD+LRRKREEQIRKEMERQDRE
Sbjct: 315 EDEDDDALQLERHRKNEEARIAREVEAHEKRIRRELEKQDMLRRKREEQIRKEMERQDRE 374

Query: 399 RRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
           RRKEEERLLREK REEERYL+EQ REL+RREKFL+KE+IRAEK RQKEE+R+ KE  RLK
Sbjct: 375 RRKEEERLLREKQREEERYLKEQMRELQRREKFLKKETIRAEKMRQKEEMRKEKEVARLK 434

Query: 459 VANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTF 518
            ANERA+AR+IAKESM L+EDERLELME+AA +KGLP++++LDFETLQNLD +RD+   F
Sbjct: 435 AANERAIARKIAKESMELIEDERLELMEVAALTKGLPSMLALDFETLQNLDEYRDKQAIF 494

Query: 519 PPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPR 578
           PP SV+LK+PFAV+PWN S++N+ NLLMVWRFLITFADVLGLWPFTLDEF QAFHDYDPR
Sbjct: 495 PPTSVKLKKPFAVKPWNGSDENVANLLMVWRFLITFADVLGLWPFTLDEFAQAFHDYDPR 554

Query: 579 LLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQ 638
           L+GEIH+ LL+++IKDIE   +T  TG+GANQN A NPGG HP +VEGAYAWGFDIRSW+
Sbjct: 555 LMGEIHIVLLKTIIKDIEGVVRTLSTGVGANQNVAANPGGGHPHVVEGAYAWGFDIRSWR 614

Query: 639 LHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNA 698
            +LN  TWPEILRQ ALSAG GPQL K NI  +  HD+NE N+ EN+I NLR G A  NA
Sbjct: 615 KNLNVFTWPEILRQLALSAGLGPQLKKMNIRTVSVHDDNEANNSENVIFNLRKGVAAENA 674

Query: 699 VAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
            A M E GLSN RRSRHRLTPGTVKFAAFHVLSLEG +GL ILEVA+KIQ
Sbjct: 675 FAKMQERGLSNPRRSRHRLTPGTVKFAAFHVLSLEGEKGLNILEVAEKIQ 724

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143341|emb|CBI21902.3| unnamed protein product [Vitis vinifera]

 Score =  825 bits (2132), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 428/546 (78%), Positives = 476/546 (87%), Gaps = 2/546 (0%)

Query: 203 DMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAASSYPYGSPADGSTARNSSLRAGHPF 262
           D+  ++ QGA R VHEY+FLPEQP+VR++T+E+  S Y YGSPADG +AR +SL  G  F
Sbjct: 366 DLGMLYLQGAGRAVHEYQFLPEQPSVRTDTYERVGSHY-YGSPADGPSAR-ASLSTGRSF 423

Query: 263 MHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGG 322
           MHG+EQ++SGYGF GQ+PNLNLLS QGR +H L S SG+Y+ + RKNS  S  MDAH G 
Sbjct: 424 MHGNEQVASGYGFQGQMPNLNLLSQQGRQNHGLSSTSGDYDTVPRKNSLGSIGMDAHFGS 483

Query: 323 QPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRR 382
            PITA+DN FISSDRRV++DEDV R E+KRKSEEARIA+EVEAHEKRIRKELEKQDILRR
Sbjct: 484 HPITALDNPFISSDRRVTNDEDVLRMERKRKSEEARIAKEVEAHEKRIRKELEKQDILRR 543

Query: 383 KREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKR 442
           KREEQ+RKEMER DRERRKEEERLLREK REEERY REQRRELERREKFLQKESIRAEK 
Sbjct: 544 KREEQMRKEMERHDRERRKEEERLLREKQREEERYQREQRRELERREKFLQKESIRAEKM 603

Query: 443 RQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDF 502
           RQKEELRR KEA R+K AN+RA+ARRIAKESM L+EDERLELMEL A SKGLP+I+SLD 
Sbjct: 604 RQKEELRREKEAARVKAANDRAIARRIAKESMELIEDERLELMELVALSKGLPSILSLDS 663

Query: 503 ETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWP 562
           ETLQNL+ FRD    FPPKSVQL+RPF +QPW DSE+NIGNLLMVWRFLITF+DVLGLWP
Sbjct: 664 ETLQNLESFRDMLTAFPPKSVQLRRPFTIQPWTDSEENIGNLLMVWRFLITFSDVLGLWP 723

Query: 563 FTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQ 622
           FT+DEFVQAFHDYDPRLLGEIHV LLRS+IKDIED A+TP  GLGANQNSA NPGG HPQ
Sbjct: 724 FTMDEFVQAFHDYDPRLLGEIHVALLRSIIKDIEDVARTPSIGLGANQNSAANPGGGHPQ 783

Query: 623 IVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNNEGNDG 682
           IVEGAYAWGFDIRSWQ HLN LTWPEILRQFALSAGFGP+L KRN+E+ Y  D+NEGND 
Sbjct: 784 IVEGAYAWGFDIRSWQRHLNPLTWPEILRQFALSAGFGPKLKKRNVEETYLRDDNEGNDC 843

Query: 683 ENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEGLTILE 742
           E+II+NLR+G+A  NAVAIM E G SN RRSRHRLTPGTVKFAAFHVLSLEGS+GLTILE
Sbjct: 844 EDIITNLRSGAAAENAVAIMQERGFSNPRRSRHRLTPGTVKFAAFHVLSLEGSKGLTILE 903

Query: 743 VADKIQ 748
           VADKIQ
Sbjct: 904 VADKIQ 909

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483496|ref|XP_002273559.2| PREDICTED: uncharacterized protein LOC100247033 [Vitis vinifera]

 Score =  776 bits (2005), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 451/749 (60%), Positives = 543/749 (72%), Gaps = 39/749 (5%)

Query: 18  EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
           EA+ K KR+MKT  QL+ LE+ YA+E YP+EA RAELS +LGLSDRQLQMWFCHRRLKD+
Sbjct: 5   EAQSKPKRQMKTPFQLQTLERAYALEPYPTEASRAELSEKLGLSDRQLQMWFCHRRLKDK 64

Query: 78  KAPTAK----RQPKDFQSLVPAGEKEL------AGSELVRGGMAVQRYYAVP------MA 121
           K   AK    ++P++  ++    E E               G +   Y  +P      M 
Sbjct: 65  KEGQAKEAASKKPRN--AVAEEFEDEARSEHGSHSGSGSLSGSSPLGYGQLPQVLSGNMG 122

Query: 122 PM--LPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFGRPIGPAAMG 179
           PM    +  PQ +I E+RVIA VE+QLGEPLR+DGPILG+EFD LPPDAFG PI  A + 
Sbjct: 123 PMGRRSYESPQ-SIFELRVIASVEAQLGEPLRDDGPILGMEFDPLPPDAFGAPI--AIVE 179

Query: 180 HQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAASS 239
           HQK S    E K YE  D K          + A R  H++ F  ++ + R + + +   S
Sbjct: 180 HQKQSAYCYEEKVYEHRDAK--------SKKAAARAFHDHPFHQDKSSTRPDAYGRVGPS 231

Query: 240 YPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHLLPSVS 299
           + Y  P DG ++  S+      F+H +E  S  YG  G + +  +LS Q +   +L S  
Sbjct: 232 HFYDRPIDGPSSETSA------FLHRTEPSSREYGEQGYVSHARVLSQQDKQERILSS-P 284

Query: 300 GEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARI 359
           G+Y+++ R +SF+++  DA   G  I   +N+++ SDR+++H+ DV R ++KRK EEARI
Sbjct: 285 GDYDSVPRSDSFMNSGKDAQFSGHSI-GPENSYVLSDRQITHNGDVLRMDRKRKGEEARI 343

Query: 360 AREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLR 419
             + EAHEKRIRKELEKQDILRRKREEQIRKEMER DRERRKEEERL+RE+ RE ER  R
Sbjct: 344 TTDAEAHEKRIRKELEKQDILRRKREEQIRKEMERHDRERRKEEERLMRERQREVERLQR 403

Query: 420 EQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVED 479
           EQRRE+ERREKFLQKES+RAEKRRQKEELRR KEA RLK + E+A ARRIA+ESM L+ED
Sbjct: 404 EQRREIERREKFLQKESLRAEKRRQKEELRREKEAVRLKASIEKATARRIARESMELIED 463

Query: 480 ERLELMELAASSKGLPTIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSED 539
           +RLELMELAA+SKGLP+IVSLD +TLQNL+ FRD    FPP SVQL+RPFAVQPW+DSE+
Sbjct: 464 DRLELMELAAASKGLPSIVSLDHDTLQNLESFRDLLSVFPPTSVQLRRPFAVQPWDDSEE 523

Query: 540 NIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAA 599
           NIGNLLMVWRFLITFADVL LWPFTLDEFVQAFHDYD RL+GEIH+ L++ +IKDIED A
Sbjct: 524 NIGNLLMVWRFLITFADVLQLWPFTLDEFVQAFHDYDSRLMGEIHIALVKLIIKDIEDVA 583

Query: 600 KTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGF 659
           +TP  GLG NQN+A  P G HP IVEGAYAWGFDIR+WQ HLN LTWPEILRQFALSAGF
Sbjct: 584 RTPSLGLGTNQNTAAGPEGGHPHIVEGAYAWGFDIRNWQRHLNPLTWPEILRQFALSAGF 643

Query: 660 GPQLNKRNIEKMYPHDNNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTP 719
           GPQL KR+ E  Y  +NNE    E+I+S LRNGSA  NAVAIM   G S  RRSRHRLTP
Sbjct: 644 GPQLKKRSSEWSYSRENNEIKGCEDIVSTLRNGSAAVNAVAIMKGKGFSLSRRSRHRLTP 703

Query: 720 GTVKFAAFHVLSLEGSEGLTILEVADKIQ 748
           GTVKFA FHVLSLEGS+GLTILE+ADKIQ
Sbjct: 704 GTVKFAVFHVLSLEGSKGLTILELADKIQ 732

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	753
TAIR|locus:2167628	1694	RLT2 "RINGLET 2" [Arabidopsis	0.415	0.184	0.725	4.9e-184
TAIR|locus:2032505	1705	HB-1 "homeobox-1" [Arabidopsis	0.413	0.182	0.691	1.9e-160
WB|WBGene00000430	134	ceh-5 [Caenorhabditis elegans	0.091	0.514	0.408	8.2e-07
UNIPROTKB|F1MJX0	142	CDX2 "Uncharacterized protein"	0.084	0.450	0.430	3.6e-06
UNIPROTKB|F8VWZ5	151	HLX "H2.0-like homeobox protei	0.092	0.463	0.383	3.6e-06
RGD|621233	123	Cdx1 "caudal type homeo box 1"	0.090	0.552	0.376	1.2e-05
UNIPROTKB|Q05095	123	Cdx1 "Homeobox protein CDX-1"	0.090	0.552	0.376	1.2e-05
UNIPROTKB|F1RWG7	353	HOXB2 "Uncharacterized protein	0.195	0.416	0.341	2e-05
FB|FBgn0000606	376	eve "even skipped" [Drosophila	0.077	0.154	0.413	3.7e-05
UNIPROTKB|F1MCF6	118	CDX1 "Uncharacterized protein"	0.083	0.533	0.390	4.3e-05

TAIR|locus:2167628 RLT2 "RINGLET 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1211 (431.4 bits), Expect = 4.9e-184, Sum P(2) = 4.9e-184
 Identities = 227/313 (72%), Positives = 263/313 (84%)

Query:   436 SIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLP 495
             +IRAEK RQKEE+R+ KE  RLK ANERA+AR+IAKESM L+EDERLELME+AA +KGLP
Sbjct:   412 TIRAEKMRQKEEMRKEKEVARLKAANERAIARKIAKESMELIEDERLELMEVAALTKGLP 471

Query:   496 TIVSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFA 555
             ++++LDFETLQNLD +RD+   FPP SV+LK+PFAV+PWN S++N+ NLLMVWRFLITFA
Sbjct:   472 SMLALDFETLQNLDEYRDKQAIFPPTSVKLKKPFAVKPWNGSDENVANLLMVWRFLITFA 531

Query:   556 DVLGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVN 615
             DVLGLWPFTLDEF QAFHDYDPRL+GEIH+ LL+++IKDIE   +T  TG+GANQN A N
Sbjct:   532 DVLGLWPFTLDEFAQAFHDYDPRLMGEIHIVLLKTIIKDIEGVVRTLSTGVGANQNVAAN 591

Query:   616 PGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHD 675
             PGG HP +VEGAYAWGFDIRSW+ +LN  TWPEILRQ ALSAG GPQL K NI  +  HD
Sbjct:   592 PGGGHPHVVEGAYAWGFDIRSWRKNLNVFTWPEILRQLALSAGLGPQLKKMNIRTVSVHD 651

Query:   676 NNEGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGS 735
             +NE N+ EN+I NLR G A  NA A M E GLSN RRSRHRLTPGTVKFAAFHVLSLEG 
Sbjct:   652 DNEANNSENVIFNLRKGVAAENAFAKMQERGLSNPRRSRHRLTPGTVKFAAFHVLSLEGE 711

Query:   736 EGLTILEVADKIQ 748
             +GL ILEVA+KIQ
Sbjct:   712 KGLNILEVAEKIQ 724

GO:0005634 "nucleus" evidence=ISM;ISS;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0009630 "gravitropism" evidence=RCA

GO:0005515 "protein binding" evidence=IPI

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=IGI

TAIR|locus:2032505 HB-1 "homeobox-1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1148 (409.2 bits), Expect = 1.9e-160, Sum P(3) = 1.9e-160
 Identities = 215/311 (69%), Positives = 260/311 (83%)

Query:   438 RAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTI 497
             RAEK++QK+E+RR K+A R K+A E+A ARRIAKESM L+EDE+LELMELAA SKGLP++
Sbjct:   449 RAEKKKQKDEIRREKDAIRRKLAIEKATARRIAKESMDLIEDEQLELMELAAISKGLPSV 508

Query:   498 VSLDFETLQNLDLFRDRPCTFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADV 557
             + LD +TLQNL+++RD   TFPPKS+QLK PFA+ PW DS++ +GNLLMVWRFLI+F+DV
Sbjct:   509 LQLDHDTLQNLEVYRDSLSTFPPKSLQLKMPFAISPWKDSDETVGNLLMVWRFLISFSDV 568

Query:   558 LGLWPFTLDEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPG 617
             L LWPFTLDEF+QAFHDYD RLLGEIHVTLLRS+I+D+ED A+TPF+G+G NQ +  NP 
Sbjct:   569 LDLWPFTLDEFIQAFHDYDSRLLGEIHVTLLRSIIRDVEDVARTPFSGIGNNQYTTANPE 628

Query:   618 GAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQLNKRNIEKMYPHDNN 677
             G HPQIVEGAYAWGFDIRSW+ HLN LTWPEILRQ ALSAGFGP+L K++       D +
Sbjct:   629 GGHPQIVEGAYAWGFDIRSWKKHLNPLTWPEILRQLALSAGFGPKLKKKHSRLTNTGDKD 688

Query:   678 EGNDGENIISNLRNGSAVGNAVAIMHEMGLSNLRRSRHRLTPGTVKFAAFHVLSLEGSEG 737
             E    E++IS +RNG+A  +A A M E GL   R+SRHRLTPGTVKFAAFHVLSLEGS+G
Sbjct:   689 EAKGCEDVISTIRNGTAAESAFASMREKGLLAPRKSRHRLTPGTVKFAAFHVLSLEGSKG 748

Query:   738 LTILEVADKIQ 748
             LT+LE+ADKIQ
Sbjct:   749 LTVLELADKIQ 759

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0009630 "gravitropism" evidence=RCA

GO:0005515 "protein binding" evidence=IPI

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=IGI

WB|WBGene00000430 ceh-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 124 (48.7 bits), Expect = 8.2e-07, P = 8.2e-07
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query:    25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR 84
             R + T  QLE LE+++    Y S + RA+L+  LGLSD Q+++WF +RR K +K  +  R
Sbjct:    39 RTVFTDEQLEKLEESFNTSGYLSGSTRAKLAESLGLSDNQVKVWFQNRRTKQKKIDS--R 96

Query:    85 QPKDFQSLVPA 95
              P   ++L PA
Sbjct:    97 DPIKPETLKPA 107

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1MJX0 CDX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 118 (46.6 bits), Expect = 3.6e-06, P = 3.6e-06
 Identities = 28/65 (43%), Positives = 41/65 (63%)

Query:    32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQS 91
             +LE LEK +    Y +   +AEL+A LGLS+RQ+++WF +RR K+RK    K Q +  Q 
Sbjct:    34 RLE-LEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQP 92

Query:    92 LVPAG 96
               P+G
Sbjct:    93 PPPSG 97

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

UNIPROTKB|F8VWZ5 HLX "H2.0-like homeobox protein" [Homo sapiens (taxid:9606)]

 Score = 118 (46.6 bits), Expect = 3.6e-06, P = 3.6e-06
 Identities = 28/73 (38%), Positives = 44/73 (60%)

Query:    36 LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQSLVPA 95
             LEK + ++ Y ++  R +L+A LGL+D Q+++WF +RR+K R +  A+ Q KD      A
Sbjct:    24 LEKRFEIQKYVTKPDRKQLAAMLGLTDAQVKVWFQNRRMKWRHSKEAQAQ-KDKDK--EA 80

Query:    96 GEKELAGSELVRG 108
             GEK   G+    G
Sbjct:    81 GEKPSGGAPAADG 93

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0001889 "liver development" evidence=IEA

GO:0007519 "skeletal muscle tissue development" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0045627 "positive regulation of T-helper 1 cell differentiation" evidence=IEA

GO:0045629 "negative regulation of T-helper 2 cell differentiation" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0048484 "enteric nervous system development" evidence=IEA

GO:0048557 "embryonic digestive tract morphogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|621233 Cdx1 "caudal type homeo box 1" [Rattus norvegicus (taxid:10116)]

 Score = 113 (44.8 bits), Expect = 1.2e-05, P = 1.2e-05
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query:    32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQS 91
             +LE LEK +    Y +   ++EL+A LGL++RQ+++WF +RR K+RK    K+Q +  Q 
Sbjct:    17 RLE-LEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQQQQ 75

Query:    92 LVPAGEKEL 100
               P    +L
Sbjct:    76 QQPMPPTQL 84

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;TAS

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007389 "pattern specification process" evidence=ISO

GO:0009952 "anterior/posterior pattern specification" evidence=IEA;ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0060349 "bone morphogenesis" evidence=IEA;ISO

UNIPROTKB|Q05095 Cdx1 "Homeobox protein CDX-1" [Rattus norvegicus (taxid:10116)]

 Score = 113 (44.8 bits), Expect = 1.2e-05, P = 1.2e-05
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query:    32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQS 91
             +LE LEK +    Y +   ++EL+A LGL++RQ+++WF +RR K+RK    K+Q +  Q 
Sbjct:    17 RLE-LEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQQQQ 75

Query:    92 LVPAGEKEL 100
               P    +L
Sbjct:    76 QQPMPPTQL 84

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1RWG7 HOXB2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 132 (51.5 bits), Expect = 2.0e-05, P = 2.0e-05
 Identities = 56/164 (34%), Positives = 77/164 (46%)

Query:    25 RKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
             R+++TA   +QL  LEK +    Y     R E++A L L++RQ+++WF +RR+K  K  T
Sbjct:   142 RRLRTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERQVKVWFQNRRMK-HKRQT 200

Query:    82 AKRQPKDFQSLVPAGEKELA-GSE--LVRGGM-AVQRYYA-VPMAP--MLPFPL--PQRN 132
               R+P D     P   K+    SE  L   G  +V R    V   P  + P PL  P   
Sbjct:   201 QHREPPDGGPACPGAPKKAGEASEEPLASPGRPSVSRAAREVCCQPPEVAPGPLGAPGLR 260

Query:   133 IVEMRVIAFVESQLGEPLREDGPILGVEFDSLPPDAFG-RPIGP 175
              +  RV        G  LR  G   G+E + LP DAF  RP  P
Sbjct:   261 PLAARVEGAGARSPGGELRGAG---GLEPERLPEDAFPERPYSP 301

GO:0005634 "nucleus" evidence=IEA

GO:0048857 "neural nucleus development" evidence=IEA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA

GO:0021612 "facial nerve structural organization" evidence=IEA

GO:0021570 "rhombomere 4 development" evidence=IEA

GO:0021569 "rhombomere 3 development" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0002011 "morphogenesis of an epithelial sheet" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

FB|FBgn0000606 eve "even skipped" [Drosophila melanogaster (taxid:7227)]

 Score = 111 (44.1 bits), Expect = 3.7e-05, Sum P(2) = 3.7e-05
 Identities = 24/58 (41%), Positives = 35/58 (60%)

Query:    29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQP 86
             T  QL  LEK +  E+Y S   R EL+AQL L +  +++WF +RR+KD++   A   P
Sbjct:    78 TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQRIAVAWP 135

GO:0005634 "nucleus" evidence=ISS;NAS;IDA

GO:0007376 "cephalic furrow formation" evidence=IMP

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA;IMP

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0007399 "nervous system development" evidence=NAS

GO:0007366 "periodic partitioning by pair rule gene" evidence=NAS;TAS

GO:0000980 "RNA polymerase II distal enhancer sequence-specific DNA binding" evidence=IDA

GO:0007350 "blastoderm segmentation" evidence=TAS

GO:0008595 "anterior/posterior axis specification, embryo" evidence=NAS

GO:0009997 "negative regulation of cardioblast cell fate specification" evidence=IMP

GO:0007517 "muscle organ development" evidence=TAS

GO:0007507 "heart development" evidence=NAS

GO:0045165 "cell fate commitment" evidence=NAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEP

GO:0001709 "cell fate determination" evidence=NAS

GO:0007417 "central nervous system development" evidence=NAS

GO:0050770 "regulation of axonogenesis" evidence=IMP

GO:0007377 "germ-band extension" evidence=IMP;TAS

GO:0035290 "trunk segmentation" evidence=TAS

GO:0035289 "posterior head segmentation" evidence=TAS

GO:0008045 "motor neuron axon guidance" evidence=IMP

UNIPROTKB|F1MCF6 CDX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 108 (43.1 bits), Expect = 4.3e-05, P = 4.3e-05
 Identities = 25/64 (39%), Positives = 41/64 (64%)

Query:    32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPKDFQS 91
             +LE LEK +    Y +   ++EL+A LGL++RQ+++WF +RR K+RK    ++Q +  Q 
Sbjct:    19 RLE-LEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKQQQQQPPQP 77

Query:    92 LVPA 95
               PA
Sbjct:    78 PPPA 81

GO:0005634 "nucleus" evidence=IEA

GO:0060349 "bone morphogenesis" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00640217 hypothetical protein (1746 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	753
pfam02791	61	pfam02791, DDT, DDT domain	2e-23
smart00571	63	smart00571, DDT, domain in different transcription	6e-17
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-15
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	4e-13
smart00389	57	smart00389, HOX, Homeodomain	1e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-07
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-07
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	5e-07
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-07
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	8e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-06
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	1e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-06
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-06
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-05
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	1e-05
pfam10186	307	pfam10186, Atg14, UV radiation resistance protein	1e-05
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
pfam12072	201	pfam12072, DUF3552, Domain of unknown function (DU	2e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	3e-05
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	3e-05
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	3e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	4e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	5e-05
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	5e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-05
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	7e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	7e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	9e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	1e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
pfam12037	276	pfam12037, DUF3523, Domain of unknown function (DU	5e-04
TIGR00570	309	TIGR00570, cdk7, CDK-activating kinase assembly fa	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	6e-04
pfam05557	722	pfam05557, MAD, Mitotic checkpoint protein	6e-04
COG3599	212	COG3599, DivIVA, Cell division initiation protein	7e-04
COG5296	521	COG5296, COG5296, Transcription factor involved in	7e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	8e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	8e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	8e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	8e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	9e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.001
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.001
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.001
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.001
PLN02316	1036	PLN02316, PLN02316, synthase/transferase	0.001
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	0.001
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.001
PLN02372	455	PLN02372, PLN02372, violaxanthin de-epoxidase	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	0.002
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.002
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.002
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.002
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.002
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.003
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
PLN02372	455	PLN02372, PLN02372, violaxanthin de-epoxidase	0.003
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.004
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.004
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.004
pfam05384	159	pfam05384, DegS, Sensor protein DegS	0.004
pfam07111	739	pfam07111, HCR, Alpha helical coiled-coil rod prot	0.004
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.004
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	0.004
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.004

>gnl|CDD|202398 pfam02791, DDT, DDT domain

 Score = 93.4 bits (233), Expect = 2e-23
 Identities = 32/61 (52%), Positives = 42/61 (68%), Gaps = 1/61 (1%)

Query: 538 EDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDPR-LLGEIHVTLLRSVIKDIE 596
            +  G+LLMVW FL TF +VLGL PFTLD+F +A    D   LLGE+H+ LL+ ++ D E
Sbjct: 1   GEAFGDLLMVWEFLNTFGEVLGLSPFTLDDFEEALLCTDSEELLGEVHIALLKLLVADEE 60

Query: 597 D 597
           D
Sbjct: 61  D 61

This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices. Length = 61

>gnl|CDD|214726 smart00571, DDT, domain in different transcription and chromosome remodeling factors

 Score = 75.0 bits (185), Expect = 6e-17
 Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 3/63 (4%)

Query: 538 EDNIGNLLMVWRFLITFADVLGLWPF--TLDEFVQAFHDYDPR-LLGEIHVTLLRSVIKD 594
            +  G+LLMV+ FL +F  VLGL PF  TL++F+ A    D   LL E+HV LLR+++KD
Sbjct: 1   NEAFGDLLMVYEFLRSFGKVLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVLLRAILKD 60

Query: 595 IED 597
             +
Sbjct: 61  EGE 63

Length = 63

>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain

 Score = 71.4 bits (176), Expect = 1e-15
 Identities = 25/57 (43%), Positives = 37/57 (64%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + KR   T  QLE LEK +    YPS   R EL+ +LGL++RQ+++WF +RR K ++
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|238039 cd00086, homeodomain, 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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 25/57 (43%), Positives = 37/57 (64%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + KR   T  QLE LEK +    YPS   R EL+ +LGL++RQ+++WF +RR K ++
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 26/56 (46%), Positives = 36/56 (64%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
          + KR   T  QLE LEK +    YPS   R EL+ +LGLS+RQ+++WF +RR K +
Sbjct: 2  RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. Length = 57

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 60.5 bits (146), Expect = 3e-09
 Identities = 40/148 (27%), Positives = 74/148 (50%), Gaps = 15/148 (10%)

Query: 342  DEDVSRTEKKRKSEEARIAREVE-----AHEKRIRKELEKQDILRRKREEQIRKEMERQD 396
             E+  + E+ +K+EE    +  E       +K+  +E +K +   +K  E ++KE E   
Sbjct: 1643 AEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAE--- 1699

Query: 397  RERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAER 456
             E +K EE  L++K  EE++   E ++  E  +   ++    AE+ ++K E  +  E E+
Sbjct: 1700 -EAKKAEE--LKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEK 1756

Query: 457  LKVAN----ERAVARRIAKESMALVEDE 480
             K+A+    E   A  I KE  A++E+E
Sbjct: 1757 KKIAHLKKEEEKKAEEIRKEKEAVIEEE 1784

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 60.2 bits (145), Expect = 4e-09
 Identities = 39/137 (28%), Positives = 73/137 (53%), Gaps = 7/137 (5%)

Query: 343  EDVSRTEKKRKSEEARIAREV-EAHEKRIRKELEKQDILR-----RKREEQIRKEMERQD 396
            E+  + ++ +K+EEA+ A E  +A EK+   EL+K + L+     +K EE  + E ++  
Sbjct: 1519 EEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNM 1578

Query: 397  RERRKEEERLLREKLREEERYLREQRRELERRE-KFLQKESIRAEKRRQKEELRRVKEAE 455
              R+ EE +   E   EE   L E+ ++++  E K  ++  I+AE+ ++ EE ++  E  
Sbjct: 1579 ALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQL 1638

Query: 456  RLKVANERAVARRIAKE 472
            + K A E+  A  + K 
Sbjct: 1639 KKKEAEEKKKAEELKKA 1655

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.8 bits (144), Expect = 5e-09
 Identities = 39/152 (25%), Positives = 85/152 (55%), Gaps = 13/152 (8%)

Query: 343  EDVSRTEKKRKSEEARIAREV-EAHEKR----IRKELEKQDILRRKREE--QIRKEMERQ 395
            ++  + E+K+K++E + A E+ +A EK+     +K  E +++  RK EE  +  +    +
Sbjct: 1537 DEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEE 1596

Query: 396  DRERRKEEERLLREKLR--EEERYLREQ-RRELERREKFLQKESIRAEKRRQKEELRRVK 452
              +  +EE+++  E+ +  EE +   E+ ++  E ++K  Q +   AE++++ EEL++ +
Sbjct: 1597 VMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAE 1656

Query: 453  EAERLKVANERAVA---RRIAKESMALVEDER 481
            E  ++K A E   A   ++ A+E+    EDE+
Sbjct: 1657 EENKIKAAEEAKKAEEDKKKAEEAKKAEEDEK 1688

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 58.2 bits (140), Expect = 1e-08
 Identities = 40/141 (28%), Positives = 68/141 (48%), Gaps = 7/141 (4%)

Query: 343  EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
             D +  E   K+EEA+     +A E R  +E +K+    RK EE  + E  R+  E RK 
Sbjct: 1089 ADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARKA 1148

Query: 403  EERLLREKLR--EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVA 460
            E+    E  R  E+ R   E R+  + ++    + + +AE+ R+ EELR+ ++A + + A
Sbjct: 1149 EDAKRVEIARKAEDARKAEEARKAEDAKKA---EAARKAEEVRKAEELRKAEDARKAEAA 1205

Query: 461  NERAVARRIAKESMALVEDER 481
             +    R+   E     ED +
Sbjct: 1206 RKAEEERKA--EEARKAEDAK 1224

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 58.2 bits (140), Expect = 2e-08
 Identities = 35/140 (25%), Positives = 70/140 (50%), Gaps = 9/140 (6%)

Query: 343  EDVSRTEKKRKSEEARIAREV-EAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
            ED  + E  RK+EE R A E  +A + +  + ++K +  ++  EE  + E ER + E RK
Sbjct: 1197 EDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRK 1256

Query: 402  EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN 461
             EE  +    R +     E+ R+ +  +K        AE++++ +E ++ +E ++   A 
Sbjct: 1257 FEEARMAHFARRQAAIKAEEARKADELKK--------AEEKKKADEAKKAEEKKKADEAK 1308

Query: 462  ERAVARRIAKESMALVEDER 481
            ++A   + A E+    E+ +
Sbjct: 1309 KKAEEAKKADEAKKKAEEAK 1328

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 3e-08
 Identities = 39/157 (24%), Positives = 73/157 (46%), Gaps = 3/157 (1%)

Query: 342  DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRE-RR 400
            +E   + E  RK+EEAR A +    E+  + E  K+  + RK E+  + E  R+  + ++
Sbjct: 1118 EEAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKK 1177

Query: 401  KEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVA 460
             E  R   E  + EE    E  R+ E   K   +E  +AE+ R+ E+ ++ +  ++ + A
Sbjct: 1178 AEAARKAEEVRKAEELRKAEDARKAEAARKA--EEERKAEEARKAEDAKKAEAVKKAEEA 1235

Query: 461  NERAVARRIAKESMALVEDERLELMELAASSKGLPTI 497
             + A   + A+E     E  + E   +A  ++    I
Sbjct: 1236 KKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAI 1272

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 3e-08
 Identities = 38/139 (27%), Positives = 73/139 (52%), Gaps = 16/139 (11%)

Query: 343  EDVSRTEKKRKSEEAR---IAREVE----AHEKRIRKELEKQDILRR----KREEQIRK- 390
            ED  + E+ RK+E+A+   IAR+ E    A E R  ++ +K +  R+    ++ E++RK 
Sbjct: 1137 EDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKA 1196

Query: 391  -EMERQDRERRKEEERLLREKLR-EEERYLREQRRELERREKFLQKESIRAEKRRQKEEL 448
             +  + +  R+ EEER   E  + E+ +     ++  E ++    +E+ +AE+ R  EE+
Sbjct: 1197 EDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKD--AEEAKKAEEERNNEEI 1254

Query: 449  RRVKEAERLKVANERAVAR 467
            R+ +EA     A  +A  +
Sbjct: 1255 RKFEEARMAHFARRQAAIK 1273

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 4e-08
 Identities = 40/167 (23%), Positives = 86/167 (51%), Gaps = 16/167 (9%)

Query: 329  DNAFISSDRRVSHDEDVSRTEKKRKSEEARIARE---VEAHEKRIRKELEKQDILRRKRE 385
            + A I    ++  +E   + E+ +K+EEA+I  E       EK+  ++L+K++   +K+ 
Sbjct: 1590 EEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKA 1649

Query: 386  EQIRKEME----RQDRERRKEEERLLR----EKLREEERYLREQ-RRELERREKFLQKES 436
            E+++K  E    +   E +K EE   +    +K  E+E+   E  ++E E  +K  + + 
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709

Query: 437  IRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLE 483
              AE++++ EEL++ +E  ++K       A++ A+E     E+ + +
Sbjct: 1710 KEAEEKKKAEELKKAEEENKIKAEE----AKKEAEEDKKKAEEAKKD 1752

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 56.3 bits (135), Expect = 6e-08
 Identities = 50/187 (26%), Positives = 85/187 (45%), Gaps = 23/187 (12%)

Query: 307  RKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREV-EA 365
            RK      A DA    +   A D   +   R+    ED  + E+ RK+E+A+ A    +A
Sbjct: 1128 RKAEEARKAEDARKAEEARKAEDAKRVEIARKA---EDARKAEEARKAEDAKKAEAARKA 1184

Query: 366  HEKRIRKELEKQDILRR----KREEQIRK--EMERQDRERRKEEERLLRE-KLREEERYL 418
             E R  +EL K +  R+    ++ E+ RK  E  + +  ++ E  +   E K   EE   
Sbjct: 1185 EEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKK 1244

Query: 419  REQRRELERREKFLQ---------KESIRAEKRRQKEELRR---VKEAERLKVANERAVA 466
             E+ R  E   KF +         + +I+AE+ R+ +EL++    K+A+  K A E+  A
Sbjct: 1245 AEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKA 1304

Query: 467  RRIAKES 473
                K++
Sbjct: 1305 DEAKKKA 1311

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.8 bits (131), Expect = 2e-07
 Identities = 37/147 (25%), Positives = 72/147 (48%), Gaps = 9/147 (6%)

Query: 342  DEDVSRTEKKRKSEEARIAREV-EAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERR 400
            DE     E K+K++EA+ A E  +A E +  +E +K D  ++  E++   E+++ +  ++
Sbjct: 1500 DEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKK 1559

Query: 401  KEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVA 460
             EE++   E  + EE      R+  E +    + E  R E+  +  E  +  +AE  K A
Sbjct: 1560 AEEKKKAEEAKKAEEDKNMALRKAEEAK----KAEEARIEEVMKLYEEEKKMKAEEAKKA 1615

Query: 461  NERAVARRIAKESMALVEDERLELMEL 487
             E     +I  E +   E+E+ ++ +L
Sbjct: 1616 EE----AKIKAEELKKAEEEKKKVEQL 1638

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.4 bits (130), Expect = 2e-07
 Identities = 39/151 (25%), Positives = 80/151 (52%), Gaps = 9/151 (5%)

Query: 349  EKKRKSEEARIAREV--EAHEKRIRKELEKQDILRRKREEQIRKEME---RQDRERRKEE 403
            E K+K+EEA+ A E   +A E +   E +K+    +K+ ++ +K  E   + D  ++ EE
Sbjct: 1461 EAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEE 1520

Query: 404  ERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANER 463
             +   E  + EE    ++ ++ E ++K    E  +AE+ ++ EE ++ +EA++ +   ++
Sbjct: 1521 AKKADEAKKAEEAKKADEAKKAEEKKK--ADELKKAEELKKAEEKKKAEEAKKAE--EDK 1576

Query: 464  AVARRIAKESMALVEDERLELMELAASSKGL 494
             +A R A+E+    E    E+M+L    K +
Sbjct: 1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKM 1607

Length = 2084

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 53.4 bits (129), Expect = 2e-07
 Identities = 48/159 (30%), Positives = 76/159 (47%), Gaps = 18/159 (11%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRK---------REEQIRKEMERQDRER 399
           +++ + +E R     E +E++ R++ EK++  +R+         REEQI ++ ER   ER
Sbjct: 196 DEREELDELRADLYQEEYERKERQK-EKEEAEKRRRQKQELQRAREEQIEEKEERLQEER 254

Query: 400 RKEEER--LLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERL 457
            +EE     + EK  E+E    EQ    +RR K L+    R E  +Q EE    + AER 
Sbjct: 255 AEEEAERERMLEKQAEDEE--LEQENAEKRRMKRLEH---RRELEQQIEEKEERRAAERE 309

Query: 458 KVANERAVARRIAKESMALVEDERLELM-ELAASSKGLP 495
           +   E    R    E  A +E+ER  L+ E A +  G  
Sbjct: 310 EELEEGERLREEEAERQARIEEERQRLLKEHAEALLGYL 348

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 53.4 bits (129), Expect = 2e-07
 Identities = 33/155 (21%), Positives = 73/155 (47%), Gaps = 13/155 (8%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKRE----EQIRKEMERQDRERRKE 402
           R + + K EE RI   +E    +   E E+++  R++        +++++E +++ R++E
Sbjct: 31  RIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEE 90

Query: 403 EERLLREK---------LREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE 453
            E  L+E+         ++EE+    +++RE +++ +    E       R++EE  R +E
Sbjct: 91  YEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKERERE 150

Query: 454 AERLKVANERAVARRIAKESMALVEDERLELMELA 488
            E   +  +R  A R  +      E +  +  E+A
Sbjct: 151 EELKILEYQREKAEREEEREAERRERKEEKEREVA 185

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 53.2 bits (127), Expect = 5e-07
 Identities = 35/141 (24%), Positives = 69/141 (48%), Gaps = 8/141 (5%)

Query: 349  EKKRKSEEARIAREVE--AHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
            E K+K+EEA+ A E +  A E +  +E +K+    +K +E  +K  E +  +  K++   
Sbjct: 1435 EAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEE 1494

Query: 407  LREKLREEERYLREQRRELERR---EKFLQKESIRAEKRRQKEELRR---VKEAERLKVA 460
             ++K  E ++    +++  E +   E     E+ +AE+ ++ +E ++    K+A+ LK A
Sbjct: 1495 AKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKA 1554

Query: 461  NERAVARRIAKESMALVEDER 481
             E   A    K   A   +E 
Sbjct: 1555 EELKKAEEKKKAEEAKKAEED 1575

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 53.2 bits (127), Expect = 5e-07
 Identities = 37/155 (23%), Positives = 79/155 (50%), Gaps = 18/155 (11%)

Query: 343  EDVSRTEKKRKSEE--------ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMER 394
            E+  + E+ +K+EE        A  A++ E  E RI + ++  +  ++ + E+ +K  E 
Sbjct: 1561 EEKKKAEEAKKAEEDKNMALRKAEEAKKAE--EARIEEVMKLYEEEKKMKAEEAKKAEEA 1618

Query: 395  QDR--ERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK 452
            + +  E +K EE   ++K+ + ++   E++++ E  +K  ++  I+A +  +K E  + K
Sbjct: 1619 KIKAEELKKAEE--EKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDK-K 1675

Query: 453  EAERLKVANERAVARRIAKESMALVEDERLELMEL 487
            +AE  K A E     + A E++    +E  +  EL
Sbjct: 1676 KAEEAKKAEED---EKKAAEALKKEAEEAKKAEEL 1707

Length = 2084

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 52.6 bits (127), Expect = 5e-07
 Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 8/117 (6%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKRE-EQIRKEMERQDRERRKE----E 403
           EKK  S E   A+ +    K+  + L+K+ +L  K E  ++R E+ER+ +ERR E    E
Sbjct: 24  EKKLGSAEEL-AKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLE 82

Query: 404 ERLLR--EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
            RLL+  E L  +   L ++   LE++EK L  +    +++ ++ E    ++ E L+
Sbjct: 83  RRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELE 139

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 52.5 bits (126), Expect = 7e-07
 Identities = 40/159 (25%), Positives = 73/159 (45%), Gaps = 11/159 (6%)

Query: 340 SHDEDVSRTEKKRKSEEARIAREVEAHEKRIR---KELEKQDILRRKREEQIRKEME--- 393
             + +    E  R+ EEA +  E+E  EK +R   +EL +   L    +E++ +++E   
Sbjct: 480 ELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLE 539

Query: 394 RQDRERRKEEERLLREKLREEERYLREQRREL-----ERREKFLQKESIRAEKRRQKEEL 448
               E  + +E+L  ++L+EE R L ++ +EL     E R    +KE +   + R KE  
Sbjct: 540 NLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELK 599

Query: 449 RRVKEAERLKVANERAVARRIAKESMALVEDERLELMEL 487
           +++KE E      E  +      E+   +E+   EL   
Sbjct: 600 KKLKELEERLSQLEELLQSLELSEAENELEEAEEELESE 638

Length = 908

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 52.4 bits (126), Expect = 8e-07
 Identities = 37/144 (25%), Positives = 65/144 (45%), Gaps = 7/144 (4%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLR 408
           EK+R+ E+A   R  +   +  +   E +++ R   EE+ R++   ++    KEE   LR
Sbjct: 312 EKERELEDAE-ERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLR 370

Query: 409 EKLREEERYLREQRRELERREKFLQK-----ESIRAEKRRQKEELRRVKEAERLKVANER 463
            +L E ++   E R EL+   + L+K       ++ E  R +EEL+R    E   +    
Sbjct: 371 AELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQR-LSEELADLNAAI 429

Query: 464 AVARRIAKESMALVEDERLELMEL 487
           A       E     ED+ LE+ + 
Sbjct: 430 AGIEAKINELEEEKEDKALEIKKQ 453

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 51.7 bits (123), Expect = 1e-06
 Identities = 33/137 (24%), Positives = 73/137 (53%), Gaps = 11/137 (8%)

Query: 342  DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRK--EMERQDRER 399
            DE   + E+K+K++EA+     +A E +   E +K+    +K EE  +K  E ++ D  +
Sbjct: 1421 DEAKKKAEEKKKADEAK----KKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAK 1476

Query: 400  RKEEERLLREKLREEERYLREQRRELERREKFLQK--ESIRAEKRRQKEELRRVKE---A 454
            +K EE    ++ +++    +++  E ++  +  +K  E+ +AE+ ++ +E ++ +E   A
Sbjct: 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKA 1536

Query: 455  ERLKVANERAVARRIAK 471
            +  K A E+  A  + K
Sbjct: 1537 DEAKKAEEKKKADELKK 1553

Length = 2084

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 50.7 bits (122), Expect = 1e-06
 Identities = 33/108 (30%), Positives = 58/108 (53%), Gaps = 13/108 (12%)

Query: 344 DVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEE 403
           D + T K++  E  R   + EA E        +Q++LR K++E+ +  ME Q+R   +E 
Sbjct: 196 DQALTAKEKAIEAERA--KAEAAEA-------EQELLREKQKEEEQM-MEAQER-SYQEH 244

Query: 404 ERLLREKL-REEERYLREQRRELERREKFLQKESIRAEKRRQKEELRR 450
            + L EK+  E E+ L EQ R LE + +  Q+E ++   + + E L++
Sbjct: 245 VKQLIEKMEAEREKLLAEQERMLEHKLQ-EQEELLKEGFKTEAESLQK 291

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 51.7 bits (123), Expect = 2e-06
 Identities = 41/151 (27%), Positives = 74/151 (49%), Gaps = 6/151 (3%)

Query: 343  EDVSRTEK-KRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
            E V + E+ K+ +EEA+ A E   +E+ IRK  E +     +R+  I+ E  R+  E +K
Sbjct: 1227 EAVKKAEEAKKDAEEAKKAEEERNNEE-IRKFEEARMAHFARRQAAIKAEEARKADELKK 1285

Query: 402  EEERLLREKLR--EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKV 459
             EE+   ++ +  EE++   E +++ E  +K  + +    E +++ +  +  K+AE  K 
Sbjct: 1286 AEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAK--KKAEEAKK 1343

Query: 460  ANERAVARRIAKESMALVEDERLELMELAAS 490
            A E A A   A    A   +E+ E  E    
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAEAAEKKKE 1374

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.9 bits (121), Expect = 2e-06
 Identities = 30/142 (21%), Positives = 70/142 (49%), Gaps = 5/142 (3%)

Query: 347  RTEKKRKSEEARIAREV-EAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEER 405
            + E+ RK++E + A E  +A E +  +E +K D  ++K EE  + +  ++  E  K++  
Sbjct: 1273 KAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1332

Query: 406  LLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAV 465
              ++K  E ++     + E E      +     AE++ +  E ++ +  ++   A ++A 
Sbjct: 1333 AAKKKAEEAKKAAEAAKAEAEAAADEAEA----AEEKAEAAEKKKEEAKKKADAAKKKAE 1388

Query: 466  ARRIAKESMALVEDERLELMEL 487
             ++ A E+    E+++ +  EL
Sbjct: 1389 EKKKADEAKKKAEEDKKKADEL 1410

Length = 2084

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 50.3 bits (121), Expect = 2e-06
 Identities = 30/119 (25%), Positives = 64/119 (53%), Gaps = 6/119 (5%)

Query: 349 EKKRKSEEARIARE---VEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEER 405
           EK+R+ E     +E   ++   +RI++E E +   +R++++++R+E++  + ER + +E 
Sbjct: 84  EKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEE 143

Query: 406 LLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERA 464
               +  EE + L  QR + ER E+   +   R E++ +KE       A++ +  +ER 
Sbjct: 144 EKEREREEELKILEYQREKAEREEEREAE---RRERKEEKEREVARLRAQQEEAEDERE 199

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 51.3 bits (123), Expect = 2e-06
 Identities = 34/152 (22%), Positives = 66/152 (43%), Gaps = 15/152 (9%)

Query: 350 KKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLRE 409
           ++ + E +R+  E+E  ++ + +  ++ + L+ + EE +R+E+E    E  + +E    E
Sbjct: 242 EELEEELSRLEEELEELQEELEEAEKEIEELKSELEE-LREELEELQEELLELKE--EIE 298

Query: 410 KLREEERYLREQRRELERREKFLQKESIRAEKRR------------QKEELRRVKEAERL 457
           +L  E   LRE+  ELE   + L++     +++               EEL ++      
Sbjct: 299 ELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEE 358

Query: 458 KVANERAVARRIAKESMALVEDERLELMELAA 489
                      + +E   L E  R EL EL A
Sbjct: 359 AKEELEEKLSALLEELEELFEALREELAELEA 390

Length = 1163

>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 37/144 (25%), Positives = 60/144 (41%), Gaps = 9/144 (6%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLR 408
           E +R++E+A I  E    E++ + E E Q     +  E     +ERQ     KE E  L 
Sbjct: 284 ETRREAEQAEILAEQAIQEEKAQAEQEVQHAKALEAREMRVGLIERQ-----KETE--LE 336

Query: 409 EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARR 468
            + R       +++ + E +      E+I A+     E  R  +EAER + A   A A  
Sbjct: 337 PQERSYFINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARETEEAERAEQAALVAAAE- 395

Query: 469 IAKESMALVEDERLELMELAASSK 492
            A E   +    R E  +  A ++
Sbjct: 396 -AAEQEQVEIAVRAEAAKAEAEAQ 418

Length = 548

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.9 bits (121), Expect = 3e-06
 Identities = 33/166 (19%), Positives = 75/166 (45%), Gaps = 7/166 (4%)

Query: 329  DNAFISSDRRVSHDEDVSRTEKKRKSEEA-RIAREVEAHEKRIRKELE---KQDILRRKR 384
            + A   ++     DE   + E+ +K++EA + A E +      +K  E   K D  ++  
Sbjct: 1460 EEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAE 1519

Query: 385  EEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQK---ESIRAEK 441
            E +   E ++ +  ++ +E +   EK + +E    E+ ++ E ++K  +    E  +   
Sbjct: 1520 EAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMA 1579

Query: 442  RRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMEL 487
             R+ EE ++ +EA   +V       +++  E     E+ +++  EL
Sbjct: 1580 LRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEEL 1625

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.5 bits (120), Expect = 3e-06
 Identities = 33/129 (25%), Positives = 68/129 (52%), Gaps = 8/129 (6%)

Query: 349  EKKRKSEEARIAREVE--AHEKRIRKELEKQDI--LRRKREEQIRK-EMERQDRERRKEE 403
            E K+K+EEA+ A E E  A E   ++  E +    L++K  E+ +K E  ++  E  K +
Sbjct: 1672 EDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIK 1731

Query: 404  ERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANER 463
                +++  E+++   E +++ E ++K      ++ E+ ++ EE+R+ KEA   +  +E 
Sbjct: 1732 AEEAKKEAEEDKKKAEEAKKDEEEKKKIAH---LKKEEEKKAEEIRKEKEAVIEEELDEE 1788

Query: 464  AVARRIAKE 472
               RR+  +
Sbjct: 1789 DEKRRMEVD 1797

Length = 2084

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.9 bits (120), Expect = 3e-06
 Identities = 37/143 (25%), Positives = 65/143 (45%), Gaps = 10/143 (6%)

Query: 349 EKKRKSEE----ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
           EK+R+ EE        RE    E+    E  ++   + +   ++R + E  + ER + +E
Sbjct: 144 EKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDE 203

Query: 405 RLLREKLREEERYLREQRRELERREKFL-QKESIRAEKRRQKEELRRVKEAERLKVANER 463
             LR  L +EE   +E+++E E  EK   QK+ ++  +  Q EE     + ER   A E 
Sbjct: 204 --LRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEER---AEEE 258

Query: 464 AVARRIAKESMALVEDERLELME 486
           A   R+ ++     E E+    +
Sbjct: 259 AERERMLEKQAEDEELEQENAEK 281

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 50.5 bits (121), Expect = 3e-06
 Identities = 37/149 (24%), Positives = 62/149 (41%), Gaps = 12/149 (8%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
           + E +    E  + RE     +   +ELE++    +++ E +++E+E ++    + E+ L
Sbjct: 294 KEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLL 353

Query: 407 --LREKLREEERYLREQRRELER-----REKFLQKESIRAEKRRQKEELRR-----VKEA 454
             L E   E E  L     ELE      RE+  + E+  AE R + EEL+R      +  
Sbjct: 354 AELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERL 413

Query: 455 ERLKVANERAVARRIAKESMALVEDERLE 483
           ERL    E         E+        LE
Sbjct: 414 ERLSERLEDLKEELKELEAELEELQTELE 442

Length = 1163

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.1 bits (119), Expect = 4e-06
 Identities = 29/135 (21%), Positives = 65/135 (48%), Gaps = 15/135 (11%)

Query: 347  RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK----- 401
            + E+ +K+EEARI   ++ +E+  + + E+    ++  E +I+ E  ++  E +K     
Sbjct: 1582 KAEEAKKAEEARIEEVMKLYEEEKKMKAEE---AKKAEEAKIKAEELKKAEEEKKKVEQL 1638

Query: 402  ----EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERL 457
                 EE+   E+L++ E   + +  E  ++    +++  +AE+ ++ EE  +       
Sbjct: 1639 KKKEAEEKKKAEELKKAEEENKIKAAEEAKKA---EEDKKKAEEAKKAEEDEKKAAEALK 1695

Query: 458  KVANERAVARRIAKE 472
            K A E   A  + K+
Sbjct: 1696 KEAEEAKKAEELKKK 1710

Length = 2084

>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription]

 Score = 46.7 bits (111), Expect = 5e-06
 Identities = 21/58 (36%), Positives = 36/58 (62%)

Query: 22  KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
           K+KR+  T  QL +LE+ + +  YPS   R +LS  L +  + +Q+WF ++R K++K 
Sbjct: 52  KSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109

Length = 156

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.8 bits (118), Expect = 6e-06
 Identities = 30/151 (19%), Positives = 71/151 (47%), Gaps = 12/151 (7%)

Query: 343  EDVSRTEKKRKSEEARIAREV--------EAHEKRIRKELEKQDILRRKREEQIRKEMER 394
            +++ + E+K+K++EA+ A E         +A E +   E +K+    +K+ +  +K+ E 
Sbjct: 1281 DELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEE 1340

Query: 395  QDR--ERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK 452
              +  E  K E     ++    E       ++ E  +K       +AE++++ +E ++  
Sbjct: 1341 AKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKA 1400

Query: 453  EAERLKV--ANERAVARRIAKESMALVEDER 481
            E ++ K     + A A++ A E+    E+++
Sbjct: 1401 EEDKKKADELKKAAAAKKKADEAKKKAEEKK 1431

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 49.7 bits (119), Expect = 6e-06
 Identities = 34/168 (20%), Positives = 63/168 (37%), Gaps = 14/168 (8%)

Query: 340 SHDEDVSRTEKKRKSEEARIAR----------EVEAHEKRIRKELEKQDILRRKREEQIR 389
             ++++   + + +     +            E+E  E  I    E+ + L  + EE   
Sbjct: 264 EAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEE 323

Query: 390 KEMERQDRERRKEEERLLREKLREEERYLR---EQRRELERREKFLQKESIRAEKRRQKE 446
           +  E +++    +EE   RE L EE   L    E+ +E    +     E +       +E
Sbjct: 324 RLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALRE 383

Query: 447 ELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGL 494
           EL  + EAE  ++ NE    +R  +     +E     L +L    K L
Sbjct: 384 ELAEL-EAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKEL 430

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 38/159 (23%), Positives = 74/159 (46%), Gaps = 5/159 (3%)

Query: 346 SRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRER--RKEE 403
              E+  K        E+E  E+ + +E E+ ++  R+  E++ KE+   + E     E 
Sbjct: 466 ELPEEHEKELLELYELELEELEEELSREKEEAEL--REEIEELEKELRELEEELIELLEL 523

Query: 404 ERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEA-ERLKVANE 462
           E  L+E+L E+   L     ELE  ++ LQ + ++ E R+ ++ L+ +KE  E L++   
Sbjct: 524 EEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRT 583

Query: 463 RAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLD 501
           R       +E +  ++ +  EL E  +  + L   + L 
Sbjct: 584 RKEELEELRERLKELKKKLKELEERLSQLEELLQSLELS 622

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 30/138 (21%), Positives = 63/138 (45%), Gaps = 3/138 (2%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLR 408
           E + K E+     E     K  + +L++     R+ E+++++  E  +  R     +   
Sbjct: 530 ELEEKLEKLENLLEELEELKE-KLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEEL 588

Query: 409 EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEA--ERLKVANERAVA 466
           E+LRE  + L+++ +ELE R   L++     E    + EL   +E     L+  N +A  
Sbjct: 589 EELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAEL 648

Query: 467 RRIAKESMALVEDERLEL 484
             + + ++  +E++  EL
Sbjct: 649 EELLQAALEELEEKVEEL 666

Length = 908

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 48.5 bits (116), Expect = 1e-05
 Identities = 38/148 (25%), Positives = 73/148 (49%), Gaps = 10/148 (6%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKR-IRKELEKQDILRRKREEQIR---KEMERQDRE 398
           E +S+ +++ +  E     E E  E     K ++K +    + EE+     +E+E   RE
Sbjct: 392 EALSKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKRE 451

Query: 399 RRKEEERL--LREKLREE---ERYLREQRRELERREKFLQKESIRAEK-RRQKEELRRVK 452
             K E  L   R ++R++   +R +R + R +ER EK L+++  R E+  R+  ELR+++
Sbjct: 452 IEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMR 511

Query: 453 EAERLKVANERAVARRIAKESMALVEDE 480
           + E         V  ++  E++   E+E
Sbjct: 512 KLELSGKGTPVKVVEKLTLEAIEEAEEE 539

Length = 652

>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and autophagy-related subunit 14

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 27/121 (22%), Positives = 53/121 (43%), Gaps = 10/121 (8%)

Query: 357 ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEER----LLREKLR 412
           AR+  E E  ++++ + LE       K    + K +E   ++ R  + R     L+E++ 
Sbjct: 30  ARLLLENEELKQKVEEALEGATNEDGKLAADLLK-LEVARKKERLNQIRARISQLKEEIE 88

Query: 413 EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK-----VANERAVAR 467
           ++   + E +R L +R   L   S + EKRR  +  +   E +R +     + +  A  R
Sbjct: 89  QKRERIEELKRALAQRRSDLSSASYQLEKRRASQLEKLQDEIKRTRSKLNALHSLLAEKR 148

Query: 468 R 468
            
Sbjct: 149 S 149

The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localisation of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex. Length = 307

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 48.6 bits (115), Expect = 1e-05
 Identities = 45/97 (46%), Positives = 59/97 (60%), Gaps = 6/97 (6%)

Query: 351 KRKSEEARIAREVEAHEKRIR-KELEKQDILRRKREEQIRKEMERQDR-ER-RKEEERLL 407
           K  +E ARI +E  AH K +  K LEK+ I R +REE+ R E ER +R ER R E ERL 
Sbjct: 432 KDHAERARIEKE-NAHRKALEMKILEKKRIERLEREERERLERERMERIERERLERERLE 490

Query: 408 REKLREEERYLREQRRELERREKFLQKESIRAEKRRQ 444
           RE+L E +R  R++   LE RE+  + E  R EK R+
Sbjct: 491 RERL-ERDRLERDRLDRLE-RERVDRLERDRLEKARR 525

Length = 1021

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.2 bits (115), Expect = 2e-05
 Identities = 39/143 (27%), Positives = 66/143 (46%), Gaps = 5/143 (3%)

Query: 348 TEKKRKSEEARIAREVEAHEKRIRK-ELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
            EK++  +E     E E  E   R   LE++     +R E++ +E+E  + E  + EE+L
Sbjct: 785 EEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKL 844

Query: 407 --LREKLREEERYLREQRRELERREKFLQKESIR-AEKRRQKEEL-RRVKEAERLKVANE 462
             L E+L E E+ L E + ELE  E   ++      E   +KEEL   ++E E      +
Sbjct: 845 DELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELK 904

Query: 463 RAVARRIAKESMALVEDERLELM 485
             + +   +      + ERLE+ 
Sbjct: 905 EEIEKLRERLEELEAKLERLEVE 927

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 37/148 (25%), Positives = 61/148 (41%), Gaps = 7/148 (4%)

Query: 346 SRTEKKRKSEEARIAREVEAHEKRIRK---ELEKQDILRRKREEQIRKEMERQDRERRKE 402
            R+   +K E   +  E+   E ++ K   EL+      R  E+ +  E+ RQ  E  ++
Sbjct: 659 KRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLE-ELRRQLEELERQ 717

Query: 403 EERLLRE--KLREEERYLREQRRELERREKFLQKESIRAEKR-RQKEELRRVKEAERLKV 459
            E L RE   L EE   L+ +  ELE   + L++E    ++R  + EE     E    K+
Sbjct: 718 LEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKL 777

Query: 460 ANERAVARRIAKESMALVEDERLELMEL 487
             E        +     +E+   EL E 
Sbjct: 778 KEEIEELEEKRQALQEELEELEEELEEA 805

Length = 1163

>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552)

 Score = 45.6 bits (109), Expect = 2e-05
 Identities = 37/127 (29%), Positives = 68/127 (53%), Gaps = 16/127 (12%)

Query: 337 RRVSHDEDVSRTEKKRKS--EEARIAREVEAHEKRIRKELEKQDILRRKREE------QI 388
           R+   +  +S  E++ K   EEA+  +E EA +K     LE ++ + + R E      + 
Sbjct: 21  RKSIAEAKISSAEEEAKQIIEEAK--KEAEALKKE--ALLEAKEEIHKLRAEAERELKER 76

Query: 389 RKEMERQDRERRKEEERLLR--EKLREEERYLREQRRELERREKFLQK--ESIRAEKRRQ 444
           R E++RQ++   ++EE L R  E L ++E  L E+ +EL  R++ L++  E +      Q
Sbjct: 77  RNELQRQEKRLLQKEETLDRKDESLEKKEESLEEKEKELAARQQQLEEKEEELEELIEEQ 136

Query: 445 KEELRRV 451
           ++EL R+
Sbjct: 137 QQELERI 143

This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with pfam00013, pfam01966. This domain has a single completely conserved residue A that may be functionally important. Length = 201

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 47.1 bits (112), Expect = 3e-05
 Identities = 29/138 (21%), Positives = 48/138 (34%), Gaps = 2/138 (1%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQ-DRERRK 401
           E +     + + E+ R+        +    ELE   I   +  E  R   E +   ER +
Sbjct: 235 EALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLE 294

Query: 402 EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRR-VKEAERLKVA 460
           E ER + E   E E          E  EK    E    +   + E+L   ++E    K  
Sbjct: 295 ELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNE 354

Query: 461 NERAVARRIAKESMALVE 478
             + +  R+ +    L E
Sbjct: 355 LAKLLEERLKELEERLEE 372

Length = 908

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 37/109 (33%), Positives = 60/109 (55%), Gaps = 8/109 (7%)

Query: 350 KKRKSEEARIAREV---EAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
           ++R ++EA    +    EA EK     LE +++L R+R +Q R+E  R+  E ++EEERL
Sbjct: 28  RQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQ-RQEARREREELQREEERL 86

Query: 407 LREKLREEERY--LREQRRELERREKFL-QKESIRAEKRRQ-KEELRRV 451
           ++++ + + R   L     +LE REK L  +E    E  +Q   EL RV
Sbjct: 87  VQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRV 135

Length = 508

>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 46.3 bits (110), Expect = 3e-05
 Identities = 27/134 (20%), Positives = 47/134 (35%), Gaps = 7/134 (5%)

Query: 375 EKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLRE-----QRRELERRE 429
           +K D  + +R E+ R+E    D  ++ E      ++  E    L E      RR      
Sbjct: 111 DKLDEEQEERVEKEREEELAGDAMKKLENRTADSKREMEVLERLEELKELQSRRADVDVN 170

Query: 430 KFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLE--LMEL 487
             L+    R +K  ++EE       + L    E    RR A +  +  ++E  +      
Sbjct: 171 SMLEALFRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSPK 230

Query: 488 AASSKGLPTIVSLD 501
           + SS        L 
Sbjct: 231 SGSSSPAKPTSILK 244

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 46.1 bits (110), Expect = 4e-05
 Identities = 35/146 (23%), Positives = 67/146 (45%), Gaps = 14/146 (9%)

Query: 351 KRKSEEARIAREVEAH--EKRIRKELEKQDILR--------RKREEQIRKEMERQDRERR 400
             K   A++ +E +A   EK+  K  EK++  R        R +     +E ER+ +E R
Sbjct: 10  NEKLRAAKVNKERDAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEER 69

Query: 401 KEEERLLREKL--REEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAER-- 456
           +E   +L+E++  RE+ R    + R  ER +     E I+ E   + +E R  ++  R  
Sbjct: 70  REGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREE 129

Query: 457 LKVANERAVARRIAKESMALVEDERL 482
           +   NE  + R+  ++     E+ ++
Sbjct: 130 IDEFNEERIERKEEEKEREREEELKI 155

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 46.9 bits (111), Expect = 4e-05
 Identities = 33/153 (21%), Positives = 67/153 (43%), Gaps = 7/153 (4%)

Query: 336 DRRVSHDEDVSRT-EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMER 394
           +RR+  +E+ + + EK++K E  +   E   +   +  +LE+  +   K +EQ +K +E 
Sbjct: 154 ERRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEY 213

Query: 395 QDRERRKEEERLLREKLR-EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE 453
                 KE+  L  E L   +   L E+R +L +     ++E I + K+  ++E   + +
Sbjct: 214 YQ---LKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQ 270

Query: 454 AERLKVANERAVA--RRIAKESMALVEDERLEL 484
             +     E+         K      E+ + EL
Sbjct: 271 VLKENKEEEKEKKLQEEELKLLAKEEEELKSEL 303

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 47.0 bits (112), Expect = 4e-05
 Identities = 38/136 (27%), Positives = 67/136 (49%), Gaps = 13/136 (9%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E+V R   +  SE   +  E+E  EK + KELE+     ++  E++ KE+E  +  +RK 
Sbjct: 203 EEVLREINEISSELPELREELEKLEKEV-KELEE----LKEEIEELEKELESLEGSKRKL 257

Query: 403 EERL-----LREKLREEERYLREQRRELER-REKFLQKESIRAEKRRQKEELRRV-KEAE 455
           EE++       E+L++E   L E+ +EL+  +EK  +   +        +ELR + K   
Sbjct: 258 EEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLS 317

Query: 456 RLKVANERAVARRIAK 471
           RL+      +  RI +
Sbjct: 318 RLE-EEINGIEERIKE 332

Length = 880

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.7 bits (110), Expect = 5e-05
 Identities = 32/137 (23%), Positives = 63/137 (45%), Gaps = 7/137 (5%)

Query: 342  DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
             E+  + E++R +EE R   E        R+   K +   RK +E  + E +++  E +K
Sbjct: 1239 AEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAE-EARKADELKKAEEKKKADEAKK 1297

Query: 402  EEERLLREKLR---EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE---AE 455
             EE+   ++ +   EE +   E +++ E  +K       +AE+ ++  E  + +    A+
Sbjct: 1298 AEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAAD 1357

Query: 456  RLKVANERAVARRIAKE 472
              + A E+A A    KE
Sbjct: 1358 EAEAAEEKAEAAEKKKE 1374

Length = 2084

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 46.6 bits (111), Expect = 5e-05
 Identities = 35/165 (21%), Positives = 75/165 (45%), Gaps = 12/165 (7%)

Query: 342 DEDVSRTEKKRKSEEARIAREVEAHEKR--IRKEL---EKQDILRRKREEQIRKEMERQD 396
             ++S+ E++    EAR+ RE+E    R  + KE    E Q++  ++ + + + +   ++
Sbjct: 797 QAELSKLEEEVSRIEARL-REIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKE 855

Query: 397 RER---RKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE 453
            E    +KEE     E+L    R L  +  +L++    L+ +    E++ ++ E +  K+
Sbjct: 856 IENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKK 915

Query: 454 AERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIV 498
            +RL    E        +E ++ +ED + E  E+      L  + 
Sbjct: 916 RKRLS---ELKAKLEALEEELSEIEDPKGEDEEIPEEELSLEDVQ 957

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 26/123 (21%), Positives = 54/123 (43%), Gaps = 9/123 (7%)

Query: 370 IRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREE----ERYLREQRREL 425
           + K  E++    ++  E+  +       +R K+ E  + E+L EE    +R L E +RE+
Sbjct: 394 LSKVKEEERPREKEGTEEEERREITVYEKRIKKLEETV-ERLEEENSELKRELEELKREI 452

Query: 426 E----RREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDER 481
           E      E+F ++   +  K R+     R  E    ++  ++     + ++   L +  +
Sbjct: 453 EKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMRK 512

Query: 482 LEL 484
           LEL
Sbjct: 513 LEL 515

Length = 652

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 46.5 bits (110), Expect = 5e-05
 Identities = 26/154 (16%), Positives = 58/154 (37%), Gaps = 6/154 (3%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
             +  +++   E      +   E+  +KE   ++ L++ + E+     ++    + K  E
Sbjct: 678 AEQELQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINE 737

Query: 405 RLLREKLR------EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
            L   + +      EEE+   ++  E E + +   KE   AE+  + E+L+  +E E   
Sbjct: 738 ELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKL 797

Query: 459 VANERAVARRIAKESMALVEDERLELMELAASSK 492
            A E  +     +        E  +L+       
Sbjct: 798 KAQEEELRALEEELKEEAELLEEEQLLIEQEEKI 831

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 46.5 bits (110), Expect = 5e-05
 Identities = 30/146 (20%), Positives = 66/146 (45%), Gaps = 7/146 (4%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
             E++    +  +  E E  E   ++  ++++IL +  +E   +E E++ +E   +    
Sbjct: 235 LNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAK 294

Query: 407 LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVA 466
             E+L+ E   L  ++ + E + K  +KE  + EK  +KE+    +E E L+   +    
Sbjct: 295 EEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEK----EEIEELEKELKEL-- 348

Query: 467 RRIAKESMALVEDERLELMELAASSK 492
             I +E+    E++  +L E     +
Sbjct: 349 -EIKREAEEEEEEQLEKLQEKLEQLE 373

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 43.9 bits (103), Expect = 5e-05
 Identities = 39/110 (35%), Positives = 66/110 (60%), Gaps = 6/110 (5%)

Query: 354 SEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLRE 413
           +E+ R ARE    E++ R+E E+QD  R +REE  R+  E + R R +E  R   E+ RE
Sbjct: 29  AEKRRQAREQREQEEQERREQEEQD--RLEREELKRRAAEERLR-REEEARRQEEERARE 85

Query: 414 EERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANER 463
           +E   + +  E E++E   Q+E  R +K++++ E R  +EAER+++  E+
Sbjct: 86  KEEKAKRKAEEEEKQE---QEEQERIQKQKEEAEARAREEAERMRLEREK 132

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 44.3 bits (105), Expect = 6e-05
 Identities = 21/86 (24%), Positives = 49/86 (56%), Gaps = 7/86 (8%)

Query: 368 KRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELER 427
           K   K+  K +  + +R+++  +E ER++R++ +E+    R++  EE    RE+++E E 
Sbjct: 2   KIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKE-EEELEEEREKKKEEEE 60

Query: 428 REKFLQKESIRAEKRRQKEELRRVKE 453
           R++  ++       R+++EE  ++K 
Sbjct: 61  RKEREEQA------RKEQEEYEKLKS 80

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 46.2 bits (110), Expect = 6e-05
 Identities = 35/167 (20%), Positives = 56/167 (33%), Gaps = 15/167 (8%)

Query: 336 DRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQ-------- 387
           +R    +E+++  E + +  EA+I +  E  +       E +  L    EE         
Sbjct: 768 ERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLE 827

Query: 388 ------IRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEK 441
                    E   +D E + EE     E L  E   L E   ELE   + L  E    E+
Sbjct: 828 SLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEE 887

Query: 442 RRQKEELRRVKEAERLKVANERAV-ARRIAKESMALVEDERLELMEL 487
                     + +E L+    +    RR  +E    +    L L  L
Sbjct: 888 ALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGL 934

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 46.2 bits (110), Expect = 7e-05
 Identities = 44/181 (24%), Positives = 81/181 (44%), Gaps = 34/181 (18%)

Query: 343 EDVSRTEKKR---KSEEARIAREVEAHEKRI---RKELEK-QDILRRKREEQIRKEMERQ 395
           ED+S  E++    KSE   +   +E  E+ +    + L   +  L   R  +I+ E+ + 
Sbjct: 744 EDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKL 803

Query: 396 DRERRKEEERL------------LREKLREEERYLREQRRELERREKFLQK--ESIRAEK 441
           + E  + E RL             +E L +E + L+EQR +L+ + K ++K  E++  +K
Sbjct: 804 EEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKK 863

Query: 442 RRQKEELRRVK-------------EAERLKVANERAVARRIAKESMALVEDERLELMELA 488
              +EEL  ++             + ER ++  +     R  +E  A +E +R  L EL 
Sbjct: 864 EELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELK 923

Query: 489 A 489
           A
Sbjct: 924 A 924

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 45.0 bits (107), Expect = 7e-05
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 375 EKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQK 434
           EK     R + E    E E   RE++KEEE+++  + R  + ++++   ++E   + L  
Sbjct: 203 EKAIEAERAKAEAAEAEQELL-REKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLA 261

Query: 435 ESIRAEKRRQKEELRRVKE 453
           E  R  + + +E+   +KE
Sbjct: 262 EQERMLEHKLQEQEELLKE 280

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.9 bits (109), Expect = 7e-05
 Identities = 27/145 (18%), Positives = 57/145 (39%), Gaps = 1/145 (0%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
           + + + +  E  +    E  E+   +  E ++ L    E   + + E ++ E +++  + 
Sbjct: 734 QLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQE 793

Query: 407 LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVA 466
             E+L EE      +   LER  + L++   R E+  ++ E    +  E+L    E    
Sbjct: 794 ELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEE 853

Query: 467 RRIAKESM-ALVEDERLELMELAAS 490
                E +   +E+   E  EL   
Sbjct: 854 LEKELEELKEELEELEAEKEELEDE 878

Length = 1163

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 46.1 bits (109), Expect = 7e-05
 Identities = 32/180 (17%), Positives = 76/180 (42%), Gaps = 2/180 (1%)

Query: 330 NAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIR 389
           +  +  +RR   DE+  +  +K   +  +  ++ +   + + KEL++ +I R   EE+  
Sbjct: 301 SELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEE 360

Query: 390 KEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEK--RRQKEE 447
           +  + Q++  + EEE L ++KL  E      + +E E   K  +++  +       Q+E+
Sbjct: 361 QLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEED 420

Query: 448 LRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQN 507
           L + ++ E LK+  E   +    +  +   ++E  +        K          +  + 
Sbjct: 421 LLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKSEDLLKETKL 480

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 45.9 bits (110), Expect = 7e-05
 Identities = 38/146 (26%), Positives = 71/146 (48%), Gaps = 16/146 (10%)

Query: 346 SRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREE--QIRKEMERQDRERRKEE 403
              E K K  E    R +E  +K    E  K++ L   +EE  ++R E E++ RERR E 
Sbjct: 27  KIAEAKIKEAEEEAKRILEEAKKEA--EAIKKEALLEAKEEIHKLRNEFEKELRERRNEL 84

Query: 404 ERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANER 463
           ++L +  L++EE         L+R+ + L+K     EK+ ++ E ++ +E E+ +   E 
Sbjct: 85  QKLEKRLLQKEEN--------LDRKLELLEKREEELEKKEKELE-QKQQELEKKEEELEE 135

Query: 464 AVARRIAK--ESMALVEDE-RLELME 486
            +  ++ +      L  +E +  L+E
Sbjct: 136 LIEEQLQELERISGLTAEEAKEILLE 161

Length = 520

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.9 bits (108), Expect = 9e-05
 Identities = 32/142 (22%), Positives = 74/142 (52%), Gaps = 6/142 (4%)

Query: 343  EDVSRTEKKRKSEEARIARE-VEAHEKRIRKELEKQDILRRKREEQIRK--EMERQDRER 399
             + ++ E +  ++EA  A E  EA EK+  +  +K D  ++K EE  +K  E +++  E 
Sbjct: 1345 AEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEE-KKKADEAKKKAEED 1403

Query: 400  RKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKV 459
            +K+ + L  +K    ++   E +++ E ++K  + +    E ++  E  ++ +EA++ + 
Sbjct: 1404 KKKADEL--KKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEE 1461

Query: 460  ANERAVARRIAKESMALVEDER 481
            A ++A   + A E+    E+ +
Sbjct: 1462 AKKKAEEAKKADEAKKKAEEAK 1483

Length = 2084

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 44.9 bits (106), Expect = 9e-05
 Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 14/124 (11%)

Query: 371 RKELEKQDILRRKREEQIRKEMERQDRERRKEEERLL---REKLREEERYLRE----QRR 423
           + E +++    +  EE   K+   Q+R ++ E+ERL    ++K  EE     +    Q+ 
Sbjct: 76  KGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQE 135

Query: 424 ELERREKFLQKESIRAEKRRQKEELRRVK-------EAERLKVANERAVARRIAKESMAL 476
           E  R+    QK+   A K +   E  ++K       +AE    A E A A+  A  +   
Sbjct: 136 EQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKK 195

Query: 477 VEDE 480
            E E
Sbjct: 196 AEAE 199

Length = 387

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.5 bits (107), Expect = 1e-04
 Identities = 35/127 (27%), Positives = 73/127 (57%), Gaps = 11/127 (8%)

Query: 337  RRVSHDEDVSRTEKKRKSEEARIAREV---EAHEKRIRKELEKQDILRRKREEQIRKEME 393
            ++   DE  +    K+++EEA+ A E+   EA EK+  +EL+K +   + + E+ +KE E
Sbjct: 1681 KKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAE 1740

Query: 394  RQDRERRKEEERLLREKLREEERYLREQRRELERR--EKFLQKESIRAEKRRQKEELRRV 451
                +++K EE    E   EE++ +   ++E E++  E   +KE++  E+  +++E RR+
Sbjct: 1741 ---EDKKKAEEAKKDE---EEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRM 1794

Query: 452  KEAERLK 458
            +  +++K
Sbjct: 1795 EVDKKIK 1801

Length = 2084

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 45.4 bits (108), Expect = 1e-04
 Identities = 38/164 (23%), Positives = 69/164 (42%), Gaps = 20/164 (12%)

Query: 349 EKKRKSEEARIAREVEAHEK---RIRKELEKQDILRRKREEQI---RKEMERQDRERRKE 402
           ++KR+ E   + +E EA E+    I ++L   +    K  E+I    K +E  ++   + 
Sbjct: 218 KEKREYEGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEEL 277

Query: 403 EERLLRE------KLREEERYLREQRRELERREKFLQKESIRAEKRRQK--EELRRVK-E 453
            +++         +++E+   L  +   LER     ++E   AE+R  K   E+ ++  E
Sbjct: 278 NKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAE 337

Query: 454 AERLKVANERAVARRIA-----KESMALVEDERLELMELAASSK 492
            E L+   E    RR        E    +ED R EL E+     
Sbjct: 338 IEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFA 381

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 31/151 (20%), Positives = 66/151 (43%), Gaps = 6/151 (3%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E++ R     + E  ++   +E  E+ + +  E+ + L+ + EE    E E +  E    
Sbjct: 719 EELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEE---LEEELESLEEALA 775

Query: 403 EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
           + +   E+L E+ + L+E+  ELE   +  ++     E+  +  E RR +  + ++   E
Sbjct: 776 KLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEE 835

Query: 463 RAVARRIAKESMALVEDERLELMELAASSKG 493
                   +E +  +E+E  EL +     K 
Sbjct: 836 E---IEELEEKLDELEEELEELEKELEELKE 863

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.4 bits (108), Expect = 1e-04
 Identities = 35/159 (22%), Positives = 65/159 (40%), Gaps = 8/159 (5%)

Query: 341 HDEDVSRTEKKRKSEEARIAR------EVEAHEKRIRKEL-EKQDILRRKREEQIRKEME 393
             E ++  E++ +  EA++        E+      + ++L E ++ L     E    E E
Sbjct: 307 LRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAE 366

Query: 394 RQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE 453
            ++ E R EE     E LR +   L  Q   L    + L+    R E RR++ +    + 
Sbjct: 367 LEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEEL 426

Query: 454 AERLKVANERAVARRIAKESMALVE-DERLELMELAASS 491
            ++L+ A  + +   + +    L E  E LE +E A   
Sbjct: 427 LKKLEEAELKELQAELEELEEELEELQEELERLEEALEE 465

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 27/123 (21%), Positives = 51/123 (41%), Gaps = 17/123 (13%)

Query: 337 RRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREE---QIRKEME 393
            R+   E+  R  +K   E    A E+E   K+  +E +  +    + EE   ++ +E  
Sbjct: 12  ERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAA 71

Query: 394 RQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE 453
             + ER +     L  ++ E    + +   E E++E          E R+ ++ELR  +E
Sbjct: 72  ASEEERER-----LEAEVDEATAEVAKLEEEREKKEA---------ETRQLQQELREAQE 117

Query: 454 AER 456
           A  
Sbjct: 118 AHE 120

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.8 bits (106), Expect = 2e-04
 Identities = 35/182 (19%), Positives = 71/182 (39%), Gaps = 20/182 (10%)

Query: 342 DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
            E     E + + EE  + +E+EA E+R+  ELE++     + + ++ +    +    + 
Sbjct: 213 KELKKLEEIQEEQEEEELEQEIEALEERL-AELEEEKERLEELKARLLEIESLELEALKI 271

Query: 402 EE------ERLLREKLREEERY-------LREQRRELERREKFLQKESIRAEKRRQKEEL 448
            E      ERLL E   + ER           +      R    + E +  + +  +E L
Sbjct: 272 REEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERL 331

Query: 449 RR-VKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQN 507
            +  ++ E+L+   E     +     +    +ERL+ +E       L   +    E L+ 
Sbjct: 332 EKLEEKLEKLESELEELAEEKNELAKLL---EERLKELEERLEE--LEKELEKALERLKQ 386

Query: 508 LD 509
           L+
Sbjct: 387 LE 388

Length = 908

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 45.1 bits (107), Expect = 2e-04
 Identities = 34/142 (23%), Positives = 58/142 (40%), Gaps = 10/142 (7%)

Query: 352 RKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKL 411
           RK E+A    E+E  E+ I        I+  KR++  R   ER+  ER +     L ++ 
Sbjct: 170 RKKEKAL--EELEEVEENIE---RLDLIIDEKRQQLERLRREREKAERYQA----LLKEK 220

Query: 412 REEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAK 471
           RE E Y   + +E   R+K    E   A    + E+L         ++     +   + K
Sbjct: 221 REYEGYELLKEKEALERQK-EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNK 279

Query: 472 ESMALVEDERLELMELAASSKG 493
           +   L E+E+L + E     + 
Sbjct: 280 KIKDLGEEEQLRVKEKIGELEA 301

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 39/179 (21%), Positives = 74/179 (41%), Gaps = 24/179 (13%)

Query: 343 EDVSRTEKKRKSEEARIA------REVEAHEKRIRKELEKQDILRRKREEQIRKEMERQD 396
           E++   E+     +  I       + ++   + + +ELE+ +      E ++    +R++
Sbjct: 765 EELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRE 824

Query: 397 R-----ERRKEEERLLREKLRE----------EERYLREQRRELERREKFLQKESIRAEK 441
           R     E  +EE   L EKL E          E   L+E+  ELE  ++ L+ E    E+
Sbjct: 825 RLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEE 884

Query: 442 RRQK--EELRRVK-EAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTI 497
            +++  EELR ++ E   LK   E+   R    E+     +  L  +E     +   T+
Sbjct: 885 EKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTL 943

Length = 1163

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 45.1 bits (106), Expect = 2e-04
 Identities = 33/89 (37%), Positives = 51/89 (57%), Gaps = 4/89 (4%)

Query: 344 DVSRTEKKRKSEEA--RIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
           D    E+ R  +E   R A E++  EK+  + LE+++  R +RE   R E ER +RER  
Sbjct: 431 DKDHAERARIEKENAHRKALEMKILEKKRIERLEREERERLERERMERIERERLERERL- 489

Query: 402 EEERLLREKLREEERYLREQRRELERREK 430
           E ERL R++L E +R  R +R  ++R E+
Sbjct: 490 ERERLERDRL-ERDRLDRLERERVDRLER 517

Length = 1021

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 42/153 (27%), Positives = 68/153 (44%), Gaps = 11/153 (7%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRI------RKELEKQDILRRKREEQIRKEMERQD 396
           E++SR     + + AR+  EVE  E+RI        ELE +     +R E+  +E+   +
Sbjct: 722 EELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAE 781

Query: 397 RERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAER 456
            E  + E ++  E+L+EE + LRE   EL      L +E+    +R +  E R      R
Sbjct: 782 AEIEELEAQI--EQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERR 839

Query: 457 LKVANERAVARRIAKESMALVEDERLELMELAA 489
           L+   E+        E +  +  E  EL EL  
Sbjct: 840 LEDLEEQI---EELSEDIESLAAEIEELEELIE 869

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 28/128 (21%), Positives = 59/128 (46%), Gaps = 5/128 (3%)

Query: 367 EKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELE 426
           E+  R++ E ++ + +  E+  R + E ++ E    E     ++  EE + L ++  ELE
Sbjct: 1   EEAEREQQELEERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELE 60

Query: 427 RREKFLQKESIRAEKRRQKEELRRVK---EAERLKVANER--AVARRIAKESMALVEDER 481
              + L++E+  +E+ R++ E    +   E  +L+   E+  A  R++ +E     E   
Sbjct: 61  EENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQELREAQEAHE 120

Query: 482 LELMELAA 489
               EL  
Sbjct: 121 RARQELLE 128

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 33/147 (22%), Positives = 78/147 (53%), Gaps = 14/147 (9%)

Query: 343  EDVSRTEKKRKSEEARIAREVE--AHEKRIRKELEKQDILRRKREEQIRK---EMERQDR 397
            E+ +   +K+K E  + A   +  A EK+   E +K+    +K+ ++++K     ++ D 
Sbjct: 1363 EEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADE 1422

Query: 398  ERRKEEERLLREKLR---EEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEA 454
             ++K EE+   ++ +   EE +   E +++ E  +K  ++   +AE+ ++ +E +  K+A
Sbjct: 1423 AKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKK-AEEAKKKAEEAKKADEAK--KKA 1479

Query: 455  ERLKVANERAVARRIAKESMALVEDER 481
            E  K A+E   A++ A+E+    ++ +
Sbjct: 1480 EEAKKADE---AKKKAEEAKKKADEAK 1503

Length = 2084

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.0 bits (104), Expect = 3e-04
 Identities = 35/147 (23%), Positives = 64/147 (43%), Gaps = 3/147 (2%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E++    ++ +  E  I    E  E       E +++L + +  + R E   +  E+ + 
Sbjct: 284 EELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLES 343

Query: 403 EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
           E   L E+  E  + L E+ +ELE R + L+KE  +A +R ++ E    +  E L     
Sbjct: 344 ELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELA-ELS 402

Query: 463 RAVARRIA--KESMALVEDERLELMEL 487
            A+       +E    +E+   EL EL
Sbjct: 403 AALEEIQEELEELEKELEELERELEEL 429

Length = 908

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 42/154 (27%), Positives = 69/154 (44%), Gaps = 16/154 (10%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E++    ++ K +   +  E+E  E  + +ELE+         E+ ++E+E +     +E
Sbjct: 319 EELEERLEELKEKIEALKEELEERET-LLEELEQL----LAELEEAKEELEEKLSALLEE 373

Query: 403 EERL---LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK------E 453
            E L   LRE+L E E  L E R ELE  ++  + ES+     R  E L  +K      E
Sbjct: 374 LEELFEALREELAELEAELAEIRNELEELKR--EIESLEERLERLSERLEDLKEELKELE 431

Query: 454 AERLKVANERAVARRIAKESMALVEDERLELMEL 487
           AE  ++  E        +E    +E+ R  L EL
Sbjct: 432 AELEELQTELEELNEELEELEEQLEELRDRLKEL 465

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 35/153 (22%), Positives = 55/153 (35%), Gaps = 8/153 (5%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK--EEE 404
           R E +   EE    R+      R    L K         EQ+ + + +  +E  +   E 
Sbjct: 704 RKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEI 763

Query: 405 RLLREKLREEERYLREQRRELERREKFLQKESIRAEK-RRQKEELRRVKEAERLKVAN-- 461
             L E+L E E  L E   E+E  E  +++     +  R   +ELR        + AN  
Sbjct: 764 EELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLR 823

Query: 462 ---ERAVARRIAKESMALVEDERLELMELAASS 491
              E    R  A E      +E++E +     S
Sbjct: 824 ERLESLERRIAATERRLEDLEEQIEELSEDIES 856

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 37/149 (24%), Positives = 67/149 (44%), Gaps = 4/149 (2%)

Query: 337 RRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQI-RKEMERQ 395
           R  S +  ++ TE++ +  E +I        + +  E+E+ + L  + E ++     ER 
Sbjct: 825 RLESLERRIAATERRLEDLEEQIEEL-SEDIESLAAEIEELEELIEELESELEALLNERA 883

Query: 396 DRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAE 455
             E      R   E+L EE R L  +R EL R  + L+++  + E R +  E+R     E
Sbjct: 884 SLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQE 943

Query: 456 RLKVANERAVARRIAKESMALVEDERLEL 484
           RL  + E ++    A+     +ED+  E 
Sbjct: 944 RL--SEEYSLTLEEAEALENKIEDDEEEA 970

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 30/133 (22%), Positives = 57/133 (42%), Gaps = 9/133 (6%)

Query: 362 EVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRE-RRKEEERLLREKLRE-----EE 415
           + E   + +++ +++      + E Q+ + +E  +      EEE    +KL E     EE
Sbjct: 168 KYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEE 227

Query: 416 RYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMA 475
             L ++   LE R   L++E  R E+ + +       E E LK+  E     R  +  + 
Sbjct: 228 EELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEEL---RELERLLE 284

Query: 476 LVEDERLELMELA 488
            +E++   L EL 
Sbjct: 285 ELEEKIERLEELE 297

Length = 908

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 27/161 (16%), Positives = 67/161 (41%), Gaps = 3/161 (1%)

Query: 348 TEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLL 407
            E++    E       +  ++   KE EK+     K  ++ ++E+E  ++E   +E  + 
Sbjct: 294 KEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKE--LKELEIK 351

Query: 408 REKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE-AERLKVANERAVA 466
           RE   EEE  L + + +LE+ E+ L  +     +R       + +E   + +   E  + 
Sbjct: 352 REAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLL 411

Query: 467 RRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQN 507
             ++++   L+++E+ E +++    +             + 
Sbjct: 412 LELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKE 452

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.5 bits (103), Expect = 5e-04
 Identities = 38/147 (25%), Positives = 64/147 (43%), Gaps = 7/147 (4%)

Query: 351 KRKSEEARIAREVEAHEK--RIRKELEK-QDILRRKREEQIRKEMERQDRERRKEEERLL 407
           +    E R         K   +RKELE+ ++ L R  EE    + E ++ E+  EE +  
Sbjct: 216 QELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSE 275

Query: 408 REKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVAR 467
            E+LREE   L+E+  EL+   + L+ E     +R ++ E    +  ERL+   E+  A 
Sbjct: 276 LEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEAL 335

Query: 468 R----IAKESMALVEDERLELMELAAS 490
           +      +  +  +E    EL E    
Sbjct: 336 KEELEERETLLEELEQLLAELEEAKEE 362

Length = 1163

>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523)

 Score = 42.4 bits (100), Expect = 5e-04
 Identities = 33/140 (23%), Positives = 66/140 (47%), Gaps = 8/140 (5%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E   + E + K +E    +  +A  +R R E E++    +++ +Q ++  + QD   RK 
Sbjct: 61  EKTRQAELEAKIKEYEAQQA-QAKLERARVEAEERRKTLQEQTQQEQQRAQYQDELARKR 119

Query: 403 EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
            ++ L ++ R+ E  L+ Q       E  L++E++R     +  E+RR    E  ++  E
Sbjct: 120 YQKELEQQRRQNEELLKMQ------EESVLRQEAMRRATEEEILEMRRETIEEEAELERE 173

Query: 463 RAVARRIAKESMALVEDERL 482
              A+  A E+    ++ER 
Sbjct: 174 NIRAKIEA-EARGRAKEERE 192

This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with pfam00004. This domain has a conserved LER sequence motif. Length = 276

>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 26/123 (21%), Positives = 55/123 (44%), Gaps = 18/123 (14%)

Query: 375 EKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQK 434
           +K +  +++ ++ I+K  E+  RE+ + EE L  EK  EE+R  R   ++ E  ++    
Sbjct: 120 KKIETYQKENKDVIQKNKEKSTREQEELEEALEFEKEEEEQR--RLLLQKEEEEQQMN-- 175

Query: 435 ESIRAEKRRQKEELRRVKEAERLKVANERA---VARRIAKESMALVEDERLELMELAASS 491
                 KR+ K+ L      + L+ +   A   +A+         ++ E+ +  +    S
Sbjct: 176 ------KRKNKQAL-----LDELETSTLPAAELIAQHKKNSVKLEMQVEKPKPEKPNTFS 224

Query: 492 KGL 494
            G+
Sbjct: 225 TGI 227

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 309

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.2 bits (102), Expect = 6e-04
 Identities = 37/146 (25%), Positives = 71/146 (48%), Gaps = 14/146 (9%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKR---IRKELEKQ-DILRRKREEQIRKEMERQDRERR 400
           VS+ +++++  E ++    E + +R   + +ELEKQ + L R+ E+   +  +    E R
Sbjct: 167 VSKYKERKEEAERKL-ERTEENLERLEDLLEELEKQLEKLERQAEK--AERYQELKAELR 223

Query: 401 KEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVA 460
           + E  LL  KL+E    LR++  ELE     L++E    ++  ++ E     E  + ++ 
Sbjct: 224 ELELALLLAKLKE----LRKELEELEEELSRLEEELEELQEELEEAEKE--IEELKSELE 277

Query: 461 NERAVARRIAKESMALVED-ERLELM 485
             R     + +E + L E+ E LE  
Sbjct: 278 ELREELEELQEELLELKEEIEELEGE 303

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.2 bits (102), Expect = 6e-04
 Identities = 31/142 (21%), Positives = 58/142 (40%), Gaps = 9/142 (6%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
            ++   +++ + + + +  E+E   + +R+EL +          +IR E+E   RE    
Sbjct: 354 AELEEAKEELEEKLSALLEELEELFEALREELAE----LEAELAEIRNELEELKREIESL 409

Query: 403 EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN- 461
           EERL R   R E+     +    E   +  + ++   E   + EEL    E  R ++   
Sbjct: 410 EERLERLSERLEDL----KEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKEL 465

Query: 462 ERAVARRIAKESMALVEDERLE 483
           ER +A    +      E   LE
Sbjct: 466 ERELAELQEELQRLEKELSSLE 487

Length = 1163

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 42.6 bits (100), Expect = 6e-04
 Identities = 28/117 (23%), Positives = 57/117 (48%), Gaps = 7/117 (5%)

Query: 380 LRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRE----LERREKFLQKE 435
           ++ ++    + E +R+ +E +  EE  L+ K   E+  L++  +E     E++++  + E
Sbjct: 67  IQSQQSSAKKGEQQRKKKEEQVAEE--LKPKQAAEQERLKQLEKERLKAQEQQKQAEEAE 124

Query: 436 SIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSK 492
                +++Q+EE  R   AE+ K A E A A+  A+ +      E  +  E AA + 
Sbjct: 125 KQAQLEQKQQEEQARKAAAEQKKKA-EAAKAKAAAEAAKLKAAAEAKKKAEEAAKAA 180

Length = 387

>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein

 Score = 43.0 bits (101), Expect = 6e-04
 Identities = 43/164 (26%), Positives = 75/164 (45%), Gaps = 20/164 (12%)

Query: 330 NAFISSDRRVSHDEDVSRTEKK--RKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQ 387
             F+S     SH   VS +     +K  E  +     A   R + +L            Q
Sbjct: 24  PKFLSQPLEGSHHLGVSTSALSSLQKQVEESMTLLQRAELIRSKSKLI-----------Q 72

Query: 388 IRKEMERQDRERRKEEERLLREKLREEERYLREQRR--ELERREKFLQKESIRAEK--RR 443
           +  E+ +++ E ++ +  L R+     E Y RE  R  ELE R K L++   +AE     
Sbjct: 73  LENELMQKELEHKRAQIELERKASTLAENYERELDRNLELEVRLKALEELEKKAENEAAE 132

Query: 444 QKEELRRVK---EAERLKVANERAVARRIAKESMALVEDERLEL 484
            +EE + +K   +AE LK+ NE+    + AKES++ ++++  E+
Sbjct: 133 AEEEAKLLKDKLDAESLKLQNEKEDQLKEAKESISRIKNDLSEM 176

This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated. Length = 722

>gnl|CDD|226127 COG3599, DivIVA, Cell division initiation protein [Cell division and chromosome partitioning]

 Score = 41.3 bits (97), Expect = 7e-04
 Identities = 31/148 (20%), Positives = 51/148 (34%), Gaps = 16/148 (10%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEME---RQDRERRKEE-- 403
               +  +A    E EA E +   E E  DIL  KR     + +    +   +R  E+  
Sbjct: 63  AADAEDSQAIQQAETEAEELKQAAEAEADDIL--KRASAQAQRVFGKAQYKADRYLEDAK 120

Query: 404 -----ERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
                E L R+   E +R   +   +L       ++E      R   +E+    E     
Sbjct: 121 IAQELEDLKRQAQVERQRLRSDIEAQLAS----AKQEDWDEILRSTVDEVEAANEEAERL 176

Query: 459 VANERAVARRIAKESMALVEDERLELME 486
               +A A R+  E    V+ +  EL  
Sbjct: 177 ADAAQADADRLRDECDIYVDTKLAELET 204

Length = 212

>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

 Score = 42.3 bits (99), Expect = 7e-04
 Identities = 37/144 (25%), Positives = 63/144 (43%), Gaps = 17/144 (11%)

Query: 346 SRTEKKRKS----EEARIAREVEAHEKRIRKELEK-----QDILRRKREE------QIRK 390
           + TE +R+S     E  I++ +E  E  IR E +       D  R  R E      + +K
Sbjct: 86  AMTEIERESILFEREEEISKLMERRELAIRMEQQHRSSGCTDTRRSTRYEPLTSAAEEKK 145

Query: 391 EMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRR 450
           +   + ++ R+ EERL  E  R  E    +  +ELE  E+ LQ+E   +      E++ R
Sbjct: 146 KKLLELKKTREREERLYSE--RHIELQRFKDYKELEESEQGLQEEYTPSYAEEAVEDISR 203

Query: 451 VKEAERLKVANERAVARRIAKESM 474
             +   L   N+  V R +   ++
Sbjct: 204 TDDFAELYDFNQCRVGRDMVARNV 227

Length = 521

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 37/140 (26%), Positives = 70/140 (50%), Gaps = 22/140 (15%)

Query: 344 DVSRTEKKRKSEEARIAR------EVEAHEKRIRKELEK------QDILRRKREEQIRKE 391
           ++ R EK+ K  E  + +      E E   + +RKELE+      ++     REE +   
Sbjct: 613 ELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELS 672

Query: 392 ME--------RQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQK-ESIRAEKR 442
            E         +  +RR+E ++ L EKL+EE     + ++ELE+ EK L++ E +R + +
Sbjct: 673 RELAGLRAELEELEKRREEIKKTL-EKLKEELEEREKAKKELEKLEKALERVEELREKVK 731

Query: 443 RQKEELRRVKEAERLKVANE 462
           + K  L+    ++  ++A+E
Sbjct: 732 KYKALLKERALSKVGEIASE 751

Length = 880

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 30/143 (20%), Positives = 54/143 (37%), Gaps = 14/143 (9%)

Query: 353 KSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDR-----------ERRK 401
           + E      E+E     +++  EK + LR +  E   +  E Q             E++K
Sbjct: 245 QEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQK 304

Query: 402 EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN 461
           +  R     L  +   L  Q  ELE +   L +E   AE   + EEL+   E+   ++  
Sbjct: 305 QILRERLANLERQLEELEAQLEELESKLDELAEEL--AELEEKLEELKEELESLEAELEE 362

Query: 462 ERAVARRIAKESMALVEDERLEL 484
             A      +  +  +E++   L
Sbjct: 363 LEAE-LEELESRLEELEEQLETL 384

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 32/111 (28%), Positives = 49/111 (44%), Gaps = 8/111 (7%)

Query: 379 ILRRKRE----EQIRKEMERQDRERRKEEERLL--REKLREEERYLREQRRELERREKFL 432
           IL R+RE    E+  +E+E +  E  K    L    E+L EE   LR++  EL R+   L
Sbjct: 672 ILERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISAL 731

Query: 433 QKESIRAEKRRQK-EELRRVKEAERLKVANERAVAR-RIAKESMALVEDER 481
           +K+  R E   ++ EE       E  ++  E      R+ +    L E E 
Sbjct: 732 RKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEA 782

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 37/151 (24%), Positives = 61/151 (40%), Gaps = 23/151 (15%)

Query: 367 EKRIRKELEKQDILR-----RKREEQIRKEMERQDRERRKEEERLLREKL-REEER---- 416
           E  I   LE+  +          EE   K++  ++ + R+ E R +RE L REE +    
Sbjct: 164 ESEIASILEESGLASDEKKLTPFEELELKKLSPEEAKARRAELRKMRELLFREEAKAKRI 223

Query: 417 -------YLREQRRELER-----REKFLQKESIRAEKRRQKEELRRVKEAERLKVANERA 464
                  Y R  ++E  +      E+ ++ +   A +  +K E RR +E   LK  N   
Sbjct: 224 KKIKSKKYHRVHKKEKLKEELKEFEELVKADPEAALEELEKLERRRAEERMTLKHKNTSK 283

Query: 465 VARRIAKESMA-LVEDERLELMELAASSKGL 494
            A+ + K   A   E+ R  L E     + L
Sbjct: 284 WAKSMLKTGRAKYDEEARKALEEQLRQGEEL 314

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 41.9 bits (99), Expect = 9e-04
 Identities = 24/73 (32%), Positives = 45/73 (61%), Gaps = 5/73 (6%)

Query: 387 QIRKE-MERQDRERRKEEERLLR--EKLREEERYLREQRRELERREKFLQKESIRAEKRR 443
           ++  E + + D+ R +EEE++L+  E+ R+EE   +++ ++ E RE  L K S   E++R
Sbjct: 252 KLSPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLS--PEEQR 309

Query: 444 QKEELRRVKEAER 456
           + EE  R K+A +
Sbjct: 310 KLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.4 bits (99), Expect = 0.001
 Identities = 37/166 (22%), Positives = 82/166 (49%), Gaps = 11/166 (6%)

Query: 334  SSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRK--E 391
              + +   D    + E+K+K++EA+   E    +K+   EL+K    ++K +E  +K  E
Sbjct: 1373 KEEAKKKADAAKKKAEEKKKADEAKKKAE---EDKKKADELKKAAAAKKKADEAKKKAEE 1429

Query: 392  MERQDRERRKEEERLLREKLR---EEERYLREQRRELERREKFLQKESIRAEKRRQKEEL 448
             ++ D  ++K EE    ++ +   EE +   E +++ E  +K   +   +AE+ ++ +E 
Sbjct: 1430 KKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKK-ADEAKKKAEEAKKADEA 1488

Query: 449  RRVKEAERLKV--ANERAVARRIAKESMALVEDERLELMELAASSK 492
            ++  E  + K   A + A A++ A E+    E ++ +  + A  +K
Sbjct: 1489 KKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAK 1534

Length = 2084

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 35/152 (23%), Positives = 62/152 (40%), Gaps = 7/152 (4%)

Query: 342 DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEME---RQDRE 398
              +   E +       I   +EA E+ +++  + ++I   + EE++ +E+E    +  E
Sbjct: 184 KAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAE 243

Query: 399 RRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRV-KEAERL 457
             +E+ERL   K R  E    E      R E+  + E +  E   + E L  + +E E L
Sbjct: 244 LEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEEL 303

Query: 458 KVANERAVA---RRIAKESMALVEDERLELME 486
           +   E   A               +ERLE +E
Sbjct: 304 EEELEGLRALLEELEELLEKLKSLEERLEKLE 335

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 34/155 (21%), Positives = 65/155 (41%), Gaps = 4/155 (2%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E   +  +  K        ++E  E ++ + LE  + L    EE++++  + ++ +  +E
Sbjct: 167 EKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQE 226

Query: 403 EERL--LREKLREEERYLREQRRELERREKFLQK-ESIRAEKRRQKEELRRVKEAERLKV 459
           EE L    E L E    L E++  LE  +  L + ES+  E  + +EE  R  E    ++
Sbjct: 227 EEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEEL 286

Query: 460 ANERAVARRIAKESMALVEDERLELMELAASSKGL 494
             +      + +E   L E+    L  L    + L
Sbjct: 287 EEKIERLEELEREIEELEEEL-EGLRALLEELEEL 320

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 21/127 (16%), Positives = 45/127 (35%), Gaps = 7/127 (5%)

Query: 346 SRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEER 405
                + + EE    RE     K+  KELE       +R  Q+ + ++  +    + E  
Sbjct: 577 ELRLLRTRKEELEELRERLKELKKKLKELE-------ERLSQLEELLQSLELSEAENELE 629

Query: 406 LLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAV 465
              E+L  E   L  Q    E  +  L++   + E+   +      +     ++  +   
Sbjct: 630 EAEEELESELEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEE 689

Query: 466 ARRIAKE 472
             ++ +E
Sbjct: 690 LEQLEEE 696

Length = 908

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 36/152 (23%), Positives = 57/152 (37%), Gaps = 6/152 (3%)

Query: 342 DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
           D++ + T  + K    ++ +      +  R+    Q+ L+R  EE           E + 
Sbjct: 377 DKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKI 436

Query: 402 EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN 461
            E    +E    E   +++Q  +LE+            E    KEE  RV E E  K+  
Sbjct: 437 NELEEEKEDKALE---IKKQEWKLEQLAA--DLSKYEQELYDLKEEYDRV-EKELSKLQR 490

Query: 462 ERAVARRIAKESMALVEDERLELMELAASSKG 493
           E A A   A+ S   V   R     L AS +G
Sbjct: 491 ELAEAEAQARASEERVRGGRAVEEVLKASIQG 522

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 33/156 (21%), Positives = 63/156 (40%), Gaps = 14/156 (8%)

Query: 358 RIAREVEAHEKRIRKELEKQDILR--------RKREEQIRKEMERQDRERRKEEERLLRE 409
           ++ R++         E  K  ++R         K +E+ R   +    E  + E  +  +
Sbjct: 363 KVERKLPELGIWKDVERIKALVIRGYPLAEALSKVKEEERPREKEGTEEEERREITVYEK 422

Query: 410 KLREEERY---LREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVA 466
           ++++ E     L E+  EL+R  + L++E  + E     E  RR    +  K    RA  
Sbjct: 423 RIKKLEETVERLEEENSELKRELEELKREIEKLESEL--ERFRREVRDKVRKDREIRARD 480

Query: 467 RRIAKESMALVEDERLELMELAASSKGLPTIVSLDF 502
           RRI +    L E+++  + EL      L  +  L+ 
Sbjct: 481 RRIERLEKEL-EEKKKRVEELERKLAELRKMRKLEL 515

Length = 652

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 28/153 (18%), Positives = 65/153 (42%), Gaps = 7/153 (4%)

Query: 342 DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
           ++  +  +  +++E+A   ++ E  +K+  +   KQ    + + E   ++  +++ +++ 
Sbjct: 95  EQRAAAEKAAKQAEQAA--KQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQA 152

Query: 402 EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN 461
           EEE   +      E   +++  E +++ +   K    A+ + + EE +   EA + K A 
Sbjct: 153 EEEAKAKAA---AEA--KKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAA 207

Query: 462 ERAVARRIAKESMALVEDERLELMELAASSKGL 494
           E A        + A  E ER           GL
Sbjct: 208 EAAAKAEAEAAAAAAAEAERKADEAELGDIFGL 240

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 25/116 (21%), Positives = 50/116 (43%), Gaps = 6/116 (5%)

Query: 380 LRRKREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIR- 438
           ++++++   +KE ERQ +  ++ EE    ++   E+   +E  +     +   Q E    
Sbjct: 55  IQQQKKPAAKKEQERQKKLEQQAEE--AEKQRAAEQARQKELEQRAAAEKAAKQAEQAAK 112

Query: 439 --AEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSK 492
              EK++Q EE +  + AE    A E    ++  +E+    E+E        A  K
Sbjct: 113 QAEEKQKQAEEAKAKQAAEAKAKA-EAEAEKKAKEEAKKQAEEEAKAKAAAEAKKK 167

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 29/129 (22%), Positives = 60/129 (46%), Gaps = 6/129 (4%)

Query: 357 ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDR-ERRKEEERLLREKLREEE 415
            RI ++ +   K+ ++  +K +    + E+Q   E  RQ   E+R   E+  ++  +  +
Sbjct: 53  NRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAK 112

Query: 416 RYLREQRRELERREKFLQKESIRAE---KRRQKEELRRVKEAERLKVANERAVARRIAKE 472
           +   +Q++  E + K   +   +AE   +++ KEE ++  E E    A   A A++ A E
Sbjct: 113 QAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKA--AAEAKKKAAE 170

Query: 473 SMALVEDER 481
           +    E E 
Sbjct: 171 AKKKAEAEA 179

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase

 Score = 42.2 bits (99), Expect = 0.001
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 13/79 (16%)

Query: 414 EERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKES 473
           E+  L E+RRELE+    L KE   AE+ RQ EE RR +E E+  +  +RA A+   ++ 
Sbjct: 247 EDFLLEEKRRELEK----LAKE--EAERERQAEEQRR-REEEKAAMEADRAQAKAEVEK- 298

Query: 474 MALVEDERL-ELMELAASS 491
                 E+L  L++ A+ S
Sbjct: 299 ----RREKLQNLLKKASRS 313

Length = 1036

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score = 41.7 bits (99), Expect = 0.001
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 409 EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK-EAERLK 458
           E L E    L EQ R+LE     L+   + AE  + + EL R+K E E+LK
Sbjct: 4   EALEERNSELEEQIRQLE-----LKLRDLEAENEKLERELERLKSELEKLK 49

Length = 389

>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 24/116 (20%), Positives = 44/116 (37%), Gaps = 9/116 (7%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLR 408
           +K+ +  E  +    +  +K+++   E  +  R    E  + E   +    +K EE L  
Sbjct: 113 DKELELLEKELDELSKELQKQLQNTAEIIEKKR----ENNKNEERLKFENEKKLEESLEL 168

Query: 409 EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERA 464
           E+         EQ  E     +F + E  R  K    ++L+R  E    +V  E  
Sbjct: 169 ERE-----KFEEQLHEANLDLEFKENEEQRESKWAILKKLKRRAELGSQQVQGEAL 219

Length = 438

>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 7/97 (7%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQI--RKEMERQDRERRKE 402
           + R EK  +  E  I +E      +I +ELEK+     K EE +  R  +E   +E  ++
Sbjct: 363 LERLEKDVEEGEKTIVKEAR----QIEEELEKEVEKLGKEEESLFKRVALEEGLKELEQD 418

Query: 403 EERLLREKLREEERYLREQRRELERREK-FLQKESIR 438
           EE  L+E  +EE+  L + + E    EK F +   +R
Sbjct: 419 EENFLKELSKEEKELLEKLKMEASEVEKLFGRALPVR 455

Length = 455

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.3 bits (96), Expect = 0.002
 Identities = 34/155 (21%), Positives = 74/155 (47%), Gaps = 17/155 (10%)

Query: 342  DEDVSRTEKKR--------KSEEARIAREV-----EAHEKRIRKELEKQDILRRKREEQI 388
            DE   + E+ +        K+EEA+ A E      EA         EK +   +K+EE  
Sbjct: 1318 DEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAK 1377

Query: 389  RK--EMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKE 446
            +K    +++  E++K +E   ++K  E+++   E ++    ++K  + +    EK++  E
Sbjct: 1378 KKADAAKKKAEEKKKADE--AKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADE 1435

Query: 447  ELRRVKEAERLKVANERAVARRIAKESMALVEDER 481
              ++ +EA++   A ++A   + A+E+    E+ +
Sbjct: 1436 AKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAK 1470

Length = 2084

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.7 bits (98), Expect = 0.002
 Identities = 26/121 (21%), Positives = 48/121 (39%), Gaps = 10/121 (8%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAH----EKRIRKELEKQDILRRKREEQIRKEMERQDRE 398
           E+++  + +         +E+E      EK + K LE+     ++ EE I++  E     
Sbjct: 346 EELAEEKNELAKLLEERLKELEERLEELEKELEKALERL----KQLEEAIQELKEELAEL 401

Query: 399 RRKEEERLLREKLREEER-YLREQRRELERREKFLQKESIRAEKRRQK-EELRRVKEAER 456
               EE     +  E+E   L  +  ELE   K L+++  + E +     EL    E   
Sbjct: 402 SAALEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCP 461

Query: 457 L 457
           +
Sbjct: 462 V 462

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 36/164 (21%), Positives = 61/164 (37%), Gaps = 9/164 (5%)

Query: 330 NAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIR 389
            +      ++  +E         + EE     E    E     ELE++    R   E++ 
Sbjct: 262 ESLELEALKIREEELRELERLLEELEEKIERLEELEREIE---ELEEELEGLRALLEELE 318

Query: 390 KEME--RQDRERRKEEERL---LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQ 444
           + +E  +   ER ++ E     L  +L E      E  + LE R K L++     EK  +
Sbjct: 319 ELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELE 378

Query: 445 KE-ELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMEL 487
           K  E  +  E    ++  E A      +E    +E+   EL EL
Sbjct: 379 KALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEEL 422

Length = 908

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 38/178 (21%), Positives = 70/178 (39%), Gaps = 22/178 (12%)

Query: 335 SDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQ--DILRRKREEQIRKEM 392
            +     +  + + E++ KS +  + R +E   + +R++LE+    +   KRE    +E 
Sbjct: 673 EEELAELEAQLEKLEEELKSLKNEL-RSLEDLLEELRRQLEELERQLEELKRELAALEEE 731

Query: 393 ERQDRERRKEEERLLREKLREEERY------LREQRRELERREKFLQKE----------- 435
             Q + R +E E  L E   E E        L E+   LE     L++E           
Sbjct: 732 LEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQAL 791

Query: 436 -SIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSK 492
                E   + EE  R  +A   ++ +      R+ +E +  +E+E  EL E     +
Sbjct: 792 QEELEELEEELEEAERRLDALERELESLEQRRERLEQE-IEELEEEIEELEEKLDELE 848

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 33/154 (21%), Positives = 63/154 (40%), Gaps = 10/154 (6%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRR------KREEQIRKEMERQD 396
           + + R  +  +    R+ +E+E  E+ I +  EK D L        K  E++++E+E  +
Sbjct: 810 DALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELE 869

Query: 397 RERRKEEERL--LREKLREEERYLREQRRELE--RREKFLQKESIRAEKRRQKEELRRVK 452
            E+ + E+ L  L E+  E E  LRE   EL   + E    +E +   + + +     + 
Sbjct: 870 AEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELP 929

Query: 453 EAERLKVANERAVARRIAKESMALVEDERLELME 486
           E E               +  +  +E+E   L  
Sbjct: 930 ELEEELEEEYEDTLETELEREIERLEEEIEALGP 963

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 32/148 (21%), Positives = 67/148 (45%), Gaps = 7/148 (4%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRK----EMERQDRE 398
           E++    ++ +     +  E+E+ E+ + K  E+ + L  KR+    +    E E ++ E
Sbjct: 747 EELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAE 806

Query: 399 RRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
           RR +      E L +    L ++  ELE   + L+++    E   + EEL +  E  + +
Sbjct: 807 RRLDALERELESLEQRRERLEQEIEELEEEIEELEEK--LDELEEELEELEKELEELKEE 864

Query: 459 VANERAVARRIAKESMALVEDERLELME 486
              E    +   ++ +  +E+E+ EL E
Sbjct: 865 -LEELEAEKEELEDELKELEEEKEELEE 891

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 38/179 (21%), Positives = 81/179 (45%), Gaps = 25/179 (13%)

Query: 337 RRVSHDEDVSRTEKKRKSEEARIA------REVEAHEKRIRKELEKQDILRRKREEQI-R 389
           RR   ++++   E++ +  E ++        E+E   + +++ELE+ +  + + E+++  
Sbjct: 822 RRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKE 881

Query: 390 KEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQ--------------KE 435
            E E+++ E    E      +L+EE   LRE+  ELE + + L+              ++
Sbjct: 882 LEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYED 941

Query: 436 SIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAASSKGL 494
           ++  E  R+ E L    E E L   N RA+     +E     E+ + +  +L  + + L
Sbjct: 942 TLETELEREIERLEE--EIEALGPVNLRAIEEY--EEVEERYEELKSQREDLEEAKEKL 996

Length = 1163

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 13/140 (9%)

Query: 343  EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQD------ 396
            E+  + EKK   EE++    +E  E  I + + ++ I+  K E +  + +  +       
Sbjct: 893  EEKEKEEKKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKE 952

Query: 397  -------RERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELR 449
                    ER K       E        + E   + ER  K   K+    E++++     
Sbjct: 953  EDNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREI 1012

Query: 450  RVKEAERLKVANERAVARRI 469
              +  +R K   E  V+   
Sbjct: 1013 IEETCQRFKEFLELFVSINR 1032

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 34/137 (24%), Positives = 70/137 (51%), Gaps = 11/137 (8%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKRE--EQIR------KEMER 394
            ++ R EK+ K  E +  R++    + + K L+K+  L + +E  EQ++      K+   
Sbjct: 459 AELKRIEKELKEIEEKE-RKLRKELRELEKVLKKESELIKLKELAEQLKELEEKLKKYNL 517

Query: 395 QDRERRKEEERLLREKLREEERYLREQRRELERREKFLQK-ESIRAEKRRQKEELRRV-K 452
           ++ E++ EE   L+EKL + +  ++  ++ELE+ E+  +K   +  +    +EEL  + K
Sbjct: 518 EELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELAELLK 577

Query: 453 EAERLKVANERAVARRI 469
           E E L   +   +  R+
Sbjct: 578 ELEELGFESVEELEERL 594

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 42/140 (30%), Positives = 67/140 (47%), Gaps = 16/140 (11%)

Query: 367 EKRIRKELEKQDILRR-------------KREEQIRKEMERQDRERRKEEERLLREKLRE 413
           EK + +E ++   L               KR E++RKE+E  +++  +EE   LRE+  E
Sbjct: 611 EKELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLE 670

Query: 414 EERYLREQRRELERREKFLQ--KESIRAEKRRQKEELRRVKEAERLKVANER-AVARRIA 470
             R L   R ELE  EK  +  K+++   K   +E  +  KE E+L+ A ER    R   
Sbjct: 671 LSRELAGLRAELEELEKRREEIKKTLEKLKEELEEREKAKKELEKLEKALERVEELREKV 730

Query: 471 KESMALVEDERLELMELAAS 490
           K+  AL+++  L  +   AS
Sbjct: 731 KKYKALLKERALSKVGEIAS 750

Length = 880

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 39.3 bits (91), Expect = 0.002
 Identities = 34/103 (33%), Positives = 64/103 (62%), Gaps = 9/103 (8%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
           R E KR++ E R+ RE EA     R++ E++    R++EE+ +++ E ++++ ++E+ER+
Sbjct: 57  REELKRRAAEERLRREEEA-----RRQEEER---AREKEEKAKRKAEEEEKQEQEEQERI 108

Query: 407 LREKLREEERYLRE-QRRELERREKFLQKESIRAEKRRQKEEL 448
            ++K   E R   E +R  LER + F Q E  R E++++ EE+
Sbjct: 109 QKQKEEAEARAREEAERMRLEREKHFQQIEQERLERKKRLEEI 151

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 397 RERRKEEERLLREKLREEERYLREQRR--ELERREKFLQKESIRAEKRRQKEELRRVKEA 454
           ++R K EE+  R + RE E   RE+R+  E +R  +  ++E +  E+ ++KEE  R +  
Sbjct: 6   KKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKERE 65

Query: 455 ERLKVANE 462
           E+ +   E
Sbjct: 66  EQARKEQE 73

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 14/85 (16%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
                KKR   E +         +R ++E E       +REE+ + E +R+   + +EE 
Sbjct: 1   KKIGAKKRAKLEEK-------QARRQQREAE-----EEEREERKKLEEKREGERKEEEEL 48

Query: 405 RLLREKLREEERYLREQRRELERRE 429
              REK +EEE   R++R E  R+E
Sbjct: 49  EEEREKKKEEEE--RKEREEQARKE 71

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 41.3 bits (98), Expect = 0.002
 Identities = 35/135 (25%), Positives = 68/135 (50%), Gaps = 18/135 (13%)

Query: 370 IRKELEKQDILRRKRE-EQIRKEMERQDRERRKEEERLLRE---KLREE-ERYLREQRRE 424
           +RK++ +  I   + E ++I +E +++    +KE     +E   KLR E E+ LRE+R E
Sbjct: 24  VRKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNE 83

Query: 425 LERREKFL-QKESI------RAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALV 477
           L++ EK L QKE          EKR ++ E +  +  ++ +   ++       +E   L+
Sbjct: 84  LQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKK------EEELEELI 137

Query: 478 EDERLELMELAASSK 492
           E++  EL  ++  + 
Sbjct: 138 EEQLQELERISGLTA 152

Length = 520

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 31/148 (20%), Positives = 59/148 (39%), Gaps = 27/148 (18%)

Query: 349 EKKRKSEEA--RIAREVEAHEKRIRKELEKQDILRRKREEQI------------------ 388
           EKKR+  E       E  A E     E+ +  +     + +                   
Sbjct: 210 EKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGFESEYEPI 269

Query: 389 --RKEMERQDR-ERRKEEERLLREKLREEERYLREQRRELER----REKFLQKESIRAEK 441
                 +R+ + +R KE+ R   E+  +EE+ L+++  +L R     ++  QKE  RA K
Sbjct: 270 NKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARK 329

Query: 442 RRQKEELRRVKEAERLKVANERAVARRI 469
           + Q++E    K+ +R K+   +     +
Sbjct: 330 KEQRKERGEKKKLKRRKLGKHKYPEPPL 357

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 29/116 (25%), Positives = 54/116 (46%), Gaps = 4/116 (3%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLR 408
            K    +E    +E    EK+ +KE  K++   RK +E+   + +R  +E+ KE+E+ + 
Sbjct: 98  PKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEE--AKEKRPPKEKEKEKEKKVE 155

Query: 409 EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERA 464
           E    EE   RE+ R   R +K    +     K+++  E  + ++A R  V  +  
Sbjct: 156 EPRDREEEKKRERVRAKSRPKK--PPKKKPPNKKKEPPEEEKQRQAAREAVKGKPE 209

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 37/129 (28%), Positives = 64/129 (49%), Gaps = 11/129 (8%)

Query: 365 AHEKRIR--KELEKQDILRRKRE-EQIRKEMERQDRERRKEEERLLREKLREEERYLREQ 421
             EK++   +EL K+ I   K+E E ++KE   +     KEE   LR +L   ER L+E+
Sbjct: 22  IAEKKLGSAEELAKRIIEEAKKEAETLKKEALLE----AKEEVHKLRAEL---ERELKER 74

Query: 422 RRELERRE-KFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKESMALVEDE 480
           R EL+R E + LQ+E     K    ++     E +  +++N+        +E   L+ ++
Sbjct: 75  RNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQ 134

Query: 481 RLELMELAA 489
           R EL  ++ 
Sbjct: 135 REELERISG 143

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 32/151 (21%), Positives = 59/151 (39%), Gaps = 17/151 (11%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           + +    +  K E + +  E+   E R+ +  ++     RK  E I KE+E+ ++E  K 
Sbjct: 677 QRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGE-IEKEIEQLEQEEEKL 735

Query: 403 EERL--LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVA 460
           +ERL  L E L   E+ +   + EL+  E              + EEL          + 
Sbjct: 736 KERLEELEEDLSSLEQEIENVKSELKELEA-------------RIEELEEDLHKLEEALN 782

Query: 461 N-ERAVARRIAKESMALVEDERLELMELAAS 490
           + E  ++     E  A +     E+  + A 
Sbjct: 783 DLEARLSHSRIPEIQAELSKLEEEVSRIEAR 813

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 33/146 (22%), Positives = 66/146 (45%), Gaps = 10/146 (6%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
           E++ R  ++ K E A +  E+E  + R+ +  E+ + L  + EE +++ +E  + E    
Sbjct: 712 EELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEE-LQERLEELEEELESL 770

Query: 403 EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
           EE L + K   EE  L E+R+ L+      + E +  E    +  L  ++          
Sbjct: 771 EEALAKLKEEIEE--LEEKRQALQ-----EELEELEEELEEAERRLDALERELESLEQRR 823

Query: 463 RAVARRIA--KESMALVEDERLELME 486
             + + I   +E +  +E++  EL E
Sbjct: 824 ERLEQEIEELEEEIEELEEKLDELEE 849

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 35/138 (25%), Positives = 61/138 (44%), Gaps = 11/138 (7%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
             + ++   +A  A   +  +  +R   E +  L   + +++RKE+E       +EE   
Sbjct: 199 EKQLEKLERQAEKAERYQELKAELR---ELELALLLAKLKELRKELEE-----LEEELSR 250

Query: 407 LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK-EAERLKVANERAV 465
           L E+L E +  L E  +E+E  +   + E +R E    +EEL  +K E E L+       
Sbjct: 251 LEEELEELQEELEEAEKEIEELKS--ELEELREELEELQEELLELKEEIEELEGEISLLR 308

Query: 466 ARRIAKESMALVEDERLE 483
            R    E+     +ERLE
Sbjct: 309 ERLEELENELEELEERLE 326

Length = 1163

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 31/181 (17%), Positives = 67/181 (37%), Gaps = 9/181 (4%)

Query: 338 RVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDR 397
                E   +  +K +   A++ +E +  EK  + + E+  +L ++ EE      E    
Sbjct: 250 EQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKS---ELLKL 306

Query: 398 ERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERL 457
           ERRK ++    +    E+   + ++   + +E+  + E    E   ++E     +E    
Sbjct: 307 ERRKVDDE--EKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEK 364

Query: 458 KVANERAVARRIA----KESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRD 513
                  +   +      ES  L    +L+  EL   ++       L   + Q  DL ++
Sbjct: 365 LQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKE 424

Query: 514 R 514
            
Sbjct: 425 E 425

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 32/143 (22%), Positives = 63/143 (44%), Gaps = 7/143 (4%)

Query: 350 KKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLRE 409
           ++ K E   + +E+E+ E   RK  EK   L  + EE  ++  E +++ +  +E +   E
Sbjct: 234 EELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAE 293

Query: 410 KLREEERYLREQRRELERREKFLQK-ESIRAEKRRQKEEL----RRVKEAERLKVANERA 464
           +  +   +  E   EL   EK L + E        + +EL     R++E ++     E+ 
Sbjct: 294 EYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKR 353

Query: 465 VARRIAKESMALVEDERLELMEL 487
           +     +E   L E+ + +  EL
Sbjct: 354 LEE--LEERHELYEEAKAKKEEL 374

Length = 880

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.2 bits (97), Expect = 0.003
 Identities = 31/115 (26%), Positives = 47/115 (40%), Gaps = 3/115 (2%)

Query: 352 RKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKL 411
           R+ E   +  ++E  E++I  ELEK   L   R+E    E E +   +  EE       L
Sbjct: 675 RRREIEELEEKIEELEEKIA-ELEKA--LAELRKELEELEEELEQLRKELEELSRQISAL 731

Query: 412 REEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVA 466
           R++   L  +  +LE R   L KE    E   ++ E R  +  E L  A      
Sbjct: 732 RKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEE 786

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 33/112 (29%), Positives = 50/112 (44%), Gaps = 20/112 (17%)

Query: 357 ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEER 416
            R+ ++VE  EK I KE             QI +E+E++  +  KEEE L       +  
Sbjct: 364 ERLEKDVEEGEKTIVKEAR-----------QIEEELEKEVEKLGKEEESLF------KRV 406

Query: 417 YLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARR 468
            L E  +ELE+ E+   KE  + EK   ++      E E+L     RA+  R
Sbjct: 407 ALEEGLKELEQDEENFLKELSKEEKELLEKLKMEASEVEKLF---GRALPVR 455

Length = 455

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 15/101 (14%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
           RTEK    + +      E HE R+ +E   +  L++K  E+IR   E++ R    E+   
Sbjct: 288 RTEKLSGLKNSGEPSLKEIHEARLNEE---ERELKKKFTEKIR---EKEKRLEELEQ--- 338

Query: 407 LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEE 447
               L EE    +E   +LE  +K L+    R EK +  + 
Sbjct: 339 ---NLIEE---RKELNSKLEEIQKKLEDLEKRLEKLKSNKS 373

Length = 373

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 36/168 (21%), Positives = 74/168 (44%), Gaps = 6/168 (3%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
              ++RK ++    +E E   K++ KEL+K+      +EE    E E ++ E ++E E  
Sbjct: 304 LKLERRKVDDEEKLKESEKELKKLEKELKKE------KEEIEELEKELKELEIKREAEEE 357

Query: 407 LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVA 466
             E+L + +  L +   EL  ++K   +    A K +++E   + +E +  K+  E +  
Sbjct: 358 EEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQ 417

Query: 467 RRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNLDLFRDR 514
                +     E + +E +E +  +K        +    Q L L +D+
Sbjct: 418 EEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDK 465

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 34/152 (22%), Positives = 68/152 (44%), Gaps = 3/152 (1%)

Query: 337 RRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQD 396
           R++   +D     K        I R +E  EK I++    +++++ K +E      E  +
Sbjct: 152 RQILGLDDYENAYKNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINE 211

Query: 397 RERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAER 456
                 E R   EKL +E + L E + E+E  EK  + ES+   KR+ +E++R ++E   
Sbjct: 212 ISSELPELREELEKLEKEVKELEELKEEIEELEK--ELESLEGSKRKLEEKIRELEERIE 269

Query: 457 LKVANERAVARRIAK-ESMALVEDERLELMEL 487
                   +  ++ + + +    +E ++L E 
Sbjct: 270 ELKKEIEELEEKVKELKELKEKAEEYIKLSEF 301

Length = 880

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 24/129 (18%), Positives = 61/129 (47%), Gaps = 5/129 (3%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
           V +   K  + + + A+E +    +  ++ ++Q    +K++++  K  E     + KEE 
Sbjct: 80  VEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKE--KPKEEPKDRKPKEE- 136

Query: 405 RLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERA 464
              +EK   +E+   ++++  E R++  +K+  R   + + ++  + K   + K   E  
Sbjct: 137 --AKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEE 194

Query: 465 VARRIAKES 473
             R+ A+E+
Sbjct: 195 KQRQAAREA 203

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 40.2 bits (95), Expect = 0.004
 Identities = 27/130 (20%), Positives = 64/130 (49%), Gaps = 11/130 (8%)

Query: 342 DEDVSRTEKKRKSEEARIAREVEAHEK---RIRKELEKQDILRRKREEQIRKEMERQDRE 398
           +E ++  E+  +  E + A E EA  K   ++++ELE++    ++ E+++ +E E++ ++
Sbjct: 519 NELIASLEELERELEQK-AEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQ 577

Query: 399 RRKE--EE-----RLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRV 451
             KE  +E     + LR+  +     ++       R+      E    +K++QKE+   +
Sbjct: 578 AIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEEL 637

Query: 452 KEAERLKVAN 461
           K  + +K  +
Sbjct: 638 KVGDEVKYLS 647

Length = 782

>gnl|CDD|147523 pfam05384, DegS, Sensor protein DegS

 Score = 38.3 bits (90), Expect = 0.004
 Identities = 34/106 (32%), Positives = 59/106 (55%), Gaps = 13/106 (12%)

Query: 348 TEKKRKSEEARIAREVEAHEKRIRK------ELEKQDILRRKREEQIRKEMER---QDRE 398
            E+ R+ E  R+ +E+E  ++ + +      +LEKQ+   RKR  ++ +  ++   +D  
Sbjct: 22  AEQARQ-EYERLEQELEEVKEEVSEVIKEVDKLEKQERRARKRLAEVSRNFDKYSEEDIR 80

Query: 399 RRKEEERLLREKL---REEERYLREQRRELERREKFLQKESIRAEK 441
              E+   L+ KL   R+EE+ LR++R ELERR K L++   RAE 
Sbjct: 81  EAYEKAHDLQVKLALLRQEEKQLRKRRDELERRLKNLKETIERAEN 126

This is small family of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterize the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon. The family also contains one sequence from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase. Length = 159

>gnl|CDD|148617 pfam07111, HCR, Alpha helical coiled-coil rod protein (HCR)

 Score = 40.4 bits (94), Expect = 0.004
 Identities = 40/162 (24%), Positives = 75/162 (46%), Gaps = 9/162 (5%)

Query: 337 RRVSHDEDVSRTEKKRKSEEA-RIAREV-EAHEKRIRKELEKQDILRRKREEQIRKEMER 394
           + V    +    E++R +E A ++ RE+ E+ E       + +     ++E        R
Sbjct: 503 QEVGRAREQGEEERQRLAEVAQQLERELQESQESLASAGAQLEAARAGQQESTEEAASLR 562

Query: 395 QDRERRKE-EERLLREKLREEERYLREQRRELERREKFLQKE------SIRAEKRRQKEE 447
           Q+  +++E   + L+EK+ E E  LREQ  + ERR    ++E      S+R  +R+  +E
Sbjct: 563 QELTQQQEVYGQALQEKVAEVETRLREQLSDTERRLNEARREHAKAVVSLRQIQRQAAQE 622

Query: 448 LRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAA 489
             R +E  RL+    +   +R+++    L  D+ L L  L  
Sbjct: 623 KERNQELRRLQEEARKEEGQRLSRRLQELERDKNLMLQRLLR 664

This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation. Length = 739

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 11/153 (7%)

Query: 344 DVSRTEKKRKSEEARIARE----VEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRER 399
              R E++RK +E + A E      A ++R+ K+LEK+    R   ++ +K+ E   ++ 
Sbjct: 73  SAKRAEEQRKKKEQQQAEELQQKQAAEQERL-KQLEKE----RLAAQEQKKQAEEAAKQA 127

Query: 400 RKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKV 459
             ++++      +       +   E +R     +K    AE +++ E     K A   K 
Sbjct: 128 ALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKK--AAAEAKKKAEAEAAKKAAAEAKK 185

Query: 460 ANERAVARRIAKESMALVEDERLELMELAASSK 492
             E   A + A E+    E E  +     A  K
Sbjct: 186 KAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKK 218

Length = 387

>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 32/132 (24%), Positives = 62/132 (46%), Gaps = 17/132 (12%)

Query: 338 RVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDR 397
           +   +E +S+ E++     AR+  +  A EK++R E E++       +E++RK+ E + R
Sbjct: 195 KEKREELLSKLEEE---LLARLESKEAALEKQLRLEFERE-------KEELRKKYEEKLR 244

Query: 398 ERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELR----RVKE 453
           +  + +     +KL+ E   L  Q  EL+R      KE +  E+  +  +L     R+K 
Sbjct: 245 QELERQAEAHEQKLKNE---LALQAIELQREFNKEIKEKVEEERNGRLAKLAELNSRLKG 301

Query: 454 AERLKVANERAV 465
            E+   +   A 
Sbjct: 302 LEKALDSRSEAE 313

Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains. Length = 493

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 23/127 (18%), Positives = 39/127 (30%), Gaps = 13/127 (10%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
            T K+  +  A IA E       + ++  +Q  L +  EE             RK+    
Sbjct: 168 ATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEE-------------RKKTLAQ 214

Query: 407 LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVA 466
           L  +L  +++ L E R    R +  +      A K R+         A       +R   
Sbjct: 215 LNSELSADQKKLEELRANESRLKNEIASAEAAAAKAREAAAAAEAAAARARAAEAKRTGE 274

Query: 467 RRIAKES 473
                  
Sbjct: 275 TYKPTAP 281

Length = 420

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	753
KOG1473	1414	consensus Nucleosome remodeling factor, subunit NU	99.86
KOG0484	125	consensus Transcription factor PHOX2/ARIX, contain	99.65
KOG0850	245	consensus Transcription factor DLX and related pro	99.61
PF02791	61	DDT: DDT domain; InterPro: IPR004022 This domain i	99.58
KOG0488	309	consensus Transcription factor BarH and related HO	99.56
KOG0489	261	consensus Transcription factor zerknullt and relat	99.55
smart00571	63	DDT domain in different transcription and chromoso	99.54
KOG0485	268	consensus Transcription factor NKX-5.1/HMX1, conta	99.54
KOG0843	197	consensus Transcription factor EMX1 and related HO	99.53
KOG0842	307	consensus Transcription factor tinman/NKX2-3, cont	99.53
KOG2251	228	consensus Homeobox transcription factor [Transcrip	99.48
KOG0487	308	consensus Transcription factor Abd-B, contains HOX	99.44
KOG0492	246	consensus Transcription factor MSH, contains HOX d	99.41
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.41
KOG0848	317	consensus Transcription factor Caudal, contains HO	99.4
KOG0844	408	consensus Transcription factor EVX1, contains HOX	99.37
KOG0491	194	consensus Transcription factor BSH, contains HOX d	99.31
KOG0493	342	consensus Transcription factor Engrailed, contains	99.31
KOG0494	332	consensus Transcription factor CHX10 and related H	99.28
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.28
KOG3802	398	consensus Transcription factor OCT-1, contains POU	99.27
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.22
COG5576	156	Homeodomain-containing transcription factor [Trans	99.2
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.19
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.16
KOG0847	288	consensus Transcription factor, contains HOX domai	99.09
KOG0486	351	consensus Transcription factor PTX1, contains HOX	99.08
KOG0483	198	consensus Transcription factor HEX, contains HOX a	99.06
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	99.01
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	98.94
KOG0490	235	consensus Transcription factor, contains HOX domai	98.75
KOG0849	354	consensus Transcription factor PRD and related pro	98.6
PF11600	216	CAF-1_p150: Chromatin assembly factor 1 complex p1	98.43
KOG0775	304	consensus Transcription factor SIX and related HOX	98.27
PTZ00121	2084	MAEBL; Provisional	98.26
PTZ00266	1021	NIMA-related protein kinase; Provisional	98.2
KOG0774	334	consensus Transcription factor PBX and related HOX	98.17
PTZ00266	1021	NIMA-related protein kinase; Provisional	98.07
KOG4364	811	consensus Chromatin assembly factor-I [Chromatin s	98.06
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	98.05
KOG4364	811	consensus Chromatin assembly factor-I [Chromatin s	97.95
KOG2252	558	consensus CCAAT displacement protein and related h	97.85
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.68
KOG0490	235	consensus Transcription factor, contains HOX domai	97.42
KOG2891	445	consensus Surface glycoprotein [General function p	97.04
KOG1146	1406	consensus Homeobox protein [General function predi	96.78
KOG1144	1064	consensus Translation initiation factor 5B (eIF-5B	96.66
KOG0163	1259	consensus Myosin class VI heavy chain [Cytoskeleto	96.35
KOG0163	1259	consensus Myosin class VI heavy chain [Cytoskeleto	96.24
KOG1144	1064	consensus Translation initiation factor 5B (eIF-5B	96.08
PF05262	489	Borrelia_P83: Borrelia P83/100 protein; InterPro:	95.87
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	95.85
KOG2507	506	consensus Ubiquitin regulatory protein UBXD2, cont	95.73
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	95.38
KOG3054	299	consensus Uncharacterized conserved protein [Funct	94.08
KOG3623	1007	consensus Homeobox transcription factor SIP1 [Tran	93.89
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	93.63
COG3064	387	TolA Membrane protein involved in colicin uptake [	93.58
KOG2412	591	consensus Nuclear-export-signal (NES)-containing p	93.54
KOG3054	299	consensus Uncharacterized conserved protein [Funct	92.98
KOG2412	591	consensus Nuclear-export-signal (NES)-containing p	92.49
KOG0773	342	consensus Transcription factor MEIS1 and related H	90.44
KOG2072	988	consensus Translation initiation factor 3, subunit	89.6
KOG2072	988	consensus Translation initiation factor 3, subunit	89.4
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	87.88
KOG3654	708	consensus Uncharacterized CH domain protein [Cytos	86.51
KOG3654	708	consensus Uncharacterized CH domain protein [Cytos	85.28
PF07946	321	DUF1682: Protein of unknown function (DUF1682); In	85.19
PRK00106	535	hypothetical protein; Provisional	84.94
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	83.66

>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]

Probab=99.86  E-value=3.8e-22  Score=231.15  Aligned_cols=126  Identities=26%  Similarity=0.480  Sum_probs=107.7

Q ss_pred             CCCcccCCCCCcCCCCCCCcccHHHHHHHHHHHHHhhhccccCCCCHHHHHHHhcC-CChhhHHHHHHHHHHHHHhhhhh
Q 004454          519 PPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHD-YDPRLLGEIHVTLLRSVIKDIED  597 (753)
Q Consensus       519 Pp~~v~l~~P~~s~pl~~~~e~v~~LL~Vw~FL~~F~~~L~Lspftlddf~~AL~~-~~s~LL~eiH~~Llk~l~~d~e~  597 (753)
                      |+.-+.+.+|.++.++.+|+++|+++|.||+||++|+.+|.||||+|+|||+||.+ ..+.||+|+|++|||+|+++++.
T Consensus       170 ~~~vPpleLP~SSedi~IPne~Vm~alsIYevLRsF~~~LrisPF~feDFcaAL~~~~~ssLlaeVHvaLLrA~lr~eD~  249 (1414)
T KOG1473|consen  170 PPLVPPLELPESSEDIGIPNEHVMDALSIYEVLRSFSRQLRISPFRFEDFCAALISHEQSSLLAEVHVALLRALLREEDR  249 (1414)
T ss_pred             cccCCCccCCCcccccCCcHHHHHHHHHHHHHHHhhcceEEeCCccHHHHHHHHHhcCchhHHHHHHHHHHHHHhhhhhh
Confidence            44455688999999999999999999999999999999999999999999999974 55589999999999999999998


Q ss_pred             hhcCCCCCCCCCCCCCCCCCCCCchhhhhhhhcccchhhhhhcCCCCCHHHHHHHHHHHhCC--CCCccccc
Q 004454          598 AAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGF--GPQLNKRN  667 (753)
Q Consensus       598 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~a~~~~~~~~~w~~~Ld~~TwpEiLR~~l~s~G~--g~~~~~~~  667 (753)
                          +++.|++  .             +..+..+++   | .+||.||||||||||+.|.|+  |+.|.-.+
T Consensus       250 ----~~Thfs~--~-------------d~KdsvnI~---l-~liD~lTWPevLrqY~ea~~~ad~~v~~~~n  298 (1414)
T KOG1473|consen  250 ----LSTHFSP--L-------------DSKDSVNID---L-YLIDTLTWPEVLRQYFEADKHADGPVWDIFN  298 (1414)
T ss_pred             ----cccccCc--c-------------ccccceeee---e-ehhccccHHHHHHHHHHhccccCcchhhhhc
Confidence                4778888  2             222233455   5 699999999999999999999  78885554

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]

Probab=99.65  E-value=1.1e-16  Score=140.71  Aligned_cols=65  Identities=32%  Similarity=0.524  Sum_probs=61.5

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +++||-||.||..||..||..|..++||++..|++||.+++|++..|||||||||+|.+|+....
T Consensus        15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            57888999999999999999999999999999999999999999999999999999999987543

>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]

Probab=99.61  E-value=8.5e-16  Score=153.55  Aligned_cols=68  Identities=31%  Similarity=0.503  Sum_probs=64.0

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccCC
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQ   85 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~~   85 (753)
                      ++|.|+.||.|+.-||..|+..|++++|+-.++|++||+.|||+..||+|||||||.|.||..++...
T Consensus       119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            57788899999999999999999999999999999999999999999999999999999999885543

>PF02791 DDT: DDT domain; InterPro: IPR004022 This domain is predicted to be a DNA binding domain

Probab=99.58  E-value=2.2e-15  Score=124.19  Aligned_cols=60  Identities=57%  Similarity=0.954  Sum_probs=56.3

Q ss_pred             cccHHHHHHHHHHHHHhhhccccCCCCHHHHHHHhcCCCh-hhHHHHHHHHHHHHHhhhhh
Q 004454          538 EDNIGNLLMVWRFLITFADVLGLWPFTLDEFVQAFHDYDP-RLLGEIHVTLLRSVIKDIED  597 (753)
Q Consensus       538 ~e~v~~LL~Vw~FL~~F~~~L~Lspftlddf~~AL~~~~s-~LL~eiH~~Llk~l~~d~e~  597 (753)
                      +++|+++||||+||++|+++|+|+|||||||++||.+.++ .+++|||++||++|+++.+|
T Consensus         1 ~~~~~~~L~v~~Fl~~F~~~L~L~~ftlddf~~AL~~~~~~~ll~ei~~~LL~~l~~~~~d   61 (61)
T PF02791_consen    1 GEAFGDLLMVWEFLNTFGEVLGLSPFTLDDFEQALLCNDPSGLLAEIHCALLKALLADEED   61 (61)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHcCCCcchhHHHHHHHHHHHHHhccCC
Confidence            3679999999999999999999999999999999998877 59999999999999999875

The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is found in foetal Alzheimer antigen and several hypothetical and uncharacterised proteins.

>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]

Probab=99.56  E-value=2.1e-15  Score=162.00  Aligned_cols=68  Identities=34%  Similarity=0.469  Sum_probs=63.8

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccCC
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQ   85 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~~   85 (753)
                      .+|+|+.||.||..||..||+.|+++.|++..+|.+||..|||++.||++||||||+||||+......
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~  236 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGE  236 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence            47888899999999999999999999999999999999999999999999999999999998877543

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]

Probab=99.55  E-value=4.9e-15  Score=156.49  Aligned_cols=70  Identities=33%  Similarity=0.508  Sum_probs=65.2

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccCCC
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQP   86 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~~~   86 (753)
                      ..++.||.||.||..|+.+||+.|+.|+|++...|.+||..|+|+++||+|||||||+||||..+.....
T Consensus       155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            3467899999999999999999999999999999999999999999999999999999999988777544

>smart00571 DDT domain in different transcription and chromosome remodeling factors

Probab=99.54  E-value=6.6e-15  Score=122.10  Aligned_cols=60  Identities=47%  Similarity=0.850  Sum_probs=55.9

Q ss_pred             cccHHHHHHHHHHHHHhhhccccCCCC--HHHHHHHhcCCCh-hhHHHHHHHHHHHHHhhhhh
Q 004454          538 EDNIGNLLMVWRFLITFADVLGLWPFT--LDEFVQAFHDYDP-RLLGEIHVTLLRSVIKDIED  597 (753)
Q Consensus       538 ~e~v~~LL~Vw~FL~~F~~~L~Lspft--lddf~~AL~~~~s-~LL~eiH~~Llk~l~~d~e~  597 (753)
                      ++.|+|+||||+||++|+++|+|+||+  ||||++||++.++ .+|++||++||+++++|+++
T Consensus         1 ~~~~~d~l~V~eFl~~F~~~L~L~~f~~~l~~f~~Al~~~~~~~ll~ei~~~LL~~i~~d~~~   63 (63)
T smart00571        1 NEAFGDLLMVYEFLRSFGKVLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEGE   63 (63)
T ss_pred             CcHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhcCCcchHHHHHHHHHHHHHHhCCCC
Confidence            367999999999999999999999999  9999999998888 59999999999999998763

>KOG0485 consensus Transcription factor NKX-5

Probab=99.54  E-value=1.3e-14  Score=143.21  Aligned_cols=65  Identities=34%  Similarity=0.498  Sum_probs=61.8

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      +.++||.||+|+..|+..||..|+..+|++..+|..||.+|.|++.||+|||||||.||||+...
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            45888999999999999999999999999999999999999999999999999999999998654

1/HMX1, contains HOX domain [Transcription]

>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]

Probab=99.53  E-value=4.7e-15  Score=143.06  Aligned_cols=64  Identities=31%  Similarity=0.465  Sum_probs=61.6

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +.||.||.||.+||..||..|+.++|....+|+.||..|+|++.||+|||||||+|.||.+...
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            7899999999999999999999999999999999999999999999999999999999987663

>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]

Probab=99.53  E-value=7.9e-15  Score=155.08  Aligned_cols=66  Identities=26%  Similarity=0.485  Sum_probs=61.9

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      .++||.|..||..|+.+||..|.+++|++.++|+.||..|+||++||||||||||-|+||+...+.
T Consensus       151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~  216 (307)
T KOG0842|consen  151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA  216 (307)
T ss_pred             ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence            467778899999999999999999999999999999999999999999999999999999877664

>KOG2251 consensus Homeobox transcription factor [Transcription]

Probab=99.48  E-value=5.6e-14  Score=140.19  Aligned_cols=67  Identities=33%  Similarity=0.544  Sum_probs=63.8

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      ..+|.||.||+||..|+++||..|.+++||+...|++||.+|+|.+.+|||||.|||+|+|+++.+.
T Consensus        33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            4578899999999999999999999999999999999999999999999999999999999988765

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]

Probab=99.44  E-value=4e-14  Score=149.83  Aligned_cols=66  Identities=33%  Similarity=0.506  Sum_probs=62.4

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .++.||||--+|..|+.+||+.|..|.|++...|.+|+..|+|+++||+|||||||+|.||..+..
T Consensus       232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            367889999999999999999999999999999999999999999999999999999999998644

>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]

Probab=99.41  E-value=9.8e-14  Score=136.38  Aligned_cols=66  Identities=33%  Similarity=0.498  Sum_probs=61.5

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+..|+.||-||.+||..||+-|...+|.++.+|.+++..|.|++.||+|||||||+|.||.+...
T Consensus       141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            455678999999999999999999999999999999999999999999999999999999987544

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.41  E-value=3e-13  Score=109.67  Aligned_cols=57  Identities=44%  Similarity=0.746  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      |++|+.||..|+..|+..|..++||+..++..||..|||+..+|++||+|+|.++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578999999999999999999999999999999999999999999999999999875

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]

Probab=99.40  E-value=9.3e-14  Score=141.18  Aligned_cols=62  Identities=39%  Similarity=0.568  Sum_probs=59.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      -|.|.++|..|+.+||+.|..++|.++..+.+||..|||+++||+|||||||+|+||..+++
T Consensus       200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            35688999999999999999999999999999999999999999999999999999988877

>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]

Probab=99.37  E-value=2.5e-13  Score=139.94  Aligned_cols=68  Identities=34%  Similarity=0.559  Sum_probs=63.2

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccCCC
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQP   86 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~~~   86 (753)
                      ..-||.||.||.+|+..||+.|-+..|.+...|.+||..|+|.+..|+|||||||+|+||+.-...+.
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWP  246 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWP  246 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCC
Confidence            45688999999999999999999999999999999999999999999999999999999987766543

>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]

Probab=99.31  E-value=9.7e-13  Score=125.10  Aligned_cols=67  Identities=31%  Similarity=0.512  Sum_probs=62.5

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccCC
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQ   85 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~~   85 (753)
                      .++++.||+|+..|+..|++.|+.++|.+..+|.+||..|+|++.||+.||||||+|.||.+.....
T Consensus        98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p  164 (194)
T KOG0491|consen   98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQP  164 (194)
T ss_pred             HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence            3567789999999999999999999999999999999999999999999999999999998877653

>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]

Probab=99.31  E-value=1.5e-12  Score=131.63  Aligned_cols=74  Identities=36%  Similarity=0.547  Sum_probs=64.8

Q ss_pred             hhcCCCccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           11 KKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        11 ~~~~~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      .+++.++..--||.||.||.+||..|+..|..++|++...|.+||..|||.+.||+|||||+|+|.||....+.
T Consensus       236 ~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn  309 (342)
T KOG0493|consen  236 PKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN  309 (342)
T ss_pred             ccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence            33444445566789999999999999999999999999999999999999999999999999999999765553

>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]

Probab=99.28  E-value=2.1e-12  Score=130.62  Aligned_cols=60  Identities=35%  Similarity=0.485  Sum_probs=57.3

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        24 ~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      -||.||..|+..||+.|...+||+...|+-||.++.|.+.+|+|||||||+||||..+.-
T Consensus       144 ~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  144 FRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             ccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            399999999999999999999999999999999999999999999999999999977655

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.28  E-value=3.6e-12  Score=103.31  Aligned_cols=53  Identities=17%  Similarity=0.313  Sum_probs=51.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCChHHHhHhhhhhh
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESY----PSEALRAELSAQLGLSDRQLQMWFCHRR   73 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~y----ps~~~r~~LA~~lgL~~~qVqiWFqNRR   73 (753)
                      +||.||.||.+|+..|+..|+.++|    |+...+.+||..|||++.+|+|||||.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            4789999999999999999999999    9999999999999999999999999965

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]

Probab=99.27  E-value=3.8e-12  Score=137.23  Aligned_cols=65  Identities=22%  Similarity=0.452  Sum_probs=62.4

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..+|+||+||.|+...+..||++|.+|+.|+..+...||.+|+|...+|+|||||||+|.||...
T Consensus       290 a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  290 AQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            45689999999999999999999999999999999999999999999999999999999999877

>smart00389 HOX Homeodomain

Probab=99.22  E-value=2.3e-11  Score=97.95  Aligned_cols=56  Identities=48%  Similarity=0.743  Sum_probs=52.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||+..+|++||+|||.+.+
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            45788899999999999999999999999999999999999999999999998864

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.20  E-value=1.6e-11  Score=119.44  Aligned_cols=71  Identities=32%  Similarity=0.579  Sum_probs=64.2

Q ss_pred             CCCccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           14 KKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        14 ~~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      ...+....+++|++.|..|+.+|+..|..|+||+...|..|+..|+|+++-|||||||||++.|+......
T Consensus        44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            33345678889999999999999999999999999999999999999999999999999999998776643

>cd00086 homeodomain 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

Probab=99.19  E-value=3.7e-11  Score=97.57  Aligned_cols=58  Identities=43%  Similarity=0.732  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|||.+.++.
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            3578899999999999999999999999999999999999999999999999998764

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]

Probab=99.16  E-value=7.8e-11  Score=120.91  Aligned_cols=67  Identities=34%  Similarity=0.547  Sum_probs=62.6

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .....||+||.||+.||+.|+..|...+.|....|++|+..+||..++|||||||||+|.||.++..
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            3467889999999999999999999999999999999999999999999999999999999987654

>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]

Probab=99.09  E-value=4.7e-11  Score=118.27  Aligned_cols=65  Identities=32%  Similarity=0.494  Sum_probs=60.4

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      .++++-.|.+|+..|+..|+..|++..|+-..+|.+||..+||++.||+|||||||+||||+...
T Consensus       164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            35677789999999999999999999999999999999999999999999999999999997643

>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]

Probab=99.08  E-value=4e-11  Score=124.94  Aligned_cols=65  Identities=29%  Similarity=0.504  Sum_probs=61.9

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      |+||.||.||.+||..||..|.+++||+...|++||..++|++..|+|||.|||+||+|.....+
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            67889999999999999999999999999999999999999999999999999999999876664

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]

Probab=99.06  E-value=1.3e-10  Score=116.92  Aligned_cols=65  Identities=28%  Similarity=0.463  Sum_probs=58.7

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      +.....++.+||.+|+..||..|+...|.....+..||..|||.++||.|||||||++||.++..
T Consensus        47 ~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   47 GSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             ccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            33455566789999999999999999999999999999999999999999999999999997743

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=99.01  E-value=1.6e-07  Score=107.48  Aligned_cols=117  Identities=35%  Similarity=0.358  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q 004454          357 ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLL-REKLREEERYLREQR-RELERREKFLQK  434 (753)
Q Consensus       357 ~r~~ke~e~~e~~~~ke~e~~e~~r~k~ee~~rke~er~~~er~keeer~~-re~~~eeer~~re~~-~e~er~ek~~~k  434 (753)
                      ..++|+++..+++.++|+|+.  +++++||+++|++||++.||+++.|+++ -|++++.|+.+.|++ ++.+++|+++  
T Consensus       327 aELerRRq~leeqqqreree~--eqkEreE~ekkererqEqErk~qlElekqLerQReiE~qrEEerkkeie~rEaar--  402 (1118)
T KOG1029|consen  327 AELERRRQALEEQQQREREEV--EQKEREEEEKKERERQEQERKAQLELEKQLERQREIERQREEERKKEIERREAAR--  402 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
Confidence            445555555555444444443  3455677778888888888877666544 556666665554443 3333333322  


Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHH
Q 004454          435 ESIRAEKRRQKE-ELRRVKEAERLKVANERAVARRIAKESMALVED  479 (753)
Q Consensus       435 e~~r~ek~~~ke-e~~~~ke~e~~k~~eek~~~~~~ake~~~~~e~  479 (753)
                        +..||+|+.| |..+.+|..-++.++++.+....++......+.
T Consensus       403 --~ElEkqRqlewErar~qem~~Qk~reqe~iv~~nak~~ql~~el  446 (1118)
T KOG1029|consen  403 --EELEKQRQLEWERARRQEMLNQKNREQEWIVYLNAKKKQLQQEL  446 (1118)
T ss_pred             --HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Confidence              2345566655 556666666667777666666655544433333

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]

Probab=98.94  E-value=1.8e-10  Score=118.33  Aligned_cols=80  Identities=30%  Similarity=0.469  Sum_probs=70.4

Q ss_pred             ChhhhhhhhhhhcCC-----CccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhh
Q 004454            1 MEAASEAEEKKKKKK-----PLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK   75 (753)
Q Consensus         1 ~~~~~~~~~~~~~~~-----~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K   75 (753)
                      +|++++..+++....     -+++-+||+||.+-......||.+|..++.|+....+.||++|+|...+|+|||||.|+|
T Consensus       284 LEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK  363 (385)
T KOG1168|consen  284 LEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK  363 (385)
T ss_pred             HHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence            367777777774333     157889999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccc
Q 004454           76 DRKAP   80 (753)
Q Consensus        76 ~kr~~   80 (753)
                      .||..
T Consensus       364 QKRm~  368 (385)
T KOG1168|consen  364 QKRMK  368 (385)
T ss_pred             HHHhh
Confidence            99843

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=98.75  E-value=5e-09  Score=108.54  Aligned_cols=64  Identities=33%  Similarity=0.404  Sum_probs=60.8

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..++|+.|+.|+..|++.|+..|.+++||+...|+.||..+++++..|+|||||||+||++...
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            4577889999999999999999999999999999999999999999999999999999999775

>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]

Probab=98.60  E-value=5e-08  Score=107.54  Aligned_cols=69  Identities=30%  Similarity=0.472  Sum_probs=63.8

Q ss_pred             CccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           16 PLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        16 ~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      ..+++.+|.||+|+..|+..|+..|..++||++..|+.||..+++++..|+|||+|||++++|.....+
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~~s  239 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRDCS  239 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccccc
Confidence            345777888999999999999999999999999999999999999999999999999999999886544

>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair []

Probab=98.43  E-value=5.9e-05  Score=78.02  Aligned_cols=13  Identities=38%  Similarity=0.488  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHHHH
Q 004454          449 RRVKEAERLKVAN  461 (753)
Q Consensus       449 ~~~ke~e~~k~~e  461 (753)
                      ++.+++++++..+
T Consensus       159 k~~keeekr~~eE  171 (216)
T PF11600_consen  159 KRKKEEEKRKKEE  171 (216)
T ss_pred             HHHHHHHHHhhHH
Confidence            3334444433333

P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].

>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]

Probab=98.27  E-value=2.6e-06  Score=88.00  Aligned_cols=52  Identities=33%  Similarity=0.523  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           28 KTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        28 ~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      |-..-...|..+|.+++||+..++.+||..+||+..||-+||.|||+++|-.
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~  234 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA  234 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence            4445578899999999999999999999999999999999999999999943

>PTZ00121 MAEBL; Provisional

Probab=98.26  E-value=5.8e-05  Score=91.90  Aligned_cols=9  Identities=0%  Similarity=-0.186  Sum_probs=5.5

Q ss_pred             cCCCCCCCC
Q 004454          218 EYKFLPEQP  226 (753)
Q Consensus       218 e~~flP~~p  226 (753)
                      .+||.|..-
T Consensus       881 p~Cf~p~Kt  889 (2084)
T PTZ00121        881 PNCQIIRKT  889 (2084)
T ss_pred             Ccccccccc
Confidence            566666654

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=98.20  E-value=6.5e-05  Score=92.33  Aligned_cols=13  Identities=15%  Similarity=0.289  Sum_probs=7.1

Q ss_pred             hhhhHHHHHHhhh
Q 004454          134 VEMRVIAFVESQL  146 (753)
Q Consensus       134 ~~~~~i~~ves~l  146 (753)
                      .++-++++|-..|
T Consensus       224 SDVWSLG~ILYEL  236 (1021)
T PTZ00266        224 SDMWALGCIIYEL  236 (1021)
T ss_pred             hHHHHHHHHHHHH
Confidence            4555666655544

>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]

Probab=98.17  E-value=3.2e-06  Score=86.45  Aligned_cols=64  Identities=27%  Similarity=0.487  Sum_probs=58.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           21 VKTKRKMKTASQLEILEKTYA---VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~---~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      .||+|..|+..-.++|..+|.   .++||+...+++||.+.|++..||-.||.|+|-+.+|.....+
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~  254 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQ  254 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhh
Confidence            567889999999999999995   5799999999999999999999999999999999999776554

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=98.07  E-value=0.00023  Score=87.69  Aligned_cols=15  Identities=0%  Similarity=-0.208  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHhhhc
Q 004454          543 NLLMVWRFLITFADV  557 (753)
Q Consensus       543 ~LL~Vw~FL~~F~~~  557 (753)
                      ..-..|+-+++|...
T Consensus       666 ~~~~~~~~~~~~~~~  680 (1021)
T PTZ00266        666 RGKDSSDHVSSYKPY  680 (1021)
T ss_pred             ccccccchhhccchh
Confidence            333444555554443

>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]

Probab=98.06  E-value=0.00025  Score=81.07  Aligned_cols=21  Identities=19%  Similarity=0.094  Sum_probs=13.2

Q ss_pred             HHHHHHHHHhCCChHHHhHhh
Q 004454           49 ALRAELSAQLGLSDRQLQMWF   69 (753)
Q Consensus        49 ~~r~~LA~~lgL~~~qVqiWF   69 (753)
                      ...+.+-..+|+...+.-+.|
T Consensus        38 ~~~e~~t~~~N~~~d~~~~d~   58 (811)
T KOG4364|consen   38 EEKESQTSSLNLEMDGLFDDF   58 (811)
T ss_pred             cccccchhhhhcccchhHHHH
Confidence            344445666777777777766

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=98.05  E-value=0.00019  Score=83.09  Aligned_cols=31  Identities=35%  Similarity=0.466  Sum_probs=14.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004454          346 SRTEKKRKSEEARIAREVEAHEKRIRKELEK  376 (753)
Q Consensus       346 ~~~ek~~~~ee~r~~ke~e~~e~~~~ke~e~  376 (753)
                      ...+++++.-++..+|++++.+++.+.|.+|
T Consensus       327 aELerRRq~leeqqqreree~eqkEreE~ek  357 (1118)
T KOG1029|consen  327 AELERRRQALEEQQQREREEVEQKEREEEEK  357 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455666654444444444443333333333

>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]

Probab=97.95  E-value=0.00057  Score=78.31  Aligned_cols=20  Identities=15%  Similarity=0.062  Sum_probs=11.5

Q ss_pred             hcCCCCCHHHHHHHHHHHhC
Q 004454          639 LHLNALTWPEILRQFALSAG  658 (753)
Q Consensus       639 ~~Ld~~TwpEiLR~~l~s~G  658 (753)
                      -|+|.-.-.-|++.|+.++-
T Consensus       664 ~hgn~ns~~~ii~E~qE~~k  683 (811)
T KOG4364|consen  664 SHGNENSINDIIDEDQEASK  683 (811)
T ss_pred             hcccccchHHHHHHHHHHHH
Confidence            35555555566666666554

>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]

Probab=97.85  E-value=3.9e-05  Score=86.59  Aligned_cols=62  Identities=21%  Similarity=0.256  Sum_probs=56.9

Q ss_pred             CCccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhh
Q 004454           15 KPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKD   76 (753)
Q Consensus        15 ~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~   76 (753)
                      +...-..||.|.+||..|...|...|..+++|+......|+.+|||....|.+||-|-|.+.
T Consensus       414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            33456788899999999999999999999999999999999999999999999999988764

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=97.68  E-value=3.7e-05  Score=58.01  Aligned_cols=34  Identities=38%  Similarity=0.709  Sum_probs=28.8

Q ss_pred             hcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhh
Q 004454           42 VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK   75 (753)
Q Consensus        42 ~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K   75 (753)
                      .++||+..++..||..+||+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4799999999999999999999999999999864

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=97.42  E-value=0.00012  Score=75.84  Aligned_cols=67  Identities=34%  Similarity=0.546  Sum_probs=62.1

Q ss_pred             CCccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           15 KPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        15 ~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      .....+.++.|+.++..|+..+...|..+++|+...+..|+..+|++...|++||||+|.+.++...
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            3345678889999999999999999999999999999999999999999999999999999998766

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=97.04  E-value=0.05  Score=56.98  Aligned_cols=18  Identities=39%  Similarity=0.638  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 004454          347 RTEKKRKSEEARIAREVE  364 (753)
Q Consensus       347 ~~ek~~~~ee~r~~ke~e  364 (753)
                      +.+.+++.+-+++..+.+
T Consensus       278 raeerrqieterlrqeee  295 (445)
T KOG2891|consen  278 RAEERRQIETERLRQEEE  295 (445)
T ss_pred             HHHHHhhhhHHHHhhhHh
Confidence            344444445555544443

>KOG1146 consensus Homeobox protein [General function prediction only]

Probab=96.78  E-value=0.0013  Score=80.98  Aligned_cols=66  Identities=26%  Similarity=0.424  Sum_probs=60.6

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .-.+|..||.++..||.++...|....||...+.+.|...+++..++|++||||-|+|.++.....
T Consensus       900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            445778999999999999999999999999999999999999999999999999999998876533

>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]

Probab=96.66  E-value=0.043  Score=64.58  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=8.8

Q ss_pred             HHHHHHhhhcCCCCCcH
Q 004454          724 FAAFHVLSLEGSEGLTI  740 (753)
Q Consensus       724 ~~~~~~l~~~g~~g~~~  740 (753)
                      -+.|.-|-..|+.=|.+
T Consensus       550 hEsFtnlRsrgsslC~~  566 (1064)
T KOG1144|consen  550 HESFTNLRSRGSSLCDL  566 (1064)
T ss_pred             chhhhhhhhccccccce
Confidence            45555555555554443

>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]

Probab=96.35  E-value=0.078  Score=62.14  Aligned_cols=25  Identities=20%  Similarity=0.254  Sum_probs=17.3

Q ss_pred             ccccCCCCHHHHHHHhc-CCChhhHH
Q 004454          557 VLGLWPFTLDEFVQAFH-DYDPRLLG  581 (753)
Q Consensus       557 ~L~Lspftlddf~~AL~-~~~s~LL~  581 (753)
                      ..+|+...+.+|-.+|. +-|-.||.
T Consensus      1064 KYDl~~wkyaeLRDtINTS~DieLL~ 1089 (1259)
T KOG0163|consen 1064 KYDLSKWKYAELRDTINTSCDIELLE 1089 (1259)
T ss_pred             ccccccccHHHHHHhhcccccHHHHH
Confidence            35677778888888886 44446664

>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]

Probab=96.24  E-value=0.11  Score=61.04  Aligned_cols=23  Identities=26%  Similarity=0.528  Sum_probs=12.0

Q ss_pred             HHHHhCCChHHHhHhhhhhhhhh
Q 004454           54 LSAQLGLSDRQLQMWFCHRRLKD   76 (753)
Q Consensus        54 LA~~lgL~~~qVqiWFqNRR~K~   76 (753)
                      -|.-|||....+++-.|-|-+..
T Consensus       376 ~a~LLGld~~elr~~L~aRvMqt  398 (1259)
T KOG0163|consen  376 AAELLGLDQTELRTGLCARVMQT  398 (1259)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHh
Confidence            34455555555555555554443

>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]

Probab=96.08  E-value=0.11  Score=61.30  Aligned_cols=9  Identities=33%  Similarity=0.571  Sum_probs=4.4

Q ss_pred             cchhhhccc
Q 004454          683 ENIISNLRN  691 (753)
Q Consensus       683 ~~~~~~~~~  691 (753)
                      ..-+.+||+
T Consensus       550 hEsFtnlRs  558 (1064)
T KOG1144|consen  550 HESFTNLRS  558 (1064)
T ss_pred             chhhhhhhh
Confidence            344445555

>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins

Probab=95.87  E-value=0.41  Score=55.20  Aligned_cols=27  Identities=26%  Similarity=0.340  Sum_probs=15.5

Q ss_pred             CCCCCchhhhhhhHHHHHHhhhCCCCc
Q 004454          125 PFPLPQRNIVEMRVIAFVESQLGEPLR  151 (753)
Q Consensus       125 ~~~~p~~~~~~~~~i~~ves~l~~p~~  151 (753)
                      .|..|+...-....|..|=+.|+..+.
T Consensus        15 Ny~gp~~~~~t~~~i~~iG~~la~~~~   41 (489)
T PF05262_consen   15 NYSGPHASIETAQQIRGIGSGLAEALK   41 (489)
T ss_pred             ecCCCCcchhHHHHHHHHHHHHHHHHh
Confidence            445555555555666666666665554

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=95.85  E-value=0.16  Score=57.87  Aligned_cols=10  Identities=30%  Similarity=0.335  Sum_probs=5.3

Q ss_pred             HHHHHHhCCC
Q 004454          651 RQFALSAGFG  660 (753)
Q Consensus       651 R~~l~s~G~g  660 (753)
                      |.|--++|.|
T Consensus       848 r~wqgs~dgG  857 (940)
T KOG4661|consen  848 RRWQGSSDGG  857 (940)
T ss_pred             hhhccCCCCc
Confidence            5555555554

>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]

Probab=95.73  E-value=0.031  Score=61.78  Aligned_cols=27  Identities=26%  Similarity=0.433  Sum_probs=20.7

Q ss_pred             CCCCcccHHHHHHHHHHHHHhhhcccc
Q 004454          534 WNDSEDNIGNLLMVWRFLITFADVLGL  560 (753)
Q Consensus       534 l~~~~e~v~~LL~Vw~FL~~F~~~L~L  560 (753)
                      |.+-.-..+-|+-+|.|+.+|...+.-
T Consensus       407 w~ll~pv~~gl~altr~~s~f~~~f~w  433 (506)
T KOG2507|consen  407 WNLLDPVSGGLFALTRRVSSFANPFSW  433 (506)
T ss_pred             hcccCccchhHHHHHHHHHHHhccCCC
Confidence            544455568899999999999887764

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=95.38  E-value=0.2  Score=57.08  Aligned_cols=16  Identities=31%  Similarity=0.416  Sum_probs=6.8

Q ss_pred             CHHHHHHHHHHHhCCC
Q 004454          645 TWPEILRQFALSAGFG  660 (753)
Q Consensus       645 TwpEiLR~~l~s~G~g  660 (753)
                      .|.-=-|.++=++|-|
T Consensus       865 rWqGGers~sG~sGpG  880 (940)
T KOG4661|consen  865 RWQGGERSHSGSSGPG  880 (940)
T ss_pred             cccCCcccccCCCCCc
Confidence            3543334444444443

>KOG3054 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.08  E-value=0.48  Score=49.14  Aligned_cols=29  Identities=14%  Similarity=0.218  Sum_probs=17.3

Q ss_pred             HHHHHhhhccccC-CCCHHHHHHHhcCCCh
Q 004454          549 RFLITFADVLGLW-PFTLDEFVQAFHDYDP  577 (753)
Q Consensus       549 ~FL~~F~~~L~Ls-pftlddf~~AL~~~~s  577 (753)
                      +||..|-+.+.-. -..|+||..++.....
T Consensus       200 nll~eFv~YIk~nKvV~ledLas~f~Lrtq  229 (299)
T KOG3054|consen  200 NLLSEFVEYIKKNKVVPLEDLASEFGLRTQ  229 (299)
T ss_pred             HHHHHHHHHHHhcCeeeHHHHHHHhCccHH
Confidence            3445555555443 3568888888875544

>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]

Probab=93.89  E-value=0.96  Score=53.42  Aligned_cols=47  Identities=23%  Similarity=0.458  Sum_probs=43.6

Q ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           33 LEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        33 l~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      +..|..+|..|..|+..+...+|.+.||+...|+.||+++++.....
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv  614 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV  614 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence            78899999999999999999999999999999999999998886553

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A

Probab=93.63  E-value=0.088  Score=42.62  Aligned_cols=42  Identities=26%  Similarity=0.341  Sum_probs=31.3

Q ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhh
Q 004454           33 LEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRL   74 (753)
Q Consensus        33 l~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~   74 (753)
                      +..|+.+|....++.......|..+.+|+..||+.||-.++.
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            456999999999999999999999999999999999976643

>COG3064 TolA Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

Probab=93.58  E-value=3.2  Score=44.74  Aligned_cols=16  Identities=19%  Similarity=0.304  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHhCCCCC
Q 004454          647 PEILRQFALSAGFGPQ  662 (753)
Q Consensus       647 pEiLR~~l~s~G~g~~  662 (753)
                      .+|-+.||...-|.-+
T Consensus       311 ~~Iq~rfl~~~sf~gK  326 (387)
T COG3064         311 SAIQSRFLDADSFAGK  326 (387)
T ss_pred             HHHHHHHhcccccCCc
Confidence            4677777777777433

>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]

Probab=93.54  E-value=1.6  Score=50.19  Aligned_cols=40  Identities=30%  Similarity=0.374  Sum_probs=25.6

Q ss_pred             CCchhhhhhhhcccchhhhhhcCCCCCHHHHHHHHHHHhCCC
Q 004454          619 AHPQIVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFG  660 (753)
Q Consensus       619 ~~~~~v~~a~~~~~~~~~w~~~Ld~~TwpEiLR~~l~s~G~g  660 (753)
                      .|+..+...|+|--.|-+-  .+..-|---||=.||-++|||
T Consensus       497 ~hpf~i~~gW~wLA~iln~--~p~~~~tatll~s~Lq~aG~~  536 (591)
T KOG2412|consen  497 VHPFGINHGWAWLARILNK--IPLLDTTATLLNSFLQTAGFG  536 (591)
T ss_pred             CCcchhhcccHHHHHHhCC--CCccchHHHHHHHHHHHHHHH
Confidence            4666667777774444443  333337777888888888874

>KOG3054 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.98  E-value=0.85  Score=47.36  Aligned_cols=11  Identities=27%  Similarity=0.277  Sum_probs=4.6

Q ss_pred             HHHHHHHHHHh
Q 004454          544 LLMVWRFLITF  554 (753)
Q Consensus       544 LL~Vw~FL~~F  554 (753)
                      |+.|-.|++.-
T Consensus       262 l~AVAkfIkqr  272 (299)
T KOG3054|consen  262 LAAVAKFIKQR  272 (299)
T ss_pred             HHHHHHHHHHc
Confidence            34444444433

>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]

Probab=92.49  E-value=1.8  Score=49.80  Aligned_cols=14  Identities=14%  Similarity=0.052  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHhhhc
Q 004454          544 LLMVWRFLITFADV  557 (753)
Q Consensus       544 LL~Vw~FL~~F~~~  557 (753)
                      |..+.+-|.+|..-
T Consensus       357 L~qI~dkl~s~~~~  370 (591)
T KOG2412|consen  357 LRQIFDKLDSLFGG  370 (591)
T ss_pred             HHHHHHHHHHHhcC
Confidence            77777777765443

>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]

Probab=90.44  E-value=0.17  Score=56.03  Aligned_cols=60  Identities=25%  Similarity=0.355  Sum_probs=49.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-h--hcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           21 VKTKRKMKTASQLEILEKTY-A--VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F-~--~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ..|.+..+......+|+.+. .  ..+||+..++..||.++||+..||.+||-|.|-+..+-.
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence            44556688889899998773 3  257999999999999999999999999999988755543

>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]

Probab=89.60  E-value=38  Score=41.31  Aligned_cols=11  Identities=55%  Similarity=0.742  Sum_probs=7.3

Q ss_pred             CCCCcccCCCC
Q 004454          155 PILGVEFDSLP  165 (753)
Q Consensus       155 P~lg~~~dplp  165 (753)
                      -+|-++|+||-
T Consensus       394 ~iLEveF~PL~  404 (988)
T KOG2072|consen  394 NILEVEFHPLK  404 (988)
T ss_pred             HHHHhcCCHHH
Confidence            45667787764

>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]

Probab=89.40  E-value=7.7  Score=46.89  Aligned_cols=12  Identities=17%  Similarity=0.268  Sum_probs=6.2

Q ss_pred             cCCCCCCCCCHH
Q 004454           20 EVKTKRKMKTAS   31 (753)
Q Consensus        20 k~rr~Rt~~t~~   31 (753)
                      +-|--|+.+|++
T Consensus       140 qdR~DR~lltPW  151 (988)
T KOG2072|consen  140 QDRSDRELLTPW  151 (988)
T ss_pred             ccccchHHHHHH
Confidence            344455565554

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=87.88  E-value=55  Score=37.30  Aligned_cols=10  Identities=20%  Similarity=0.039  Sum_probs=4.4

Q ss_pred             HHHHHHHHHH
Q 004454          647 PEILRQFALS  656 (753)
Q Consensus       647 pEiLR~~l~s  656 (753)
                      +|-.|.-|.+
T Consensus       465 SEaqRsaLNA  474 (630)
T KOG0742|consen  465 SEAQRSALNA  474 (630)
T ss_pred             cHHHHHHHHH
Confidence            4444444433

>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]

Probab=86.51  E-value=48  Score=38.20  Aligned_cols=35  Identities=17%  Similarity=0.290  Sum_probs=22.1

Q ss_pred             hhhhhhhcccchhhhhhcCCCCCHHHHHHHHHHHhCCCCCc
Q 004454          623 IVEGAYAWGFDIRSWQLHLNALTWPEILRQFALSAGFGPQL  663 (753)
Q Consensus       623 ~v~~a~~~~~~~~~w~~~Ld~~TwpEiLR~~l~s~G~g~~~  663 (753)
                      +++-+|--||-.   +.+-..+|=+|.+|..   .|.||..
T Consensus       617 FliLfrds~cqf---ralyT~~~ETeei~kl---~gmgpk~  651 (708)
T KOG3654|consen  617 FLILFRDSGCQF---RALYTYMPETEEIRKL---TGMGPKM  651 (708)
T ss_pred             hhhhhhhcccee---ecccccCccHHHHhhh---hccCchh
Confidence            334444446663   3366778888888865   4778776

>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]

Probab=85.28  E-value=4.6  Score=46.01  Aligned_cols=15  Identities=27%  Similarity=0.384  Sum_probs=8.0

Q ss_pred             HhHhhhhhhhhhccc
Q 004454           65 LQMWFCHRRLKDRKA   79 (753)
Q Consensus        65 VqiWFqNRR~K~kr~   79 (753)
                      +---|-..|+|.-|.
T Consensus       118 mea~fakqrqklgks  132 (708)
T KOG3654|consen  118 MEAIFAKQRQKLGKS  132 (708)
T ss_pred             HHHHHHHHHHHhchh
Confidence            444565556665543

>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function

Probab=85.19  E-value=2.9  Score=46.04  Aligned_cols=11  Identities=27%  Similarity=0.628  Sum_probs=6.5

Q ss_pred             hHHHhHhhhhh
Q 004454           62 DRQLQMWFCHR   72 (753)
Q Consensus        62 ~~qVqiWFqNR   72 (753)
                      .+.+..||.-.
T Consensus        29 ~~~A~~w~~~~   39 (321)
T PF07946_consen   29 RRIAKAWFESH   39 (321)
T ss_pred             HHHHHHHHHHH
Confidence            45566777543

One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.

>PRK00106 hypothetical protein; Provisional

Probab=84.94  E-value=90  Score=36.93  Aligned_cols=12  Identities=33%  Similarity=0.520  Sum_probs=8.1

Q ss_pred             HHHHHHHHhhhc
Q 004454          741 LEVADKIQVTLE  752 (753)
Q Consensus       741 ~~~~~~~~~~~~  752 (753)
                      .|||++|+..|.
T Consensus       504 ~~ia~~Ie~~~~  515 (535)
T PRK00106        504 HKVREKIENNLD  515 (535)
T ss_pred             HHHHHHHHHhCc
Confidence            367788776654

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=83.66  E-value=1.9  Score=34.59  Aligned_cols=46  Identities=17%  Similarity=0.214  Sum_probs=34.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhh
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHR   72 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNR   72 (753)
                      ||+|..+|-.+-..+-..++...     ....||..+|++..+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            57899999988887777777665     57889999999999999999885

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	753
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		8e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		1e-04
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		1e-04
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		1e-04
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-04
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		3e-04

>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain Length = 60

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T+ QLE LEK ++   YP    R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 7  TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T+ QLE LEK ++   YP    R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 14 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63

>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 35/54 (64%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          R   T+ QLE LEK ++   YP    R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 3  RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna Length = 60

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 33/50 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T  QL  LEK +  E+Y S   R EL+AQL L +  +++WF +RR+KD++
Sbjct: 9  TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 97

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T  QL  LEK +    Y S A R E++A L L++ Q+++WF +RR+K +K
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo Box B13 Length = 70

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 33/48 (68%)
Query: 32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
          QL  LE+ YA   + ++  R ++SA   LS+RQ+ +WF +RR+K++K+
Sbjct: 18 QLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	753
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-15
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-15
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	5e-15
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	7e-14
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	3e-13
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	6e-13
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	7e-13
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	3e-11
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	3e-09
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-11
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	1e-11
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-11
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-11
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	7e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-06
1e3o_C	160	Octamer-binding transcription factor 1; transcript	6e-11
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	7e-11
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-10
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	6e-10
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-10
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-05
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-09
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-09
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-09
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	6e-09
1uhs_A	72	HOP, homeodomain only protein; structural genomics	9e-09
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-08
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-08
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-08
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	4e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-05
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	8e-08
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	8e-08
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	8e-08
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	4e-06
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	6e-06
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	9e-08
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	1e-07
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-07
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-07
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	2e-07
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	2e-07
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-07
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	4e-07
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	4e-07
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-07
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-07
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	5e-07
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	5e-07
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	6e-07
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	6e-07
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	7e-07
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	7e-07
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	8e-07
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	9e-07
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	9e-07
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	1e-06
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	1e-06
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	1e-06
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-06
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-06
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	2e-06
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-06
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	3e-06
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	3e-06
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	5e-05
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	7e-05
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	7e-04
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	8e-05
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	4e-04
2e19_A	64	Transcription factor 8; homeobox domain, structura	5e-04
3iyk_A	526	VP5; icosahedral virus; HET: MNA; 7.00A {Bluetongu	5e-04
3iyk_A	526	VP5; icosahedral virus; HET: MNA; 7.00A {Bluetongu	9e-04
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	6e-04
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	7e-04

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 71.0 bits (174), Expect = 1e-15
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 24 KRKMKTASQLEILEKTYAVES-YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA 82
               TA    ILEK +   + +P E     LS QL    R +Q WF  RR +++ +  +
Sbjct: 3  SGSSGTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGPS 62

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 70.6 bits (173), Expect = 2e-15
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 21 VKTKRKMKTASQLEILEKTYAVES-YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
          +K           + LEK +   + YP E     LS QL  S R++Q WF HRR +D+ +
Sbjct: 9  IKDSPV-NKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67

Query: 80 PTA 82
            +
Sbjct: 68 GPS 70

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 69.4 bits (170), Expect = 5e-15
 Identities = 16/65 (24%), Positives = 30/65 (46%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
             +  K+  QL  L+ ++    +P ++    L+   GLS R+++ WF  RR   R    
Sbjct: 9  SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG 68

Query: 82 AKRQP 86
          ++  P
Sbjct: 69 SRSGP 73

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 66.1 bits (161), Expect = 7e-14
 Identities = 19/65 (29%), Positives = 29/65 (44%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
           TK K +   QL  LE ++A    P +     L ++  ++ R++  WF  RR K     T
Sbjct: 8  PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET 67

Query: 82 AKRQP 86
           K  P
Sbjct: 68 KKSGP 72

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89

 Score = 65.0 bits (158), Expect = 3e-13
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
            K K KTA QL +L+ ++   S  ++     L AQ  L+ R++  WF  ++ K +    
Sbjct: 12 PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK-KSKALKE 70

Query: 82 AKRQPKDFQSLVPAGE 97
           K +  +  +   +G 
Sbjct: 71 EKMEIDESNAGSSSGP 86

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89

 Score = 64.2 bits (156), Expect = 6e-13
 Identities = 20/62 (32%), Positives = 30/62 (48%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
            K K KT  Q++ILE ++   S+P++A    L  +  LS R++  WF  RR        
Sbjct: 14 PQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ 73

Query: 82 AK 83
          A 
Sbjct: 74 AV 75

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 71.4 bits (174), Expect = 7e-13
 Identities = 27/172 (15%), Positives = 64/172 (37%), Gaps = 1/172 (0%)

Query: 337 RRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQD 396
               H+      E + + E  +I  + EA + R      +   +  +     + E E + 
Sbjct: 671 AAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRA 730

Query: 397 RERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAER 456
              R E E  + +   + +    E   ELER +K  + E +   + + + E+ + ++   
Sbjct: 731 EAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREME-LIYARAQLELEVSKAQQLAN 789

Query: 457 LKVANERAVARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFETLQNL 508
           ++    + +   +   ++  +     E+      S GL + +  D  +  NL
Sbjct: 790 VEAKKFKEMTEALGPGTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSSPINL 841

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 66.0 bits (160), Expect = 3e-11
 Identities = 31/144 (21%), Positives = 59/144 (40%), Gaps = 1/144 (0%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLR 408
           E    S+EA    E +  E+  R  LE+Q IL +   E+ RKE+   +      E     
Sbjct: 663 EITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNA 722

Query: 409 EKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARR 468
           +   E          E    +  L+ +++  E   + E +++V+E E +    +  +   
Sbjct: 723 KAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVS 782

Query: 469 IAKESMALVEDERLELMELAASSK 492
            A++ +A VE ++ + M  A    
Sbjct: 783 KAQQ-LANVEAKKFKEMTEALGPG 805

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 59.4 bits (143), Expect = 3e-09
 Identities = 34/173 (19%), Positives = 60/173 (34%), Gaps = 21/173 (12%)

Query: 336 DRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQ 395
           D+ V     +  +    +S E    R  +A ++ ++  +E   I    +E   + E +R 
Sbjct: 624 DQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIE---ITTNSQEAAAKHEAQRL 680

Query: 396 DRERRKEEERLLREKLREEERY------LREQRRELERREKFLQKESIRAEKRRQKEE-- 447
           ++E R   ER       E E+       L      +E       +   RAE  R + E  
Sbjct: 681 EQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGS 740

Query: 448 ----------LRRVKEAERLKVANERAVARRIAKESMALVEDERLELMELAAS 490
                     L    EAE  +V   R +    A+  + L   +  +L  + A 
Sbjct: 741 VLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVSKAQQLANVEAK 793

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 16/57 (28%), Positives = 30/57 (52%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          K  R   T  QL +L + + + + PSE    E++ + GL  + ++ WF +   K+R+
Sbjct: 8  KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 59.4 bits (144), Expect = 1e-11
 Identities = 12/56 (21%), Positives = 26/56 (46%)

Query: 24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
            + KT  Q+  L+ ++    +P +A    L    GL+  +++ WF   R + ++ 
Sbjct: 7  HHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 58.3 bits (141), Expect = 5e-11
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 3  AASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSD 62
           +S     ++ ++      K  R   T  QLEIL + Y ++S P+  +   ++ ++GL  
Sbjct: 4  GSSGGTGGEEPQRD-----KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKK 58

Query: 63 RQLQMWFCHRRLKDRK 78
          R +Q+WF + R ++RK
Sbjct: 59 RVVQVWFQNTRARERK 74

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 61.3 bits (148), Expect = 6e-11
 Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 15/92 (16%)

Query: 365 AHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLRE-EERYLREQRR 423
           A   R+ +E E    +R+ REEQ RK ++  D   +  E+    +  ++ EE    +++ 
Sbjct: 75  AQADRLTQEPES---IRKWREEQ-RKRLQELDAASKVMEQEWREKAKKDLEEWN--QRQS 128

Query: 424 ELERREKFLQKESIRAEKRRQKEELRRVKEAE 455
           E        Q E  +   R   +   +  +A+
Sbjct: 129 E--------QVEKNKINNRIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 52.5 bits (125), Expect = 7e-08
 Identities = 13/82 (15%), Positives = 39/82 (47%), Gaps = 7/82 (8%)

Query: 348 TEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIR----KEMERQDRERRKEE 403
            +  R ++E    R+    E++ RK L++ D   +  E++ R    K++E  ++ + ++ 
Sbjct: 75  AQADRLTQEPESIRK--WREEQ-RKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQV 131

Query: 404 ERLLREKLREEERYLREQRREL 425
           E+        ++ + ++   ++
Sbjct: 132 EKNKINNRIADKAFYQQPDADI 153

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 47.1 bits (111), Expect = 4e-06
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 13/88 (14%)

Query: 395 QDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEE--LRRVK 452
           Q     +E E +   K REE+R   ++     +      ++  R + ++  EE   R+ +
Sbjct: 76  QADRLTQEPESI--RKWREEQRKRLQELDAASKV----MEQEWREKAKKDLEEWNQRQSE 129

Query: 453 EAERLKVANERAVARRIAKESMALVEDE 480
           + E+ K+ N     R   K      + +
Sbjct: 130 QVEKNKINN-----RIADKAFYQQPDAD 152

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 60.4 bits (146), Expect = 6e-11
 Identities = 13/57 (22%), Positives = 28/57 (49%)

Query: 22  KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
           + KR     +    LEK++     P+      ++ QL +    +++WF +RR K+++
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 60.4 bits (146), Expect = 7e-11
 Identities = 17/75 (22%), Positives = 29/75 (38%)

Query: 4   ASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDR 63
           +S        K   +   + KR          LE  +     PS      L+  L L   
Sbjct: 82  SSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKE 141

Query: 64  QLQMWFCHRRLKDRK 78
            +++WFC+RR K+++
Sbjct: 142 VVRVWFCNRRQKEKR 156

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 59.2 bits (143), Expect = 1e-10
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 5   SEAEEKKKKKKPLEAEVKTKRKMKT---ASQLEILEKTYAVESYPSEALRAELSAQLGLS 61
            EAE+            + KRK +T    +  + LE+ +   S PS      ++ +L L 
Sbjct: 68  EEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLE 127

Query: 62  DRQLQMWFCHRRLKDRK 78
              +++WFC+RR ++++
Sbjct: 128 KEVVRVWFCNRRQREKR 144

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 54.8 bits (132), Expect = 6e-10
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 22 KTKRKMKTASQLEILEKTYA-VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             R   +   L IL+     V  YP +     LSAQL L    +  +F ++R   + 
Sbjct: 8  PRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 61.4 bits (149), Expect = 8e-10
 Identities = 27/147 (18%), Positives = 62/147 (42%), Gaps = 3/147 (2%)

Query: 343  EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
            E   + E + K  E +  +  E       K   + ++     E ++R   ++Q+ E    
Sbjct: 871  ERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILH 930

Query: 403  EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
            E     E+  E  + L+ ++++++++   L+++    E  RQK +L +V    ++K   +
Sbjct: 931  EMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMED 990

Query: 463  RAVARRIAKESMALVEDERLELMELAA 489
                  I ++    +  ER  L E  +
Sbjct: 991  DI---LIMEDQNNKLTKERKLLEERVS 1014

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 57.9 bits (140), Expect = 9e-09
 Identities = 24/148 (16%), Positives = 70/148 (47%), Gaps = 5/148 (3%)

Query: 336  DRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQ 395
             +     E+ +  ++K ++E    A   EA E R+R   +KQ++     E + R E E +
Sbjct: 885  QKHTQLCEEKNLLQEKLQAETELYA---EAEEMRVRLAAKKQELEEILHEMEARIEEEEE 941

Query: 396  DRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAE 455
              ++ + E++ +++++ + E  L E+    ++ +   +K +   + ++ ++++  +++  
Sbjct: 942  RSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQL--EKVTADGKIKKMEDDILIMEDQN 999

Query: 456  RLKVANERAVARRIAKESMALVEDERLE 483
                   + +  R++  +  L E+E   
Sbjct: 1000 NKLTKERKLLEERVSDLTTNLAEEEEKA 1027

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 56.4 bits (136), Expect = 3e-08
 Identities = 27/151 (17%), Positives = 72/151 (47%), Gaps = 13/151 (8%)

Query: 347  RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
              E + K EE +  +E +   +   KELE++     + +  ++++++ +     + EE  
Sbjct: 856  EEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMR 915

Query: 407  LREKLREEERYLREQRRELERREKFLQKE--SIRAEKRRQKEEL----RRVKEAERLKVA 460
            +R   +++E  L E   E+E R +  ++    ++AEK++ ++++     +++E E  +  
Sbjct: 916  VRLAAKKQE--LEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQK 973

Query: 461  NERAVARRIAK-----ESMALVEDERLELME 486
             +        K     + + ++ED+  +L +
Sbjct: 974  LQLEKVTADGKIKKMEDDILIMEDQNNKLTK 1004

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 54.5 bits (131), Expect = 1e-07
 Identities = 26/152 (17%), Positives = 71/152 (46%), Gaps = 12/152 (7%)

Query: 343  EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
            E++    + R  EE   +++++A +K++++++   +  + + EE  R++++    E+   
Sbjct: 926  EEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLE-EQLEEEEAARQKLQ---LEKVTA 981

Query: 403  EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
            + ++  +K+ ++   + +Q  +L +  K L++          +EE  + K   +LK  +E
Sbjct: 982  DGKI--KKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEE-EKAKNLTKLKNKHE 1038

Query: 463  RAVARRIAKESMALVEDERLELMELAASSKGL 494
              ++     E    ++ E     EL    + L
Sbjct: 1039 SMIS-----ELEVRLKKEEKSRQELEKIKRKL 1065

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 27/156 (17%), Positives = 67/156 (42%), Gaps = 10/156 (6%)

Query: 357 ARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERLLREKLREEER 416
             +    +  E + + E  ++   R+++ E   KE+E++   +  EE+ LL+EKL+ E  
Sbjct: 848 PLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQK-HTQLCEEKNLLQEKLQAETE 906

Query: 417 YLREQRRELER---REKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAVARRIAKES 473
              E      R   +++ L++     E R ++EE    + +++L+   ++   + +  E 
Sbjct: 907 LYAEAEEMRVRLAAKKQELEEILHEMEARIEEEE----ERSQQLQAEKKKMQQQMLDLEE 962

Query: 474 MALVEDERLELMELAASSKGLPTIVSLDFETLQNLD 509
              +E+E     +L          +    + +  ++
Sbjct: 963 Q--LEEEEAARQKLQLEKVTADGKIKKMEDDILIME 996

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 50.2 bits (120), Expect = 2e-06
 Identities = 31/146 (21%), Positives = 58/146 (39%), Gaps = 10/146 (6%)

Query: 343  EDVSRTEKKRKSEEARIAREVEAHEKRIRKEL-EKQDILRRKREEQIRKEMERQDRERRK 401
            E   + E+K + E  +I R++E     + +++ E Q  +   + +  +KE E Q    R 
Sbjct: 1045 EVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARL 1104

Query: 402  EEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN 461
            E+E   +    ++ R L     +L+   +  +    +AEK  QK +L    E E LK   
Sbjct: 1105 EDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEK--QKRDLSE--ELEALKTEL 1160

Query: 462  ERAVARRIAKESMALVEDERLELMEL 487
            E          +    E    +  + 
Sbjct: 1161 EDT-----LDTTATQQELRGSDYKDD 1181

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 46.0 bits (109), Expect = 5e-05
 Identities = 36/165 (21%), Positives = 74/165 (44%), Gaps = 17/165 (10%)

Query: 336  DRRVSHDEDVSRTEKKRKSEEARIAR------EVEAHEKRIRKELEKQDILRRKREEQIR 389
            D  +  ++  ++  K+RK  E R++       E E   K + K   K + +  + E +++
Sbjct: 990  DDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLK 1049

Query: 390  KE-MERQDRERRK----EEERLLREKLREEERYLREQRRELERREKFLQ--KESIRAEKR 442
            KE   RQ+ E+ K     E   L E++ E +  + E + +L ++E+ LQ     +  E  
Sbjct: 1050 KEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETS 1109

Query: 443  RQKEELRRVKEAE-RLKVANERAVARRIAKESMALVEDERLELME 486
            ++   L++++E E  +    E        K +    E ++ +L E
Sbjct: 1110 QKNNALKKIRELESHISDLQEDL---ESEKAARNKAEKQKRDLSE 1151

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T  QL +L+  +   +YP +    +LS  L L  R + +WF + R K RK
Sbjct: 15 TDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             QL  L   YA    P   ++ +L    GLS R +++WF ++R KD+K
Sbjct: 11 NEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 11/70 (15%), Positives = 32/70 (45%), Gaps = 11/70 (15%)

Query: 6  EAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQL 65
          + E+  K K  +           +      LE+ +  +   +   + E++ + G++  Q+
Sbjct: 1  KKEKSPKGKSSI-----------SPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQV 49

Query: 66 QMWFCHRRLK 75
          ++WF ++R++
Sbjct: 50 RVWFINKRMR 59

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73

 Score = 52.1 bits (125), Expect = 6e-09
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 22 KTKRKMKTASQLEILEKTYA-VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
                 T  Q+EILE  +  V  +P       ++A+ GL++ Q Q WF  R  + R+
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 60

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 29 TASQLEILEKTYA-VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T  Q+EILE  +  V  +P       ++A+ GL++ Q Q WF  R  + R+
Sbjct: 9  TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 59

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155

 Score = 53.2 bits (127), Expect = 2e-08
 Identities = 16/59 (27%), Positives = 25/59 (42%)

Query: 20  EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             K KR          LE  +     PS      ++ QLGL    +++WF +RR K ++
Sbjct: 95  ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 4  ASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDR 63
           S      KK+  +  + +  R + +++QL +L   +  + Y S     ELS  L LS +
Sbjct: 5  TSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYK 64

Query: 64 QLQMWFCHRRLKDRKAPTAKRQPKD 88
          Q++ WF ++R+K      +KR  K+
Sbjct: 65 QVKTWFQNQRMK------SKRWQKN 83

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 15/59 (25%), Positives = 27/59 (45%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPK 87
             QL  ++  +A+   P      +L+ + GL+ R LQ+WF + R K R+    +    
Sbjct: 15 KHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGG 73

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 52.7 bits (126), Expect = 3e-08
 Identities = 11/57 (19%), Positives = 24/57 (42%)

Query: 22  KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
           + +R   T   +E L   +     P+     E++ +L      +++WF +RR   + 
Sbjct: 94  RKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.4 bits (135), Expect = 3e-08
 Identities = 66/443 (14%), Positives = 129/443 (29%), Gaps = 121/443 (27%)

Query: 361 REVEAHEKRIRKELEKQDILRRK-REEQIRKEMERQDRERRKEEERLLREKLREEERYLR 419
           ++V+   K I  + E   I+  K       +       ++ +  ++ + E LR   ++L 
Sbjct: 36  KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95

Query: 420 EQRRELERREKFLQKESIRAEKRR--------QKEELRRVKEAERLKVA-NERAVARRIA 470
              +  E+R+  +       ++ R         K  + R++   +L+ A  E   A+ + 
Sbjct: 96  SPIKT-EQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154

Query: 471 --------KESMAL--VEDERLEL-MELAAS--SKGLPTIVSLDFETLQNLDLFRDRP-C 516
                   K  +AL      +++  M+      +           E LQ L    D    
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214

Query: 517 TFPPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRF---LITFADVLGLWPFTLD-EFVQAF 572
           +    S  +K        +  +  +  LL    +   L+   +V        + +   AF
Sbjct: 215 SRSDHSSNIKLRI-----HSIQAELRRLLKSKPYENCLLVLLNV---Q----NAKAWNAF 262

Query: 573 HDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGANQNSAVNPGGAHPQIVEGAYAWGF 632
            +   ++L    +T     + D   AA T                  H  +         
Sbjct: 263 -NLSCKIL----LTTRFKQVTDFLSAATT-----------------THISLDH------- 293

Query: 633 DIRSWQLHLNALTWPEILRQFALSAGFGPQ-LNKRNIEKMYPHDNNEGN----------- 680
                  H   LT  E+           PQ L         P +    N           
Sbjct: 294 -------HSMTLTPDEVKSLLLKYLDCRPQDL---------PREVLTTNPRRLSIIAESI 337

Query: 681 -DGENIISNLR--NGSAVGNAVAIMHEMGLSNLRRS--RHRLTPGTVKFAAF-------- 727
            DG     N +  N   +   +    E  L+ L  +  R        + + F        
Sbjct: 338 RDGLATWDNWKHVNCDKLTTII----ESSLNVLEPAEYRKMF----DRLSVFPPSAHIPT 389

Query: 728 HVLSL--EGSEGLTILEVADKIQ 748
            +LSL         ++ V +K+ 
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLH 412

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 6e-07
 Identities = 95/698 (13%), Positives = 175/698 (25%), Gaps = 247/698 (35%)

Query: 178 MGHQKHSVRPL----EAKEYERLDVKPFKDMFTIHPQGATRTV---HEYKFLPEQPTVRS 230
            G  ++  + +    E    +  D K  +DM         +++    E   +       S
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNFDCKDVQDM--------PKSILSKEEIDHIIMSKDAVS 62

Query: 231 ETH-------EKAASSYPYGSPADGSTARNSSLRAGHPFMHGSEQISSGYGFPGQLPNLN 283
            T         K                          F+    +I+  Y F        
Sbjct: 63  GTLRLFWTLLSKQEEMVQK-------------------FVEEVLRIN--YKF-------- 93

Query: 284 LLSHQGRHSHLLPSVSGEY-ENILRKNSFISAAMDAHVGGQPITAMDNAFISSDRRVSHD 342
                     L+  +  E  +  +    +I      +   Q     +             
Sbjct: 94  ----------LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN------------- 130

Query: 343 EDVSRTEK----KRKSEEARIAREVEAH----------------EKRIRKELEKQ----D 378
             VSR +     ++   E R A+ V                     +++ +++ +    +
Sbjct: 131 --VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188

Query: 379 ILRRKREEQIRKEME----RQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQK 434
           +      E + + ++    + D       +     KLR     ++ + R L + + +  +
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS--IQAELRRLLKSKPY--E 244

Query: 435 ES--IRAEKRRQKEELRRVKEAERLK--------------------VANERAVARRIAKE 472
               +          L  V+ A+                       ++        +   
Sbjct: 245 NCLLV----------LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294

Query: 473 SMALVEDERLELMELAASSK----------GLPTIVSLDFETLQNLDLFRDRPCTF---- 518
           SM L  DE   L+      +            P  +S+  E        RD   T+    
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE------SIRDGLATWDNWK 348

Query: 519 ----PPKSVQLKRPFAVQPWNDSEDNIGNLLMVWRF----LITFADVLG-LW----PFTL 565
                  +  ++    V    +       L +   F     I    +L  +W       +
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV---FPPSAHIP-TILLSLIWFDVIKSDV 404

Query: 566 DEFVQAFHDYDPRLLGEIHVTLLRSVIKDIEDAAKTPFTGLGA---------NQNSAVNP 616
              V   H Y   L+ E         I  I    K       A         N     + 
Sbjct: 405 MVVVNKLHKY--SLV-EKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461

Query: 617 GGAHPQIVEGAYAW--GFDIRSWQLHLNALTWPE---ILRQFALSAGF------------ 659
               P  ++  +    G        HL  +  PE   + R   L   F            
Sbjct: 462 DDLIPPYLDQYFYSHIGH-------HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW 514

Query: 660 ---GPQLNKRNIEKMY-PH--DNNEGNDG--ENIISNLRNGSAVGNAVAIMHEMGLSNLR 711
              G  LN     K Y P+  DN+   +     I+  L              E    NL 
Sbjct: 515 NASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPK-----------IE---ENLI 560

Query: 712 RSRHRLTPGTVKFAAFHVLSLEGSEGLTILEVADKIQV 749
            S++      ++ A    L  E      I E A K QV
Sbjct: 561 CSKYT---DLLRIA----LMAEDEA---IFEEAHK-QV 587

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 5e-05
 Identities = 67/463 (14%), Positives = 120/463 (25%), Gaps = 132/463 (28%)

Query: 4   ASEAEEKKKKKKPLEAEV---KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
           A +     K +  ++ ++     K      + LE+L+K       P+   R++ S+ + L
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID-PNWTSRSDHSSNIKL 225

Query: 61  SDRQLQMWFCHRRL-KDRKAPTA---------KRQPKDF----QSLVPAGEKELAGSELV 106
               +Q     RRL K +               +    F    + L+    K++      
Sbjct: 226 RIHSIQAEL--RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF--- 280

Query: 107 RGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGEPLREDGPILGVEFDSLPP 166
              ++      + +              +   +     ++   L +    L      LP 
Sbjct: 281 ---LSAATTTHISL--------------DHHSMTLTPDEVKSLLLK---YLDCRPQDLPR 320

Query: 167 DAFGRPIGP------AAMGHQ--------KH------------SVRPLEAKE----YERL 196
           +       P      A             KH            S+  LE  E    ++RL
Sbjct: 321 EVLT--TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL 378

Query: 197 -----DVK-------------PFKDMFTI------------HPQGATRTVHE-YKFLPEQ 225
                                   D+  +             P+ +T ++   Y  L  +
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVK 438

Query: 226 PTVRSETHEKAASSYPYGSPADGSTARNSSLRA------GHPFMH--GSEQISSGYGFPG 277
                  H      Y      D        L        GH   H    E       F  
Sbjct: 439 LENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH---HLKNIEHPERMTLFRM 495

Query: 278 QLPNLNLLSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAHVGGQPITAMDNAFISSDR 337
              +   L  + RH     + SG   N L                  I   D  +   +R
Sbjct: 496 VFLDFRFLEQKIRHDSTAWNASGSILNTL---------QQLKFYKPYICDNDPKY---ER 543

Query: 338 RVSHDEDVSRT--EKKRKSEEARIAR-EVEAHEKRIRKELEKQ 377
            V+   D      E    S+   + R  + A ++ I +E  KQ
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73

 Score = 49.8 bits (119), Expect = 4e-08
 Identities = 23/61 (37%), Positives = 37/61 (60%)

Query: 18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
            E + KR   T  QL+ LE+ YA   + ++  R  +SA   LS+RQ+ +WF +RR+K++
Sbjct: 4  MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63

Query: 78 K 78
          K
Sbjct: 64 K 64

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 55.1 bits (133), Expect = 7e-08
 Identities = 26/152 (17%), Positives = 54/152 (35%), Gaps = 10/152 (6%)

Query: 349  EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQI------RKEMERQDRERRKE 402
              + K +      +    +K +R  L +    R  +          R   +R+ ++ + E
Sbjct: 853  LVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIE 912

Query: 403  EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
               +  E+ ++    L  +  +L+R+     KE     ++    E+    E E+L+   E
Sbjct: 913  ARSV--ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVE 970

Query: 463  RAVARRIAKESMALVEDERLELMELAASSKGL 494
            R   R   +E+            E+A   K L
Sbjct: 971  R--LRMSEEEAKNATNRVLSLQEEIAKLRKEL 1000

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.0 bits (130), Expect = 2e-07
 Identities = 23/148 (15%), Positives = 57/148 (38%), Gaps = 10/148 (6%)

Query: 347  RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRK---EMERQDRERRKEE 403
            + E +      ++   +E    ++++++++Q+   +   E++         +  + R + 
Sbjct: 910  KIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDV 969

Query: 404  ERLLREKLREEERYLREQRRELERREKFLQK--ESIRAEKRRQKEELRRVKEAERLKVAN 461
            ERL      EE +    +   L+     L+K     + EK+  +E   + K      V+ 
Sbjct: 970  ERL--RMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSE 1027

Query: 462  ERAVARRIAKESMAL---VEDERLELME 486
             +     +  E   L   + D+  E+ E
Sbjct: 1028 LKEQNTLLKTEKEELNRRIHDQAKEITE 1055

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 52.4 bits (126), Expect = 5e-07
 Identities = 23/142 (16%), Positives = 57/142 (40%), Gaps = 4/142 (2%)

Query: 343  EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
            ++     +K  + E   + E E     + + L   +   +    ++   ++ +  + RKE
Sbjct: 942  KEYKSLLEKMNNLEITYSTETEKLRSDV-ERLRMSEEEAKNATNRV-LSLQEEIAKLRKE 999

Query: 403  EERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
              +   EK   EE    + + E E+    L++++   +  +++   R   +A+ +    E
Sbjct: 1000 LHQTQTEKKTIEEW-ADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETME 1058

Query: 463  RAVARRIAKESMALVEDERLEL 484
            + +     +  + L  DERL  
Sbjct: 1059 KKLVEETKQLELDL-NDERLRY 1079

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 50.5 bits (121), Expect = 2e-06
 Identities = 23/149 (15%), Positives = 52/149 (34%), Gaps = 11/149 (7%)

Query: 350  KKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRK----EMERQDRERRKEEE- 404
               ++ +A +  +        ++EL+K  I  R  E   +     E +    +R+ +E+ 
Sbjct: 882  HYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQN 941

Query: 405  ---RLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVAN 461
               + L EK+   E     +  +L    + L+      E+ +         + E  K+  
Sbjct: 942  KEYKSLLEKMNNLEITYSTETEKLRSDVERLRMS---EEEAKNATNRVLSLQEEIAKLRK 998

Query: 462  ERAVARRIAKESMALVEDERLELMELAAS 490
            E    +   K      +  + E  +L + 
Sbjct: 999  ELHQTQTEKKTIEEWADKYKHETEQLVSE 1027

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 49.7 bits (119), Expect = 4e-06
 Identities = 25/150 (16%), Positives = 62/150 (41%), Gaps = 11/150 (7%)

Query: 347  RTEKKRKSEEARIAREVE--AHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
              E K    +  +   +    + + ++  +  Q   RR   ++  K+++ +   R  E  
Sbjct: 862  LREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIE--ARSVERY 919

Query: 405  RLLREKLREEERYLREQRRELERREKFL--QKESIRAEKRRQKEELRRVKEAERLKVANE 462
            + L   L  +   L+ +  E  +  K L  +  ++      + E+LR   + ERL+++ E
Sbjct: 920  KKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLR--SDVERLRMSEE 977

Query: 463  RAVARRIAKESMALVEDERLELMELAASSK 492
             A   + A   +  +++E  +L +    ++
Sbjct: 978  EA---KNATNRVLSLQEEIAKLRKELHQTQ 1004

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 49.3 bits (118), Expect = 4e-06
 Identities = 28/149 (18%), Positives = 50/149 (33%), Gaps = 21/149 (14%)

Query: 357 ARIAREVEAHEKRIRKELEKQDILR----RKREEQIRKEMERQDRERRKEEERLLREKLR 412
              AR      +R R  +  Q   R    RKR + +R          R    R   + + 
Sbjct: 803 GHQARCYATFLRRTRAAIIIQKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMML 862

Query: 413 EEERYLREQ---RRELERREKFLQKESI------------RAEKRRQKEELRRVKEAERL 457
            E + +  Q   R  L R       ++I            + E ++ K E R V+  ++L
Sbjct: 863 REHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKL 922

Query: 458 KVANERAVARRIAKESMALVEDERLELME 486
            +  E  + +   +  +     E   L+E
Sbjct: 923 HIGLENKIMQ--LQRKIDEQNKEYKSLLE 949

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.6 bits (116), Expect = 8e-06
 Identities = 19/140 (13%), Positives = 47/140 (33%), Gaps = 13/140 (9%)

Query: 349  EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRK----------EMERQDRE 398
             K+ KS   ++   +E       ++L       R  EE+ +           E+ +  +E
Sbjct: 941  NKEYKSLLEKM-NNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKE 999

Query: 399  RRKEEERL--LREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAER 456
              + +     + E   + +    +   EL+ +   L+ E     +R   +     +  E+
Sbjct: 1000 LHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEK 1059

Query: 457  LKVANERAVARRIAKESMAL 476
              V   + +   +  E +  
Sbjct: 1060 KLVEETKQLELDLNDERLRY 1079

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.6 bits (116), Expect = 8e-06
 Identities = 27/154 (17%), Positives = 67/154 (43%), Gaps = 8/154 (5%)

Query: 337  RRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMER-- 394
            R V   + +    + +  +  R   E     K + +++   +I      E++R ++ER  
Sbjct: 914  RSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLR 973

Query: 395  -QDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKE 453
              + E +    R+    L+EE   LR++  + +  +K +++     + + + E+L    +
Sbjct: 974  MSEEEAKNATNRV--LSLQEEIAKLRKELHQTQTEKKTIEEW--ADKYKHETEQLVSELK 1029

Query: 454  AERLKVANERA-VARRIAKESMALVEDERLELME 486
             +   +  E+  + RRI  ++  + E    +L+E
Sbjct: 1030 EQNTLLKTEKEELNRRIHDQAKEITETMEKKLVE 1063

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 20/144 (13%), Positives = 52/144 (36%), Gaps = 7/144 (4%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
           V +  +  +     +   +  +  R + ++  ++      ++ +R  + R    R  +  
Sbjct: 831 VRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAI 890

Query: 405 RLLREKLREE--ERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANE 462
             L+   R    +R L++ + E    E+  +K  I  E   +  +L+R  + +      +
Sbjct: 891 VYLQCCYRRMMAKRELKKLKIEARSVER-YKKLHIGLEN--KIMQLQR--KIDEQNKEYK 945

Query: 463 RAVARRIAKESMALVEDERLELME 486
             + +    E     E E+L    
Sbjct: 946 SLLEKMNNLEITYSTETEKLRSDV 969

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 17/87 (19%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 342  DEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRK 401
             +++ +T+ ++K+ E    +     E+ + +  E+  +L+ ++EE     + R+  ++ K
Sbjct: 997  RKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEE-----LNRRIHDQAK 1051

Query: 402  EEERLLREKLREEERYLREQRRELERR 428
            E    + +KL EE + L     +   R
Sbjct: 1052 EITETMEKKLVEETKQLELDLNDERLR 1078

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 48.9 bits (117), Expect = 8e-08
 Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 3/65 (4%)

Query: 22 KTKRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
           + RK +T     QL  L++ +    Y +   RAEL+A LGL+  Q+++WF ++R K +K
Sbjct: 5  SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

Query: 79 APTAK 83
          +  + 
Sbjct: 65 SGPSS 69

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query: 21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          V+  R   T  QL  LEK +  E+Y S   R EL+AQL L +  +++WF +RR+KD++
Sbjct: 1  VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 54.6 bits (130), Expect = 8e-08
 Identities = 22/125 (17%), Positives = 64/125 (51%), Gaps = 3/125 (2%)

Query: 323 QPITAMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRR 382
           +   +M +A + +D+ ++  E     E+ +       A+ +   +++  + +E+++   +
Sbjct: 466 KSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQ 525

Query: 383 KREEQIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKR 442
           +  +Q+ ++ME    +  KE+ER L  KL+E+E+ L+E     ++  + ++ E    + +
Sbjct: 526 EHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKE---GFQKESRIMKNEIQDLQTK 582

Query: 443 RQKEE 447
            ++ +
Sbjct: 583 MRRRK 587

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 49.2 bits (116), Expect = 4e-06
 Identities = 18/91 (19%), Positives = 50/91 (54%), Gaps = 4/91 (4%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
              + ++  E  + ++  ++++ +++  EK +  R     Q+ KE ER    + +E+E+L
Sbjct: 505 MLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDR----VQLLKEQERTLALKLQEQEQL 560

Query: 407 LREKLREEERYLREQRRELERREKFLQKESI 437
           L+E  ++E R ++ + ++L+ + +  +  +I
Sbjct: 561 LKEGFQKESRIMKNEIQDLQTKMRRRKACTI 591

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 48.4 bits (114), Expect = 6e-06
 Identities = 21/110 (19%), Positives = 55/110 (50%), Gaps = 4/110 (3%)

Query: 348 TEKKRKSEEARIAREVEAHEKRIRKE-LEKQDILRRKREEQIRKEMERQDRERRKEEERL 406
           T+   ++++    +E E   +R++ E  +    +  + + +  + ME+++R  ++  ++L
Sbjct: 472 TDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQL 531

Query: 407 LREKLREEERYLREQRRELERR---EKFLQKESIRAEKRRQKEELRRVKE 453
             +   +  + L+EQ R L  +   ++ L KE  + E R  K E++ ++ 
Sbjct: 532 TEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQT 581

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)

Query: 23 TKRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          TK+KM+T    +QL  L+  +  + Y S     ELS+ L LS +Q++ WF ++R+K ++
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97

 Score = 49.5 bits (118), Expect = 1e-07
 Identities = 25/83 (30%), Positives = 39/83 (46%)

Query: 1  MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
          M+      +  K  +P        R   T  QL  LEK +    Y S A R E++A L L
Sbjct: 14 MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 73

Query: 61 SDRQLQMWFCHRRLKDRKAPTAK 83
          ++ Q+++WF +RR+K +K     
Sbjct: 74 NETQVKIWFQNRRMKQKKREREG 96

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 5  SEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQ 64
          +      KK+K         R + T +Q   LE+ +  + Y S   R  L++ + L+  Q
Sbjct: 1  ASDGLPNKKRKR--------RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQ 52

Query: 65 LQMWFCHRRLKDRKAPTAKR 84
          +++WF + R K ++A   K 
Sbjct: 53 VKIWFQNHRYKTKRAQNEKG 72

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 48.6 bits (115), Expect = 2e-07
 Identities = 16/77 (20%), Positives = 29/77 (37%)

Query: 2  EAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLS 61
             S   E   +    ++    K   KT  QL +L+  +    +PS     +L+ + GL+
Sbjct: 6  HHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLA 65

Query: 62 DRQLQMWFCHRRLKDRK 78
             +  WF   R   + 
Sbjct: 66 RTDIVSWFGDTRYAWKN 82

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 20/50 (40%), Positives = 33/50 (66%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T +QL  LE+ +  + Y S A RAE S+ L L++ Q+++WF +RR K ++
Sbjct: 8  TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T +Q+E+LE  + V  YP   +  +L+ +L L   ++Q+WF +RR K ++
Sbjct: 9  TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 49.9 bits (118), Expect = 3e-07
 Identities = 15/59 (25%), Positives = 24/59 (40%)

Query: 20  EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             K  R + T  Q   L   +     PS+ L+  +S QLGL    +  +F + R +   
Sbjct: 96  TPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 24 KRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK 75
          +RK +     +Q+  LE+ +  + Y S   R +L++ L L+  Q+++WF +RR K
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 21/60 (35%), Positives = 37/60 (61%)

Query: 19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +  + KR   +  QL  LE+ YA   + ++  R ++SA   LS+RQ+ +WF +RR+K++K
Sbjct: 5  SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 22 KTKRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          K  R+ +T     QL  LEK +  + Y S   R +L+  LGLS  Q++ W+ +RR+K +K
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56

 Score = 46.2 bits (110), Expect = 4e-07
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + SQ+  LE+ +  + Y + A RA L+  L ++D Q++ WF +RR K R+
Sbjct: 5  SRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 19/58 (32%), Positives = 37/58 (63%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
          K  R   ++ QL  L++ +    Y +E  R +LS++LGL++ Q+++WF ++R K +K+
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 24 KRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP 80
          +RK +     +Q+  LE+ +  + Y S   R  L++ + L+  Q+++WF + R K     
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYK----- 56

Query: 81 TAKRQPKD 88
            KRQ KD
Sbjct: 57 -MKRQAKD 63

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68

 Score = 46.3 bits (110), Expect = 6e-07
 Identities = 22/65 (33%), Positives = 36/65 (55%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
          K  R+  T  Q   LEK +    Y +   R E++  L L++RQ+++WF +RR+K +K   
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

Query: 82 AKRQP 86
           K +P
Sbjct: 63 TKGEP 67

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68

 Score = 46.3 bits (110), Expect = 6e-07
 Identities = 18/64 (28%), Positives = 33/64 (51%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
          +  R   T+SQ+  LE+ +    Y +    A+LSA+L L   Q+++WF +RR + +    
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 82 AKRQ 85
            + 
Sbjct: 63 QHKD 66

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 18/50 (36%), Positives = 33/50 (66%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T +QL++LE  +A   YP   +R E++ ++ L + ++Q+WF +RR K R+
Sbjct: 15 TRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93

 Score = 46.8 bits (111), Expect = 7e-07
 Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 22 KTKRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
            ++K +T+    Q+  LEK +  + Y + A RA L+  L ++D Q++ WF +RR K R+
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74

Query: 79 APTAKRQ 85
              +R+
Sbjct: 75 QTAEERE 81

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 20/67 (29%), Positives = 35/67 (52%)

Query: 19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             + KR   T  Q   LEK +    Y +   R E++  L L++RQ+++WF +RR+K +K
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

Query: 79 APTAKRQ 85
              + +
Sbjct: 71 INKDRAK 77

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T+ QLE LEK ++   YP    R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 7  TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63

 Score = 45.8 bits (109), Expect = 9e-07
 Identities = 22/60 (36%), Positives = 33/60 (55%)

Query: 19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             K  R   T +QL  LEK +    Y S   R EL+  L L++R +++WF +RR+K +K
Sbjct: 1  GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 13/51 (25%), Positives = 20/51 (39%)

Query: 23 TKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR 73
          +  K KT  QL IL+  +    +       +L    GL   ++  WF   R
Sbjct: 5  SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTR 55

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T+ QL+ LE T+    YP  + R E++    L++ ++++WF +RR K RK
Sbjct: 11 TSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 17/50 (34%), Positives = 29/50 (58%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          T  QLE LE  +    YP    R +L+ ++ L + ++++WF +RR K R+
Sbjct: 15 TDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 24 KRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP 80
               +    +Q+  LE+ ++ + Y S   RA L+  L L++ Q+++WF +RR K ++  
Sbjct: 4  HHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

Query: 81 TAK 83
           + 
Sbjct: 64 LSS 66

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 18 EAEVKTKRKMK------TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCH 71
          E  +  KRK +      +ASQL+ LE+ +    YP    R EL+ +  L++ ++Q+WF +
Sbjct: 9  EPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN 68

Query: 72 RRLKDRK 78
          RR + RK
Sbjct: 69 RRARLRK 75

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
            E K +R   T  Q   LEK +    Y +   R E++  L L++RQ+++WF +RR+K +
Sbjct: 25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84

Query: 78 K 78
          K
Sbjct: 85 K 85

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 19/66 (28%), Positives = 33/66 (50%)

Query: 13 KKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHR 72
                   +  R+  T  Q   LEK +    Y +   R E++  L L++RQ+++WF +R
Sbjct: 12 AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71

Query: 73 RLKDRK 78
          R+K +K
Sbjct: 72 RMKLKK 77

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
          K  +   +  Q   LEK +  + Y S   R  L+  L LS+RQ++ WF +RR K R++  
Sbjct: 8  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP 67

Query: 82 AK 83
          + 
Sbjct: 68 SS 69

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 20/59 (33%), Positives = 33/59 (55%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQPK 87
          T  Q+E LEK +    YP    R  L+A++ L + ++Q+WF +RR K R+    + Q +
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRR 73

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 43.0 bits (100), Expect = 5e-05
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 17/46 (36%)

Query: 9  EKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAEL 54
          EK+  KK L+A +K                 YA +S P+ A++A +
Sbjct: 18 EKQALKK-LQASLKL----------------YADDSAPALAIKATM 46

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 44.8 bits (105), Expect = 7e-05
 Identities = 19/121 (15%), Positives = 54/121 (44%), Gaps = 2/121 (1%)

Query: 333 ISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEM 392
           +++      D + ++ +  +           E   K  + E+E + +   K +E+++K  
Sbjct: 295 LAAVTYNGVDNNKNKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQKLK 354

Query: 393 ERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVK 452
           + +   +R+ E+  +++ L  + + L E+RR+ E  +   + +    E++     L + K
Sbjct: 355 DSEAELQRRHEQ--MKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRTLEKNK 412

Query: 453 E 453
           +
Sbjct: 413 K 413

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 41.7 bits (97), Expect = 7e-04
 Identities = 20/122 (16%), Positives = 45/122 (36%), Gaps = 10/122 (8%)

Query: 347 RTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDR--------- 397
           R+ K        +       +       + ++  R    +  + EME +           
Sbjct: 291 RSRKLAAVTYNGVDNNKNKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKV 350

Query: 398 ERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKR-RQKEELRRVKEAER 456
           ++ K+ E  L+ +  + ++ L  Q +ELE + +  + E    E + R  E+    +  E+
Sbjct: 351 QKLKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRTLEK 410

Query: 457 LK 458
            K
Sbjct: 411 NK 412

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 44.7 bits (105), Expect = 8e-05
 Identities = 20/128 (15%), Positives = 52/128 (40%), Gaps = 8/128 (6%)

Query: 335 SDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRK---ELEKQDILRRKREEQIRKE 391
             +        +  + K  S +     +       ++K   E+ +  + R K +E   KE
Sbjct: 300 RCKLEEMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKE 359

Query: 392 MERQDRERRKEEERLLREKLREEERYLREQRRELER-REKFLQKESIRAEKRRQKEELRR 450
            E++  E+       L++  ++E++ L ++++ L+     F Q+++     + Q  +   
Sbjct: 360 AEKELHEKFDR----LKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQGSQAGG 415

Query: 451 VKEAERLK 458
            +  +R K
Sbjct: 416 SQTLKRDK 423

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12 Length = 430

 Score = 42.8 bits (101), Expect = 4e-04
 Identities = 20/151 (13%), Positives = 49/151 (32%), Gaps = 13/151 (8%)

Query: 342 DEDVSRTEKKRKSEEARI---AREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQ-DR 397
            + VS  +     E   I   A+     +  + +   +  +   +  E++   ++ + + 
Sbjct: 123 GKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQYKKEY 182

Query: 398 ERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERL 457
           E  KE+   L +   E  +  R    EL+  +    +   +  +          +   R 
Sbjct: 183 EELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPR---GSRYDEAEG--RF 237

Query: 458 KVANER----AVARRIAKESMALVEDERLEL 484
           +V N          +        ++ +R EL
Sbjct: 238 EVINNETEQLKAEEKKILNQFLKIKKKRKEL 268

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 9/47 (19%), Positives = 21/47 (44%)

Query: 32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
           L +L+  YA+ + PS    ++++  + L    ++ WF   +     
Sbjct: 14 LLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60

>3iyk_A VP5; icosahedral virus; HET: MNA; 7.00A {Bluetongue virus} Length = 526

 Score = 42.3 bits (99), Expect = 5e-04
 Identities = 23/125 (18%), Positives = 50/125 (40%), Gaps = 23/125 (18%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEERL-- 406
           E ++++E  R       +  +I+++         K  E++   M  +     ++E++   
Sbjct: 103 EDEQRNELVR-----LKYNDKIKEKF-------GKELEEVYNFMNGEANAEIEDEKQFDI 150

Query: 407 LREKLREEERYLREQRRELERREKFLQKES---------IRAEKRRQKEELRRVKEAERL 457
           L + +    + L E+  ++ R    LQKE          +  E R + + L+   E ER 
Sbjct: 151 LNKAVTSYNKILTEEDLQMRRLATALQKEIGERTHAETVMVKEYRDKIDALKNAIEVERD 210

Query: 458 KVANE 462
            +  E
Sbjct: 211 GMQEE 215

>3iyk_A VP5; icosahedral virus; HET: MNA; 7.00A {Bluetongue virus} Length = 526

 Score = 41.5 bits (97), Expect = 9e-04
 Identities = 19/124 (15%), Positives = 47/124 (37%), Gaps = 6/124 (4%)

Query: 389 RKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKE-SIRAEKRRQKEE 447
            + ++ + +E   E+      +L+  ++   +  +ELE    F+  E +   E  +Q + 
Sbjct: 92  ERGIQAKLKELEDEQRNE-LVRLKYNDKIKEKFGKELEEVYNFMNGEANAEIEDEKQFDI 150

Query: 448 LRRVKEAERLKVANERA----VARRIAKESMALVEDERLELMELAASSKGLPTIVSLDFE 503
           L +   +    +  E      +A  + KE       E + + E       L   + ++ +
Sbjct: 151 LNKAVTSYNKILTEEDLQMRRLATALQKEIGERTHAETVMVKEYRDKIDALKNAIEVERD 210

Query: 504 TLQN 507
            +Q 
Sbjct: 211 GMQE 214

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95

 Score = 38.9 bits (90), Expect = 6e-04
 Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 15/65 (23%)

Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLG---------------LSDRQLQMWFCHRR 73
              L ++E  +    YP EA R E++                   ++  ++  WF +RR
Sbjct: 15 RKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRR 74

Query: 74 LKDRK 78
           + ++
Sbjct: 75 KEIKR 79

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 42.0 bits (99), Expect = 7e-04
 Identities = 10/108 (9%), Positives = 27/108 (25%), Gaps = 7/108 (6%)

Query: 337  RRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQD 396
               +   D     + +         E ++ E +   +L            Q+ +      
Sbjct: 909  LGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSI-------LAQLTELNYNGV 961

Query: 397  RERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQ 444
             E  + ++    ++    +      +  L    + LQK          
Sbjct: 962  PELTERKDTFFAQQWTGVKSSAETYKNTLLAELERLQKIEDLHHHHHH 1009

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	753
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.66
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.65
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.65
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.65
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.64
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.64
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.64
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.64
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.63
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.63
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.63
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.63
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.63
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.63
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.62
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.62
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.62
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.62
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.62
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.62
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.62
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.61
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.61
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.61
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.61
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.6
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.6
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.6
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.59
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.59
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.59
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.59
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.59
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.59
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.59
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.59
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.58
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.57
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.57
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.57
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.57
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.56
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.56
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.56
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.56
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.55
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.55
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.54
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.54
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.54
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.53
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.53
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.52
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.51
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.5
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.5
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.5
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.49
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.49
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.48
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.47
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.47
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.47
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.47
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.47
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.47
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.46
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.45
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.44
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.44
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.41
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.29
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.2
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.16
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.05
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.02
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	98.84
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.11
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	89.67
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	87.26
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	81.51

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.66  E-value=1.4e-16  Score=133.83  Aligned_cols=65  Identities=32%  Similarity=0.540  Sum_probs=61.4

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..++.|++||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            45678899999999999999999999999999999999999999999999999999999999753

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.65  E-value=2.2e-16  Score=136.09  Aligned_cols=67  Identities=28%  Similarity=0.520  Sum_probs=63.1

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+++.|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~   69 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ   69 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHcc
Confidence            4567889999999999999999999999999999999999999999999999999999999977655

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.65  E-value=1.1e-16  Score=131.23  Aligned_cols=62  Identities=27%  Similarity=0.402  Sum_probs=53.7

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ++.|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.+
T Consensus         1 g~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~q   62 (62)
T 2vi6_A            1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ   62 (62)
T ss_dssp             -------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGGC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhcC
Confidence            35788999999999999999999999999999999999999999999999999999999863

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.65  E-value=2.3e-16  Score=132.47  Aligned_cols=66  Identities=27%  Similarity=0.442  Sum_probs=61.9

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ..++.|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+....
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            456788999999999999999999999999999999999999999999999999999999997543

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-16  Score=132.36  Aligned_cols=65  Identities=28%  Similarity=0.496  Sum_probs=61.4

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      .++..|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+...
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            45678899999999999999999999999999999999999999999999999999999998654

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-16  Score=132.33  Aligned_cols=65  Identities=29%  Similarity=0.488  Sum_probs=61.4

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      .+++.|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             SCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            46678899999999999999999999999999999999999999999999999999999998653

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=3.1e-16  Score=135.19  Aligned_cols=65  Identities=32%  Similarity=0.452  Sum_probs=61.3

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..++.|+.||.||..|+..|+..|..++||+..++..||..|||++.||+|||||||+|+|+...
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            35678889999999999999999999999999999999999999999999999999999999754

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.64  E-value=2.2e-16  Score=132.48  Aligned_cols=65  Identities=25%  Similarity=0.444  Sum_probs=61.6

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..++.|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+...
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            45678899999999999999999999999999999999999999999999999999999999764

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.63  E-value=2.1e-16  Score=129.93  Aligned_cols=61  Identities=36%  Similarity=0.560  Sum_probs=56.3

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ..|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            5788999999999999999999999999999999999999999999999999999999853

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.63  E-value=4.4e-16  Score=135.40  Aligned_cols=65  Identities=26%  Similarity=0.440  Sum_probs=61.6

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..++.|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+..+
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            45678899999999999999999999999999999999999999999999999999999999764

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=5e-16  Score=133.77  Aligned_cols=67  Identities=25%  Similarity=0.362  Sum_probs=62.5

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+++.|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A            3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            3567889999999999999999999999999999999999999999999999999999999976544

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.63  E-value=4.5e-16  Score=134.13  Aligned_cols=62  Identities=15%  Similarity=0.153  Sum_probs=58.9

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAV----ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~----~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      ..+++||.||.||..|+..|+..|..    ++||+..+|.+||..|||++.+|+|||||||+|+|+
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            34678899999999999999999999    999999999999999999999999999999999886

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.63  E-value=3.1e-16  Score=135.19  Aligned_cols=68  Identities=29%  Similarity=0.499  Sum_probs=63.5

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      .++..|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+......
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            45678899999999999999999999999999999999999999999999999999999999876553

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.63  E-value=6.8e-16  Score=131.14  Aligned_cols=69  Identities=30%  Similarity=0.453  Sum_probs=64.0

Q ss_pred             CccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           16 PLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        16 ~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      ++.+++++.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....+
T Consensus         4 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q   72 (75)
T 2m0c_A            4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQ   72 (75)
T ss_dssp             CCCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhh
Confidence            456788899999999999999999999999999999999999999999999999999999999876543

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A

Probab=99.62  E-value=3.5e-16  Score=127.74  Aligned_cols=59  Identities=32%  Similarity=0.571  Sum_probs=53.4

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      ..|+.||.||..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            36789999999999999999999999999999999999999999999999999999987

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.62  E-value=6.9e-16  Score=130.69  Aligned_cols=66  Identities=35%  Similarity=0.517  Sum_probs=62.1

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      ..+.|++|+.||..|+..|+..|..++||+..++..||..+||++.+|+|||||||+|+|+.....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKL   69 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhccc
Confidence            456788999999999999999999999999999999999999999999999999999999986654

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P

Probab=99.62  E-value=2.5e-16  Score=131.56  Aligned_cols=65  Identities=29%  Similarity=0.470  Sum_probs=61.2

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +++|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         1 g~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CCSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            46788999999999999999999999999999999999999999999999999999999976654

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.62  E-value=5.2e-16  Score=130.31  Aligned_cols=65  Identities=31%  Similarity=0.384  Sum_probs=60.9

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      .+...+++|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||||||+|+|+...
T Consensus         3 ~~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            3 SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            35678889999999999999999999999999999999999999999999999999999998654

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.62  E-value=5.8e-16  Score=128.49  Aligned_cols=62  Identities=29%  Similarity=0.536  Sum_probs=59.1

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ++|+.||.||..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            47889999999999999999999999999999999999999999999999999999998753

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.62  E-value=5.5e-16  Score=125.21  Aligned_cols=58  Identities=36%  Similarity=0.578  Sum_probs=55.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      |++||.||..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   58 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhccC
Confidence            5789999999999999999999999999999999999999999999999999999873

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.62  E-value=5.1e-16  Score=129.66  Aligned_cols=64  Identities=28%  Similarity=0.466  Sum_probs=60.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      +|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+......
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~~   65 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHK   65 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcccc
Confidence            5789999999999999999999999999999999999999999999999999999999776553

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A

Probab=99.61  E-value=6.8e-16  Score=132.04  Aligned_cols=66  Identities=26%  Similarity=0.456  Sum_probs=61.7

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      ..++|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            457788999999999999999999999999999999999999999999999999999999876544

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A

Probab=99.61  E-value=4.8e-16  Score=129.84  Aligned_cols=63  Identities=33%  Similarity=0.509  Sum_probs=59.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~   64 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK   64 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcccc
Confidence            578999999999999999999999999999999999999999999999999999999976544

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.61  E-value=8e-16  Score=128.44  Aligned_cols=63  Identities=24%  Similarity=0.459  Sum_probs=59.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~   64 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHh
Confidence            578999999999999999999999999999999999999999999999999999999987654

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.61  E-value=6e-16  Score=133.21  Aligned_cols=65  Identities=31%  Similarity=0.525  Sum_probs=61.1

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ...+.|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+...
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            35678889999999999999999999999999999999999999999999999999999999754

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=5.1e-16  Score=133.81  Aligned_cols=65  Identities=15%  Similarity=0.171  Sum_probs=61.0

Q ss_pred             CccCcCCCCCCCCCHHHHHHHHHHHhhc----CCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           16 PLEAEVKTKRKMKTASQLEILEKTYAVE----SYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        16 ~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~----~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      +..++.|+.||.||..|+.+|+..|..+    +||+..++..||..|||++.+|+|||||||+|+|+..
T Consensus         3 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            3 SGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            3456788999999999999999999999    9999999999999999999999999999999999854

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.60  E-value=1e-15  Score=131.87  Aligned_cols=61  Identities=18%  Similarity=0.235  Sum_probs=57.8

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAV-----ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~-----~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      ...++||.||.||..|+..|+ .|..     ++||+..+|.+||..|||++.+|+|||||||+|+++
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            456788999999999999999 7999     999999999999999999999999999999999986

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.60  E-value=9.7e-16  Score=124.71  Aligned_cols=58  Identities=40%  Similarity=0.642  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      |+.||.||..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            6789999999999999999999999999999999999999999999999999999985

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*

Probab=99.59  E-value=9.9e-16  Score=132.34  Aligned_cols=63  Identities=30%  Similarity=0.475  Sum_probs=54.9

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      .++.|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+..
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            456788999999999999999999999999999999999999999999999999999999865

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.59  E-value=1.5e-15  Score=126.34  Aligned_cols=63  Identities=29%  Similarity=0.536  Sum_probs=59.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .|++||.||..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+.....
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~~   63 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRES   63 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCTT
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchhc
Confidence            368899999999999999999999999999999999999999999999999999999976543

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A

Probab=99.59  E-value=1e-15  Score=130.96  Aligned_cols=65  Identities=31%  Similarity=0.457  Sum_probs=61.1

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      .++.|++||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+....
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            45678899999999999999999999999999999999999999999999999999999987653

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.59  E-value=1.2e-15  Score=133.85  Aligned_cols=64  Identities=33%  Similarity=0.512  Sum_probs=55.8

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ..++.|+.||.||..|+..|+..|..++||+..+|..||..|||++.+|+|||||||+|+|+..
T Consensus        24 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            3467889999999999999999999999999999999999999999999999999999999865

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.59  E-value=1.8e-15  Score=121.99  Aligned_cols=57  Identities=28%  Similarity=0.515  Sum_probs=55.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      +|+.|+.||..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            567899999999999999999999999999999999999999999999999999986

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=99.59  E-value=1.1e-15  Score=131.95  Aligned_cols=65  Identities=34%  Similarity=0.567  Sum_probs=59.5

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ..++.|+.||.||..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|+...
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            45678889999999999999999999999999999999999999999999999999999998653

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.7e-15  Score=128.01  Aligned_cols=66  Identities=23%  Similarity=0.458  Sum_probs=60.7

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .....+.|+.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         5 ~~~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~   70 (76)
T 2dn0_A            5 SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSR   70 (76)
T ss_dssp             CSCCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccC
Confidence            345566799999999999999999999999999999999999999999999999999999976654

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.59  E-value=1.4e-15  Score=134.86  Aligned_cols=67  Identities=31%  Similarity=0.430  Sum_probs=62.4

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      ...+.|+.||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            3467888999999999999999999999999999999999999999999999999999999976554

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*

Probab=99.58  E-value=1.5e-15  Score=124.00  Aligned_cols=59  Identities=14%  Similarity=0.378  Sum_probs=48.6

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      ++.++.|+.||..|+.+|+..|..++||+..++..||..+||++.||++||||||+++|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            46788999999999999999999999999999999999999999999999999999975

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.57  E-value=2.2e-15  Score=122.64  Aligned_cols=57  Identities=39%  Similarity=0.601  Sum_probs=50.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        24 ~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      .||.||..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            589999999999999999999999999999999999999999999999999999865

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=4.8e-15  Score=126.18  Aligned_cols=62  Identities=29%  Similarity=0.460  Sum_probs=57.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .++|+.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~   69 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK   69 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSS
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcc
Confidence            35677899999999999999999999999999999999999999999999999999987654

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.57  E-value=3.3e-15  Score=126.43  Aligned_cols=63  Identities=25%  Similarity=0.344  Sum_probs=58.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+++||.||..|+.+|+..|.. ++||+..++..||..+||++.+|+|||||||+|+|+.....
T Consensus         2 ~~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~   65 (73)
T 2hi3_A            2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   65 (73)
T ss_dssp             CCSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCC
Confidence            3578999999999999999995 99999999999999999999999999999999999976443

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.57  E-value=2.8e-15  Score=127.11  Aligned_cols=61  Identities=21%  Similarity=0.281  Sum_probs=56.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           23 TKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        23 r~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+|+.||.+|+.+|+..|..++||+..+|.+||..+||++.||+|||||||+|+|+..-.-
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w   65 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKW   65 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHH
Confidence            4677899999999999999999999999999999999999999999999999999876544

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.56  E-value=3.7e-15  Score=125.82  Aligned_cols=62  Identities=26%  Similarity=0.367  Sum_probs=57.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .++|+.||..|+..|+..|.. ++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~   64 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   64 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCC
Confidence            468999999999999999996 99999999999999999999999999999999999976443

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1

Probab=99.56  E-value=2.2e-15  Score=134.61  Aligned_cols=66  Identities=33%  Similarity=0.475  Sum_probs=56.7

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ..+..+++||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+....
T Consensus        30 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            346788899999999999999999999999999999999999999999999999999999987543

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.56  E-value=8.1e-15  Score=128.43  Aligned_cols=57  Identities=25%  Similarity=0.375  Sum_probs=54.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           27 MKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        27 ~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .||..|+.+|+..|..++||+..+|.+||..|||+++||+|||||||+||++.....
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~   73 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   73 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHh
Confidence            899999999999999999999999999999999999999999999999999876554

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.56  E-value=3e-15  Score=120.15  Aligned_cols=54  Identities=33%  Similarity=0.491  Sum_probs=51.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           26 KMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        26 t~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      |.||..|+..|+..|..++||+..++..||..+||++.+|+|||||||+|+||+
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            689999999999999999999999999999999999999999999999999985

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.55  E-value=7.1e-15  Score=124.65  Aligned_cols=64  Identities=23%  Similarity=0.423  Sum_probs=59.8

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      ..++.|+.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   68 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQ   68 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCC
Confidence            4577899999999999999999999999999999999999999999999999999999976543

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.55  E-value=4.8e-15  Score=131.92  Aligned_cols=67  Identities=19%  Similarity=0.352  Sum_probs=63.1

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------CChHHHhHhhhhhhhhhccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLG---------------LSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lg---------------L~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ...++|+.|+.||..|+.+|+..|..++||+..++..||..||               |++.+|++||||||+|+|+...
T Consensus         3 ~~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            4567889999999999999999999999999999999999999               9999999999999999999876


Q ss_pred             cc
Q 004454           82 AK   83 (753)
Q Consensus        82 ~~   83 (753)
                      ..
T Consensus        83 ~~   84 (95)
T 2cuf_A           83 IA   84 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.54  E-value=9.9e-15  Score=123.45  Aligned_cols=65  Identities=20%  Similarity=0.309  Sum_probs=60.4

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      .++.|++|+.|+..|+.+|+..|..   ++||+..++..||..+||++.||++||||||+|+++....
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            4678889999999999999999987   9999999999999999999999999999999999987543

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=99.54  E-value=4.8e-15  Score=142.15  Aligned_cols=64  Identities=20%  Similarity=0.503  Sum_probs=56.5

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ..+++||+||.||..|+..|+..|..++||+..+|..||..|||++++|+|||||||+|+||.+
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~k  146 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK  146 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhccC
Confidence            4567888999999999999999999999999999999999999999999999999999999863

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.54  E-value=7.4e-15  Score=120.99  Aligned_cols=60  Identities=25%  Similarity=0.497  Sum_probs=57.1

Q ss_pred             cCCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           20 EVKTKRKMKTASQLEILEKTY---AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F---~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      ..+++|+.||..|+.+|+..|   ..++||+..++..||..+||++.||++||||||+|+||.
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   64 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   64 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhccC
Confidence            467899999999999999999   999999999999999999999999999999999999873

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=99.53  E-value=1e-14  Score=123.34  Aligned_cols=63  Identities=27%  Similarity=0.490  Sum_probs=59.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTY---AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F---~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .|++|+.||..|+.+|+..|   ..++||+..++..||..+||++.||++||||||+|+|+.....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   66 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccc
Confidence            37899999999999999999   9999999999999999999999999999999999999876654

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.53  E-value=1.1e-14  Score=119.01  Aligned_cols=62  Identities=23%  Similarity=0.268  Sum_probs=57.7

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      .++.+||.||.|+.+||.+|+..|+. ++||+...|..||..|||++++|+|||||+|.-.+.
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~~   65 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeecC
Confidence            35678899999999999999999999 999999999999999999999999999999986554

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.52  E-value=1.1e-14  Score=129.86  Aligned_cols=64  Identities=22%  Similarity=0.352  Sum_probs=57.0

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ....+++|+.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.+.
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~l   85 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL   85 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcc
Confidence            4566789999999999999999999999999999999999999999999999999999999753

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.51  E-value=3.2e-14  Score=123.48  Aligned_cols=67  Identities=24%  Similarity=0.269  Sum_probs=61.3

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+.++|++|+.|+..|+.+|+.+|..   ++||+..++..||..+||++.||+|||||||+|+++.....
T Consensus         3 ~~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A            3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            45678889999999999999999987   59999999999999999999999999999999998865544

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=99.50  E-value=2.4e-14  Score=116.36  Aligned_cols=56  Identities=25%  Similarity=0.350  Sum_probs=54.1

Q ss_pred             CCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           24 KRKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        24 ~Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      +|+.||..|+.+|+..|..   ++||+..++..||..+||++.||++||||||+|+|+.
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            4789999999999999999   9999999999999999999999999999999999985

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=2.8e-14  Score=127.38  Aligned_cols=66  Identities=18%  Similarity=0.268  Sum_probs=61.8

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHh---------------------CCChHHHhHhhhhhhhhh
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQL---------------------GLSDRQLQMWFCHRRLKD   76 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~l---------------------gL~~~qVqiWFqNRR~K~   76 (753)
                      .+++||.|+.|+..|+.+|+..|..++||+..+|++||..|                     +|++.+|+|||||||+++
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            45788999999999999999999999999999999999999                     799999999999999999


Q ss_pred             ccccccc
Q 004454           77 RKAPTAK   83 (753)
Q Consensus        77 kr~~~~~   83 (753)
                      ++.....
T Consensus        83 kr~~~~~   89 (102)
T 2da6_A           83 AFRQKLA   89 (102)
T ss_dssp             HHHHHHH
T ss_pred             HHhhHhh
Confidence            9976655

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.50  E-value=2.4e-14  Score=125.19  Aligned_cols=63  Identities=27%  Similarity=0.490  Sum_probs=58.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTY---AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F---~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .||+|+.||..|+.+|+..|   ..++||+..++..||..+||++.||++||||||+|+|+.....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            36889999999999999999   9999999999999999999999999999999999999987654

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.49  E-value=1.9e-14  Score=140.57  Aligned_cols=66  Identities=24%  Similarity=0.416  Sum_probs=52.7

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ..+++||+||.||..|+..|+..|..++||+..+|..||..|||++++|+|||||||+|+||....
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            356788899999999999999999999999999999999999999999999999999999997643

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.49  E-value=1.4e-14  Score=122.28  Aligned_cols=60  Identities=33%  Similarity=0.507  Sum_probs=55.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           21 VKTKRKMKTASQLEILEKTY-AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F-~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ..+.|+.++..|+..||..| ..++||+...|.+||..|||+++||+|||||||+|+|+..
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            45567788899999999999 9999999999999999999999999999999999999864

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=6.9e-14  Score=122.93  Aligned_cols=61  Identities=33%  Similarity=0.470  Sum_probs=55.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccccC
Q 004454           24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        24 ~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      ++..||..|+.+|+..|..++||+..+|..||..|||++++|+|||||||+|+++......
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~   76 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL   76 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCC
T ss_pred             ccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhh
Confidence            3345999999999999999999999999999999999999999999999999998776553

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.47  E-value=4.9e-14  Score=117.78  Aligned_cols=57  Identities=28%  Similarity=0.526  Sum_probs=53.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           26 KMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        26 t~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ..+|..|+..||..|..++||+...|..||..|||++++|+|||||||+|+|+....
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~   65 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS   65 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhh
Confidence            468999999999999999999999999999999999999999999999999997643

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.47  E-value=5.1e-14  Score=123.19  Aligned_cols=61  Identities=23%  Similarity=0.315  Sum_probs=57.5

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      ..+++++|+.||..|+.+|+..|..   ++||+..++..||..+||++.||++||||||+|+|.
T Consensus        24 ~~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             EESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            4567778999999999999999999   999999999999999999999999999999999874

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.47  E-value=3.7e-14  Score=138.01  Aligned_cols=61  Identities=21%  Similarity=0.416  Sum_probs=55.2

Q ss_pred             CcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           19 AEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        19 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      .++||+||.||..|+..|+..|..++||+..+|..||..|||++.+|+|||||||+|+||.
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            5788899999999999999999999999999999999999999999999999999999986

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.47  E-value=3.7e-14  Score=116.29  Aligned_cols=52  Identities=23%  Similarity=0.488  Sum_probs=49.9

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           28 KTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        28 ~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      .|..|+..|+..|..++||+..++.+||..|||++++|++||||||+|+|+.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            4789999999999999999999999999999999999999999999999974

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.47  E-value=4.3e-14  Score=126.41  Aligned_cols=66  Identities=21%  Similarity=0.348  Sum_probs=54.4

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHH------------------hC---CChHHHhHhhhhhhhhh
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQ------------------LG---LSDRQLQMWFCHRRLKD   76 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~------------------lg---L~~~qVqiWFqNRR~K~   76 (753)
                      .++.|+.|+.||..|+.+|+..|..++||+...|.+||..                  ||   |++.+|+|||||||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4578889999999999999999999999999999999999                  88   99999999999999999


Q ss_pred             ccccccc
Q 004454           77 RKAPTAK   83 (753)
Q Consensus        77 kr~~~~~   83 (753)
                      ++.+...
T Consensus        86 k~k~~~~   92 (99)
T 1lfb_A           86 AFRHKLA   92 (99)
T ss_dssp             SCCC---
T ss_pred             HHhchhh
Confidence            8876543

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.47  E-value=6e-14  Score=121.72  Aligned_cols=60  Identities=23%  Similarity=0.307  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      +++|+.||..|+.+|+..|..   ++||+..++..||..+||++.||++||||||+|+|+...
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            456777999999999999999   999999999999999999999999999999999998643

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=99.46  E-value=4.2e-14  Score=136.92  Aligned_cols=62  Identities=26%  Similarity=0.374  Sum_probs=58.8

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      .+++||+||.||..|+..|+..|..++||+..++..||..|||++++|+|||||||+|+||.
T Consensus        93 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           93 VQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             ccCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            35788899999999999999999999999999999999999999999999999999999985

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=99.45  E-value=7.6e-14  Score=134.54  Aligned_cols=61  Identities=18%  Similarity=0.395  Sum_probs=58.8

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      .+++||+||.||..|+..|+..|..++||+..++..||..|||++.+|+|||||||+|+||
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            4678889999999999999999999999999999999999999999999999999999987

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=1.3e-13  Score=113.73  Aligned_cols=56  Identities=16%  Similarity=0.274  Sum_probs=51.9

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        25 Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      +..++..|+..|+..|..++||+..+|..||..|||++++|+|||||||+|.++.+
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~~   62 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ   62 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCSS
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCCC
Confidence            45567999999999999999999999999999999999999999999999988743

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.44  E-value=7.2e-14  Score=114.65  Aligned_cols=51  Identities=35%  Similarity=0.519  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           30 ASQLEILEKTY-AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        30 ~~Ql~~Le~~F-~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      ..|+..||..| ..++||+...|.+||..|||+++||+|||||||+|+|+..
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~   60 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG   60 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence            45899999999 6799999999999999999999999999999999999754

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.41  E-value=1.9e-13  Score=133.57  Aligned_cols=66  Identities=23%  Similarity=0.236  Sum_probs=55.2

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ...+.||+||.||..|+..|+..|..++||+..+|..||..|||++.||+|||||||+|+|+....
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            356788999999999999999999999999999999999999999999999999999999986543

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.29  E-value=2.9e-12  Score=106.58  Aligned_cols=57  Identities=21%  Similarity=0.331  Sum_probs=50.7

Q ss_pred             CCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           27 MKTASQLEILEKTYA---VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        27 ~~t~~Ql~~Le~~F~---~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .|+..|+.+|+..|.   .++||+..++..||..+||+..||++||||||+|+++.....
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   63 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQ   63 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC---
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHH
Confidence            699999999999999   999999999999999999999999999999999999875543

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=99.20  E-value=7e-12  Score=125.15  Aligned_cols=61  Identities=20%  Similarity=0.330  Sum_probs=54.0

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------------CChHHHhHhhhhhhhhh
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLG---------------------LSDRQLQMWFCHRRLKD   76 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lg---------------------L~~~qVqiWFqNRR~K~   76 (753)
                      .++.||.|+.|+..|+.+|+..|..++||+...|.+||..+|                     |++.+|++||||||+++
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            357789999999999999999999999999999999999999                     99999999999999998


Q ss_pred             cc
Q 004454           77 RK   78 (753)
Q Consensus        77 kr   78 (753)
                      +.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            74

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=2.5e-11  Score=100.05  Aligned_cols=46  Identities=22%  Similarity=0.476  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhh
Q 004454           30 ASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK   75 (753)
Q Consensus        30 ~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K   75 (753)
                      .+|+..|+.+|..+++|+..++..||..+||+.++|+|||||||+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999999974

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.05  E-value=1.3e-10  Score=117.11  Aligned_cols=59  Identities=20%  Similarity=0.402  Sum_probs=53.6

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------------CChHHHhHhhhhhhhhh
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLG---------------------LSDRQLQMWFCHRRLKD   76 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lg---------------------L~~~qVqiWFqNRR~K~   76 (753)
                      .++.||.|+.|+..|+.+|+..|..++||+..+|++||..+|                     |++.+|++||||||+..
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~  218 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE  218 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTC
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhh
Confidence            467788999999999999999999999999999999999988                     89999999999999874

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=99.02  E-value=3e-10  Score=98.96  Aligned_cols=59  Identities=31%  Similarity=0.327  Sum_probs=54.3

Q ss_pred             CCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           25 RKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        25 Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      -.+|+..++.+|+.+|..   ++||+..++..||..+||++.||++||+|+|.|+++.....
T Consensus         9 ~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A            9 SHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            457999999999999987   99999999999999999999999999999999998876544

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=98.84  E-value=1.6e-09  Score=119.38  Aligned_cols=56  Identities=14%  Similarity=0.392  Sum_probs=53.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      ++.|+.|+..|+..|+..|..++||+..+|.+||..+||+++||+|||||||+|+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            45678899999999999999999999999999999999999999999999999986

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.11  E-value=2.6e-07  Score=67.07  Aligned_cols=22  Identities=36%  Similarity=0.687  Sum_probs=19.3

Q ss_pred             HHHhHhhhhhhhhhcccccccC
Q 004454           63 RQLQMWFCHRRLKDRKAPTAKR   84 (753)
Q Consensus        63 ~qVqiWFqNRR~K~kr~~~~~~   84 (753)
                      +||+|||||||+|||+......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            4899999999999999887653

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=89.67  E-value=0.27  Score=56.67  Aligned_cols=14  Identities=21%  Similarity=0.394  Sum_probs=9.6

Q ss_pred             HHHHHHHHhCCChH
Q 004454           50 LRAELSAQLGLSDR   63 (753)
Q Consensus        50 ~r~~LA~~lgL~~~   63 (753)
                      ....++..|||.+.
T Consensus        29 ll~~V~~~LgL~e~   42 (575)
T 2i1j_A           29 LFDQVVKTIGLREV   42 (575)
T ss_dssp             HHHHHHHHHTCCCG
T ss_pred             HHHHHHHHcCCCCc
Confidence            34457888998763

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.26  E-value=0.7  Score=37.98  Aligned_cols=43  Identities=26%  Similarity=0.334  Sum_probs=38.5

Q ss_pred             CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhh
Q 004454           29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCH   71 (753)
Q Consensus        29 t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqN   71 (753)
                      ++.-.+.|+.+|.....+.......|..+.+|+..||+-||-.
T Consensus        14 ~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           14 PPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            3344578999999999999999999999999999999999954

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=81.51  E-value=0.87  Score=52.45  Aligned_cols=9  Identities=11%  Similarity=0.453  Sum_probs=3.8

Q ss_pred             HHHHhhhhh
Q 004454          589 RSVIKDIED  597 (753)
Q Consensus       589 k~l~~d~e~  597 (753)
                      +.|-.|++.
T Consensus       521 ~~L~~el~~  529 (575)
T 2i1j_A          521 KALKQDLAR  529 (575)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            344444443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	753
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	6e-13
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-12
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-12
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	4e-12
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	5e-12
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	5e-12
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-11
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	6e-11
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	2e-10
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	2e-10
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-10
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-10
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-10
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-10
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-10
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-10
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	5e-10
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	5e-10
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	6e-10
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-10
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-09
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-09
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-09
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-09
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	4e-09
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	6e-09
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-08
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-08
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-08
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	9e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	3e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	3e-07
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	3e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-04
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-06
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-06

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.7 bits (150), Expect = 6e-13
 Identities = 19/54 (35%), Positives = 32/54 (59%)

Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          R+  T  Q   LEK +    Y +   R E++  L L++RQ+++WF +RR+K +K
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.9 bits (148), Expect = 1e-12
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 29 TASQLEILEKTYAVES-YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          TA    ILEK +   + +P E     LS QL    R +Q WF  RR +++ 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.0 bits (148), Expect = 2e-12
 Identities = 20/57 (35%), Positives = 33/57 (57%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + KR   T  Q   LEK +    Y +   R E++  L L++RQ+++WF +RR+K +K
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.5 bits (144), Expect = 4e-12
 Identities = 21/57 (36%), Positives = 36/57 (63%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + KR   +  QL  LE+ YA   + ++  R ++SA   LS+RQ+ +WF +RR+K++K
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (144), Expect = 5e-12
 Identities = 21/66 (31%), Positives = 35/66 (53%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
          +  R   T  Q+E LEK +    YP    R  L+A++ L + ++Q+WF +RR K R+   
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 82 AKRQPK 87
           + Q +
Sbjct: 62 LRNQRR 67

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (143), Expect = 5e-12
 Identities = 20/57 (35%), Positives = 30/57 (52%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          K  +   +  Q   LEK +  + Y S   R  L+  L LS+RQ++ WF +RR K R+
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 56.8 bits (137), Expect = 3e-11
 Identities = 13/55 (23%), Positives = 30/55 (54%)

Query: 24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +R   + +  + LE+ +   S PS      ++ +L L    +++WFC+RR ++++
Sbjct: 2  RRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.9 bits (135), Expect = 6e-11
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 24 KRKMKTASQLEILEKTYAVES-YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
             +      + LEK +   + YP E     LS QL  S R++Q WF HRR +D+
Sbjct: 4  DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 21 VKTKRK--MKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +KT R   +    QL  L   YA    P   ++ +L    GLS R +++WF ++R KD+K
Sbjct: 1  MKTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 17 LEAEVKTKRKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR 73
          +E  V+ +++ +T+        LE  +     PS      ++ QLGL    +++WFC+RR
Sbjct: 1  METLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRR 60

Query: 74 LKDRKA 79
           K +++
Sbjct: 61 QKGKRS 66

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + +R   T+ QL+ LE T+    YP  + R E++    L++ ++++WF +RR K RK
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 58

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
           R   T  QL  LEK +  E+Y S   R EL+AQL L +  +++WF +RR+KD++
Sbjct: 2  YRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 54.9 bits (132), Expect = 2e-10
 Identities = 20/57 (35%), Positives = 34/57 (59%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +  R   +ASQL+ LE+ +    YP    R EL+ +  L++ ++Q+WF +RR + RK
Sbjct: 3  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 59

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 21/57 (36%), Positives = 35/57 (61%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +  R   T +QL  LE+ +  + Y S A RAE S+ L L++ Q+++WF +RR K ++
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 54.7 bits (131), Expect = 3e-10
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 9/83 (10%)

Query: 4  ASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDR 63
          AS+    KK+K+         R + T +Q   LE+ +  + Y S   R  L++ + L+  
Sbjct: 1  ASDGLPNKKRKR---------RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPT 51

Query: 64 QLQMWFCHRRLKDRKAPTAKRQP 86
          Q+++WF + R K ++A   K   
Sbjct: 52 QVKIWFQNHRYKTKRAQNEKGYE 74

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.0 bits (130), Expect = 3e-10
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 24 KRKMKTASQLEILEKTYA---VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +    T   + ILE  +A      Y        L     LS  Q++ W  +RR K++ 
Sbjct: 1  RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.3 bits (128), Expect = 5e-10
 Identities = 14/49 (28%), Positives = 22/49 (44%)

Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR 73
          R + T  Q   L   +     PS+ L+  +S QLGL    +  +F + R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 5e-10
 Identities = 25/78 (32%), Positives = 39/78 (50%)

Query: 1  MEAASEAEEKKKKKKPLEAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGL 60
          M+      +  K  +P        R   T  QL  LEK +    Y S A R E++A L L
Sbjct: 7  MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 66

Query: 61 SDRQLQMWFCHRRLKDRK 78
          ++ Q+++WF +RR+K +K
Sbjct: 67 NETQVKIWFQNRRMKQKK 84

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 6e-10
 Identities = 16/63 (25%), Positives = 27/63 (42%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT 81
            K K KTA QL +L+ ++   S  ++     L AQ  L+ R++  WF  ++        
Sbjct: 5  PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 82 AKR 84
             
Sbjct: 65 KME 67

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 7e-10
 Identities = 13/55 (23%), Positives = 27/55 (49%)

Query: 24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          KR     +    LEK++     P+      ++ QL +    +++WF +RR K+++
Sbjct: 1  KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 52.6 bits (126), Expect = 1e-09
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          +  R   T+SQ+  LE+ +    Y +    A+LSA+L L   Q+++WF +RR + + 
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI 58

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 51.8 bits (124), Expect = 2e-09
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK 75
           R   ++ QL  L++ +    Y +E  R +LS++LGL++ Q+++WF + R K
Sbjct: 2  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.8 bits (124), Expect = 2e-09
 Identities = 8/53 (15%), Positives = 28/53 (52%)

Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
          +   +      LE+ +  +   +   + E++ + G++  Q+++WF ++R++ +
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 51.9 bits (124), Expect = 3e-09
 Identities = 14/57 (24%), Positives = 33/57 (57%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + +R + + +Q+  LE+ +  + Y S   R  L++ + L+  Q+++WF + R K ++
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.5 bits (123), Expect = 4e-09
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 24 KRKMKTASQLEILEKTYAVE-SYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA 82
               T  Q+EILE  +     +P       ++A+ GL++ Q Q WF  R  + R++   
Sbjct: 4  GAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL 63

Query: 83 KRQ 85
            +
Sbjct: 64 PSE 66

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (121), Expect = 6e-09
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 22 KTKRKMKTASQLEILEKTYA---VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          K KR +       ++           YP+E  + +++AQ  L+  Q+  WF + R +  +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 22 KTKRKMKTASQLEILEKTYAVES---YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
          + KR+       EIL + +       YPSE  + EL+ + G++  Q+  WF ++R++ +K
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 79 A 79
           
Sbjct: 62 N 62

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 15/70 (21%)

Query: 24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQ---------------LGLSDRQLQMW 68
           R       L ++E  +    YP EA R E++                   ++  ++  W
Sbjct: 3  SRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNW 62

Query: 69 FCHRRLKDRK 78
          F +RR + ++
Sbjct: 63 FANRRKEIKR 72

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 4/62 (6%)

Query: 22 KTKRKMKTASQLEILE----KTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
          K  R   TA Q E +     +         +    +  A+ G+  + L++W  + +    
Sbjct: 18 KRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP 77

Query: 78 KA 79
           +
Sbjct: 78 SS 79

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 1e-07
 Identities = 13/57 (22%), Positives = 21/57 (36%)

Query: 22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
           +  K KT  QL IL+  +    +       +L    GL   ++  WF   R   + 
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 2e-07
 Identities = 22/122 (18%), Positives = 62/122 (50%), Gaps = 8/122 (6%)

Query: 327 AMDNAFISSDRRVSHDEDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREE 386
           +M +A + +D+ ++  E     E+ +       A+ +   +++  + +E+++   ++  +
Sbjct: 187 SMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLK 246

Query: 387 QIRKEMERQDRERRKEEERLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKE 446
           Q+ ++ME    +  KE+ER L  KL+E+E+ L+E  ++        +   ++ E +  + 
Sbjct: 247 QLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQK--------ESRIMKNEIQDLQT 298

Query: 447 EL 448
           ++
Sbjct: 299 KM 300

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 5e-07
 Identities = 24/117 (20%), Positives = 51/117 (43%), Gaps = 4/117 (3%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKE 402
              S T+   ++++    +E E   +R++ E  +         ++  ++M  Q     +E
Sbjct: 184 SKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQE 243

Query: 403 EERLLREKLREE-ERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
             + L EK+  +  + L+EQ R L  +   LQ++    ++  QKE      E + L+
Sbjct: 244 HLKQLTEKMENDRVQLLKEQERTLALK---LQEQEQLLKEGFQKESRIMKNEIQDLQ 297

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 9e-06
 Identities = 18/135 (13%), Positives = 50/135 (37%), Gaps = 5/135 (3%)

Query: 343 EDVSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILR-RKREEQIRKEMERQDRERRK 401
            +  R   + +       +  E+    I +  +           E+++ E  +   +   
Sbjct: 165 YEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLH 224

Query: 402 EEERLLREKLREEERYLREQRRELERR----EKFLQKESIRAEKRRQKEELRRVKEAERL 457
           E +R   + + ++ER  +E  ++L  +       L KE  R    + +E+ + +KE  + 
Sbjct: 225 EMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQK 284

Query: 458 KVANERAVARRIAKE 472
           +    +   + +  +
Sbjct: 285 ESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 3e-05
 Identities = 24/138 (17%), Positives = 48/138 (34%), Gaps = 5/138 (3%)

Query: 349 EKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREE---QIRKEMERQDRERRKEEER 405
           +K  +     I  E         KE     IL+  +     +   E+ER   E  +   +
Sbjct: 162 KKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAK 221

Query: 406 LLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLKVANERAV 465
           +L E  R+ E+ + ++ R  +   K  Q        R Q  + +    A +L+   +   
Sbjct: 222 MLHEMQRKNEQMMEQKERSYQEHLK--QLTEKMENDRVQLLKEQERTLALKLQEQEQLLK 279

Query: 466 ARRIAKESMALVEDERLE 483
                +  +   E + L+
Sbjct: 280 EGFQKESRIMKNEIQDLQ 297

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 22 KTKRKMKTASQLEILEKTYA-VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
             R   +   L IL+     V  YP +     LSAQL L    +  +F ++R   + 
Sbjct: 8  PRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 46.3 bits (109), Expect = 3e-07
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 21/75 (28%)

Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQL---------------------GLSDR 63
          R     +  +IL + Y  +  PS+  R  L  +                       +++ 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 64 QLQMWFCHRRLKDRK 78
          ++  WF +RR ++  
Sbjct: 61 RVYNWFANRRKEEAF 75

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 21/104 (20%), Positives = 45/104 (43%), Gaps = 4/104 (3%)

Query: 346 SRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEER 405
            R +   +  + ++    E  + +  + L+     R    E I+K +E  +   +  +E+
Sbjct: 38  RRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEK 97

Query: 406 LLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELR 449
           L ++    +E         LER    LQ++   AE+ R+ +EL+
Sbjct: 98  LAQKMESNKENREAHLAAMLER----LQEKDKHAEEVRKNKELK 137

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 18/114 (15%), Positives = 41/114 (35%), Gaps = 5/114 (4%)

Query: 345 VSRTEKKRKSEEARIAREVEAHEKRIRKELEKQDILRRKREEQIRKEMERQDRERRKEEE 404
                +   S   R    +E  +K++    E++     +  + + ++ E +    +K  E
Sbjct: 26  FDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIE 85

Query: 405 RLLREKLREEERYLREQRRELERREKFLQKESIRAEKRRQKEELRRVKEAERLK 458
                    +E+  ++     E RE  L      A   R +E+ +  +E  + K
Sbjct: 86  ENNNFIKMAKEKLAQKMESNKENREAHLA-----AMLERLQEKDKHAEEVRKNK 134

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	753
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.72
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.7
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.7
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.69
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.69
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.69
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.68
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.67
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.66
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.66
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.66
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.64
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.64
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.63
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.63
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.63
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.63
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.62
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.59
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.58
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.58
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.56
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.52
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.5
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.47
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.47
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.41
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.4
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.33
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.31
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.28

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.9e-18  Score=136.41  Aligned_cols=57  Identities=37%  Similarity=0.647  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      |++||.||..|+.+|+..|..++||+..++.+||..|||++.+|+|||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            678999999999999999999999999999999999999999999999999999986

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=7.3e-18  Score=134.43  Aligned_cols=58  Identities=36%  Similarity=0.578  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      ||+||.||..|+.+|+..|..++||+..++.+||..|||++.+|+|||||||+|+||.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   58 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhccC
Confidence            5789999999999999999999999999999999999999999999999999999874

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.70  E-value=8.1e-18  Score=137.96  Aligned_cols=63  Identities=29%  Similarity=0.459  Sum_probs=59.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +||+||+||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+|+|+.....
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~   63 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   63 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhc
Confidence            467899999999999999999999999999999999999999999999999999999866544

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.69  E-value=8.6e-18  Score=132.50  Aligned_cols=55  Identities=35%  Similarity=0.565  Sum_probs=53.9

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        25 Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      ||.||..|+..|+..|..++||+...|.+||..|||++++|+|||||||+|+||.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7999999999999999999999999999999999999999999999999999985

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.69  E-value=1e-17  Score=133.01  Aligned_cols=57  Identities=40%  Similarity=0.638  Sum_probs=55.2

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           23 TKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        23 r~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      |.||.||..|+..|+..|..++||+...+.+||..|||++.+|+|||||||+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            579999999999999999999999999999999999999999999999999999874

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.4e-17  Score=132.21  Aligned_cols=57  Identities=35%  Similarity=0.469  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      |+.|+.||..|+.+|+..|..++||+..++..||..|||++.||+|||||||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            578999999999999999999999999999999999999999999999999999986

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.68  E-value=2.3e-17  Score=138.86  Aligned_cols=66  Identities=26%  Similarity=0.456  Sum_probs=61.2

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      ..++|+.||+||..|+.+|+..|..++||+..++..||..|||++.||+|||||||+|+|+.....
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   71 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhcc
Confidence            456788999999999999999999999999999999999999999999999999999999865544

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.67  E-value=2.5e-17  Score=128.87  Aligned_cols=53  Identities=32%  Similarity=0.596  Sum_probs=51.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhh
Q 004454           23 TKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK   75 (753)
Q Consensus        23 r~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K   75 (753)
                      |+||.||..|+..|+..|..++||+..+|.+||..|||++.+|+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            57999999999999999999999999999999999999999999999999987

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=3.1e-17  Score=137.93  Aligned_cols=65  Identities=31%  Similarity=0.457  Sum_probs=60.3

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      .+..|++||+||..|+.+|+..|..++||+...|..||..|||++.+|+|||||||+|+|+....
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            34567889999999999999999999999999999999999999999999999999999986543

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.66  E-value=4.7e-17  Score=133.69  Aligned_cols=63  Identities=24%  Similarity=0.459  Sum_probs=59.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      +||+||+||..|+.+|+..|..++||+...+..||..|||++.+|+|||||||+|+|+.....
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~   64 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccch
Confidence            577999999999999999999999999999999999999999999999999999999875443

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.66  E-value=3.8e-17  Score=133.11  Aligned_cols=62  Identities=34%  Similarity=0.569  Sum_probs=58.8

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ++|+.||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||+|+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            46889999999999999999999999999999999999999999999999999999998643

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=6.7e-17  Score=132.78  Aligned_cols=60  Identities=33%  Similarity=0.583  Sum_probs=57.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ||+||+||..|+.+|+..|..|+||+...+..||..|||++.+|+|||||+|+|+|+...
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            678999999999999999999999999999999999999999999999999999998654

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=5.9e-17  Score=139.62  Aligned_cols=63  Identities=35%  Similarity=0.521  Sum_probs=55.7

Q ss_pred             cCcCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           18 EAEVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        18 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      .+++++.|+.||..|+.+|+..|..++||+..++.+||..|||++.+|+|||||||+|+|+..
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            456788999999999999999999999999999999999999999999999999999999864

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=6.4e-17  Score=129.79  Aligned_cols=59  Identities=32%  Similarity=0.542  Sum_probs=56.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           21 VKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      .||.||+||..|+.+|+..|..++||+..++..||..+||++.+|++||||+|+|+|+.
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            36789999999999999999999999999999999999999999999999999999875

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.8e-16  Score=131.38  Aligned_cols=60  Identities=27%  Similarity=0.389  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPT   81 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~   81 (753)
                      ++.|+.||..|+.+|+..|.. ++||+...+..||..+||++++|+|||||||+|+|+...
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            578999999999999999987 689999999999999999999999999999999998654

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.8e-16  Score=129.75  Aligned_cols=60  Identities=28%  Similarity=0.444  Sum_probs=57.5

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      .+||+||.||..|+..|+..|..++||+..++..||..+||++.+|+|||||+|+++|+.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            457899999999999999999999999999999999999999999999999999999885

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.63  E-value=2.1e-16  Score=129.05  Aligned_cols=63  Identities=29%  Similarity=0.524  Sum_probs=59.6

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           20 EVKTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        20 k~rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      +.+|.||.||.+|+.+|+..|..|+||+..++..||..+||++.+|++||||||++.|+....
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~~   64 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIM   64 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCCS
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHHh
Confidence            578899999999999999999999999999999999999999999999999999999987543

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.62  E-value=2.9e-16  Score=124.93  Aligned_cols=58  Identities=22%  Similarity=0.548  Sum_probs=55.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccc
Q 004454           23 TKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        23 r~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~   80 (753)
                      |+||.||..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+++|+.+
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~k   58 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK   58 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhcC
Confidence            5799999999999999999999999999999999999999999999999999999853

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.59  E-value=6.3e-16  Score=120.71  Aligned_cols=53  Identities=15%  Similarity=0.431  Sum_probs=51.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        25 Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      ||.||++|+.+|+..|..++||+..++..||..+||++.+|++||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            78999999999999999999999999999999999999999999999999975

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1e-15  Score=121.28  Aligned_cols=56  Identities=23%  Similarity=0.440  Sum_probs=54.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        24 ~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      +||.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            59999999999999999999999999999999999999999999999999999985

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1e-15  Score=126.89  Aligned_cols=63  Identities=22%  Similarity=0.270  Sum_probs=58.1

Q ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           17 LEAEVKTKRKMKTASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        17 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      .++..+++|+.||.+|+.+|+.+|.. ++||+..++..||..|||+..+|++||||+|++.|+.
T Consensus         3 s~~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            34567789999999999999999974 8999999999999999999999999999999999873

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.2e-15  Score=129.87  Aligned_cols=62  Identities=21%  Similarity=0.406  Sum_probs=57.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------CChHHHhHhhhhhhhhhccccccc
Q 004454           22 KTKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLG---------------LSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lg---------------L~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      |++|++||..|+.+|+..|..++||+..+|.+||..+|               |++.+|+|||||||+|+|+.....
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a   77 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIA   77 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHH
Confidence            68999999999999999999999999999999999875               999999999999999999976544

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.52  E-value=6.6e-15  Score=124.64  Aligned_cols=63  Identities=16%  Similarity=0.161  Sum_probs=57.7

Q ss_pred             CccCcCCCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           16 PLEAEVKTKRKMKTASQLEILEKTYAV----ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        16 ~~~~k~rr~Rt~~t~~Ql~~Le~~F~~----~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      +..+++||.||.||..|+..|+.+|+.    ++||+..++.+||..|||++.+|+|||||+|++.|+
T Consensus        12 ~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            345677889999999999999998886    799999999999999999999999999999998775

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=5e-15  Score=114.21  Aligned_cols=50  Identities=28%  Similarity=0.373  Sum_probs=49.0

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhh
Q 004454           24 KRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR   73 (753)
Q Consensus        24 ~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR   73 (753)
                      +||+||..|+.+|+..|..++||+..++..||..|||++.+|++||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999999999999999999999999999999999998

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=3.7e-14  Score=118.82  Aligned_cols=57  Identities=25%  Similarity=0.375  Sum_probs=52.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccccccc
Q 004454           27 MKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK   83 (753)
Q Consensus        27 ~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~~   83 (753)
                      .+|.+|+.+|+..|..++||+..++..||..|||++.+|++||||||++.++.....
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~   66 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   66 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhh
Confidence            459999999999999999999999999999999999999999999999987765544

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.4e-14  Score=118.45  Aligned_cols=60  Identities=22%  Similarity=0.305  Sum_probs=55.2

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           23 TKRKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        23 r~Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ..++.+|.+|+.+|+..|..|+||+..++..||..|||+..+|++||||+|+++|+....
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~~   64 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchHH
Confidence            345568999999999999999999999999999999999999999999999999986544

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=4.8e-14  Score=117.24  Aligned_cols=61  Identities=28%  Similarity=0.518  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcccccc
Q 004454           22 KTKRKMKTASQLEILEKTYA---VESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA   82 (753)
Q Consensus        22 rr~Rt~~t~~Ql~~Le~~F~---~~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~~~~   82 (753)
                      ||+|+.||.+|+.+|+.+|.   .++||+..++..||..+||+..||++||||+|+++++....
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~~   65 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccchh
Confidence            67899999999999999997   48899999999999999999999999999999999876543

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.41  E-value=7.7e-14  Score=117.08  Aligned_cols=56  Identities=21%  Similarity=0.345  Sum_probs=53.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------------CChHHHhHhhhhhhhhhcccc
Q 004454           25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLG---------------------LSDRQLQMWFCHRRLKDRKAP   80 (753)
Q Consensus        25 Rt~~t~~Ql~~Le~~F~~~~yps~~~r~~LA~~lg---------------------L~~~qVqiWFqNRR~K~kr~~   80 (753)
                      |++||+.|+.+|+..|..++||+..+|..||..||                     |++.+|++||||||++.|+..
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            78999999999999999999999999999999994                     899999999999999999864

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.40  E-value=7e-14  Score=108.38  Aligned_cols=50  Identities=36%  Similarity=0.517  Sum_probs=47.1

Q ss_pred             CHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhcc
Q 004454           29 TASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK   78 (753)
Q Consensus        29 t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr   78 (753)
                      |++|..+||..|.. ++||+...+..||..+||+.++|+|||||||+++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            56799999999987 689999999999999999999999999999999886

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.33  E-value=2.6e-13  Score=107.92  Aligned_cols=55  Identities=35%  Similarity=0.560  Sum_probs=51.1

Q ss_pred             CCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           23 TKRKMKTASQLEILEKTYAV-ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        23 r~Rt~~t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      +.++.++.++..+||..|.. ++||+..++..||..+||++++|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            46778888899999999986 68999999999999999999999999999999986

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.31  E-value=1.2e-12  Score=104.50  Aligned_cols=53  Identities=26%  Similarity=0.355  Sum_probs=49.4

Q ss_pred             CCCHHHHHHHHHHHhhc---CCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhccc
Q 004454           27 MKTASQLEILEKTYAVE---SYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA   79 (753)
Q Consensus        27 ~~t~~Ql~~Le~~F~~~---~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~kr~   79 (753)
                      +||.+|+.+|+.+|..+   +||+..++..||..+||+..||++||||+|++.|..
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~~   59 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccccccC
Confidence            49999999999999765   799999999999999999999999999999998764

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=2.4e-12  Score=103.35  Aligned_cols=57  Identities=23%  Similarity=0.336  Sum_probs=52.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHhHhhhhhhhhhc
Q 004454           21 VKTKRKMKTASQLEILEKTYAV---ESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR   77 (753)
Q Consensus        21 ~rr~Rt~~t~~Ql~~Le~~F~~---~~yps~~~r~~LA~~lgL~~~qVqiWFqNRR~K~k   77 (753)
                      .|++|+.|+.+++.+|+.+|..   ++||+..++..||..+||+..||++||||+|.|..
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            3567889999999999999985   78999999999999999999999999999998753