Psyllid ID: psy17256

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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-------760-------77
Protein Sequence
GADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQNRPKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKVNQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQN
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccEEEEcccHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHcccccccEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHcHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccEEcccccccEEEEcccHHHHHHHHHHHHHccccccccccccccccccHHHHHcccccccccccEEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEcccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHEEEEEEEEHHHHcccccccccccccccccccccccEEEEcccccccEEEEEEEcccccccccccccccccEEEcccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHcccccEEEEEccccHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEcccccccEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHcccEEEEccccccccccccccccHHHHcHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHccccccHHcccccccccccccHHHHHHHHHHHHcccccccccccccccccccccEEEccccccEEEEcHHHHHHHHHHHHHHHHHHcccccEEEccccccccHHHHEEEccEEccccEEEEEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccHHHHHHHHHHHHHHHHHHccccccEEEEEEcccHHHHHHHHHHHHHccccEEEEEEEEcccccccccccEEEEcccEEEHHHHHHHcccHHcccccccHHHHHHHHHccEEEHHHHHHHHHHHccccccEEEEEcccEEEcccHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHccc
Coil and Loop (DISEMBL)
gadsesshskskAKRVRTTFTEEQLQVLQANfqldsnpdgfgadstdhtdsesshskskAKRVRTTFTEEQLQVLQANfqldsnpdgqdlERIAQITGLSKRVTQVWFQNSRARQKkhlhtgkmkssqnrpkygyypepnksflvIKPQFLEEASLLFHDLHVQIVTEKrflggvigngdekkNYVKEKVNQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHcqdeyiplreiihstlvpsifeheisssehelfhlptrfgglgindpvetaQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEgqsshwlnvipkssdnfdlspvQFRDALALRYNhglkglptycdgcggemsvthalnckkgglvkhghdylRDECIMMASYAWngivkepimrdssstspalIADFKingvweaggtaffdnrivnadapsyssqtWNTIAKRHAQEKHLKYNTAAEdlrasftplvcstdgalhLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGtrqivkpygfddgaGLMYIRVRILLKGRLSVLICFRSfgakcskccrgiassDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLelvdggttssddgadsesshsksKAKRVRTTFTEEQLQVLQANfqldsnpdgqdlERIAQITGLSKRVTQVWFQNSRARQKkhlhtgkmkssqn
Flexible Loop (DISEMBL)
gadsesshskskakrvrtTFTEEQLQVLQANFQLDSNPDGFGADStdhtdsesshskskakrVRTTFTEEQLQVLQANfqldsnpdgQDLERIAQITGLSKRVTQVWFQNSrarqkkhlhtgkmkssqnrpkyGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRflggvigngdekknyvKEKVNQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQerilsslppakqRVLTRIVegqsshwlnviPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKavslrlrgtrqivkpygfddgaglMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGgttssddgadsesshskskakrVRTTFTEEQLQVLQANfqldsnpdgQDLERIAQITGLSKRVTQVWFQnsrarqkkhlhtgkmkssqn
Low Complexity Region (SEG)
GADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGFGadstdhtdsesshskskakRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQNRPKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKVNQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPsifeheisssehelfhlPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVdggttssddgadsesshsKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQN
Disordered region (IsUnstruct)
*******************************************************************************************RIAQITGLSKRVTQVWFQ************************GYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKVNQWIDCVKKLSEAA****QAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELV**********************RVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMR******PALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD****************************************************RIAQITGLSKRVTQVWFQ********************
Disordered Region (DISOPRED)
*******************************************************************TEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR**************************************************************************************************SVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPV***************VLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQERILSSLPPAK*RVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRD********IADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTI**********KYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGE*FALHEDRVLCKSHYLELVDGGTTSSD***************************************D**DLERIAQITGLSKRVTQVWFQNS******************
Disordered Region (DISEMBL)
******************TFTEEQLQVLQANFQLDSNPDGFGA**********************TFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNS******************RPKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKVNQWIDCVKKLS************VVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGT***********************TFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNS******************
Disordered Region (DISPRO)
*************************************************************RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK*******************************QFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKVNQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVKNAINTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG*********************RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
GADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQNRPKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKVNQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQEHNQCVxxxxxxxxxxxxxxxxxxxxxILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQN
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	768	2.2.26 [Sep-21-2011]
Q8IRC7	275	LIM/homeobox protein Awh	yes	N/A	0.196	0.549	0.796	5e-68
Q9UPM6	363	LIM/homeobox protein Lhx6	no	N/A	0.190	0.402	0.545	8e-44
Q9R1R0	363	LIM/homeobox protein Lhx6	no	N/A	0.190	0.402	0.545	9e-44
Q68G74	356	LIM/homeobox protein Lhx8	no	N/A	0.190	0.410	0.560	4e-43
O35652	367	LIM/homeobox protein Lhx8	no	N/A	0.190	0.397	0.554	2e-42
Q9UBR4	397	LIM/homeobox protein Lhx3	no	N/A	0.170	0.329	0.424	4e-26
P50481	400	LIM/homeobox protein Lhx3	no	N/A	0.170	0.327	0.424	4e-26
O97581	383	LIM/homeobox protein Lhx3	no	N/A	0.170	0.342	0.424	5e-26
P53412	395	LIM/homeobox protein Lhx3	no	N/A	0.170	0.331	0.431	6e-26
P50212	340	Insulin gene enhancer pro	N/A	N/A	0.187	0.423	0.387	6e-26

>sp|Q8IRC7|AWH_DROME LIM/homeobox protein Awh OS=Drosophila melanogaster GN=Awh PE=1 SV=1

 Score =  259 bits (663), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 121/152 (79%), Positives = 138/152 (90%), Gaps = 1/152 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           ++FGAKCSKCCRGI++SDWVR+AR+ V+HLACFAC+ C RQLSTGE+FAL +DRVLCK+H
Sbjct: 63  KNFGAKCSKCCRGISASDWVRRARELVFHLACFACDQCGRQLSTGEQFALMDDRVLCKAH 122

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE V+GGTTSSD+G D +  H KSK KRVRTTFTEEQLQVLQANFQ+DSNPDGQDLERI
Sbjct: 123 YLETVEGGTTSSDEGCDGDGYH-KSKTKRVRTTFTEEQLQVLQANFQIDSNPDGQDLERI 181

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMK 764
           A +TGLSKRVTQVWFQNSRARQKKH+H GK K
Sbjct: 182 ASVTGLSKRVTQVWFQNSRARQKKHIHAGKNK 213

Probable transcription factor. Required for the establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings.
Drosophila melanogaster (taxid: 7227)

>sp|Q9UPM6|LHX6_HUMAN LIM/homeobox protein Lhx6 OS=Homo sapiens GN=LHX6 PE=2 SV=2

 Score =  179 bits (454), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 84/154 (54%), Positives = 108/154 (70%), Gaps = 8/154 (5%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           F  FG KC++C R I +SDWVR+AR + YHLACFAC +CKRQLSTGEEF L E++VLC+ 
Sbjct: 124 FSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRI 183

Query: 672 HYLELVDGGTTSSDDG--------ADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSN 723
           HY  +++    ++++G          SE       AKR RT+FT EQLQV+QA F  D+N
Sbjct: 184 HYDTMIENLKRAAENGNGLTLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNN 243

Query: 724 PDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           PD Q L+++A +TGLS+RV QVWFQN RAR KKH
Sbjct: 244 PDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKH 277

Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex.

Homo sapiens (taxid: 9606)

>sp|Q9R1R0|LHX6_MOUSE LIM/homeobox protein Lhx6 OS=Mus musculus GN=Lhx6 PE=1 SV=2

 Score =  179 bits (453), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 84/154 (54%), Positives = 108/154 (70%), Gaps = 8/154 (5%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           F  FG KC++C R I +SDWVR+AR + YHLACFAC +CKRQLSTGEEF L E++VLC+ 
Sbjct: 124 FSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRI 183

Query: 672 HYLELVDGGTTSSDDG--------ADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSN 723
           HY  +++    ++++G          SE       AKR RT+FT EQLQV+QA F  D+N
Sbjct: 184 HYDTMIENLKRAAENGNGLTLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNN 243

Query: 724 PDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           PD Q L+++A +TGLS+RV QVWFQN RAR KKH
Sbjct: 244 PDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKH 277

Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex.

Mus musculus (taxid: 10090)

>sp|Q68G74|LHX8_HUMAN LIM/homeobox protein Lhx8 OS=Homo sapiens GN=LHX8 PE=2 SV=2

 Score =  177 bits (448), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 88/157 (56%), Positives = 115/157 (73%), Gaps = 11/157 (7%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct: 129 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 188

Query: 672 HYLELVD-------GGTTSSDDGA---DSESSHSKSKAKRVRTTFTEEQLQVLQANFQLD 721
           HY  ++D        G   S +GA   + + +H K  AKR RT+FT +QLQV+QA F  D
Sbjct: 189 HYDCMLDNLKREVENGNGISVEGALLTEQDVNHPK-PAKRARTSFTADQLQVMQAQFAQD 247

Query: 722 SNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL 758
           +NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+
Sbjct: 248 NNPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHV 284

Transcription factor involved in differentiation of certain neurons and mesenchymal cells.

Homo sapiens (taxid: 9606)

>sp|O35652|LHX8_MOUSE LIM/homeobox protein Lhx8 OS=Mus musculus GN=Lhx8 PE=2 SV=4

 Score =  174 bits (442), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 87/157 (55%), Positives = 115/157 (73%), Gaps = 11/157 (7%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct: 150 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 209

Query: 672 HYLELVD-------GGTTSSDDGA---DSESSHSKSKAKRVRTTFTEEQLQVLQANFQLD 721
           H+  ++D        G   S +GA   + + +H K  AKR RT+FT +QLQV+QA F  D
Sbjct: 210 HFDCMLDNLKREVENGNGISVEGALLTEQDVNHPKP-AKRARTSFTADQLQVMQAQFAQD 268

Query: 722 SNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL 758
           +NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+
Sbjct: 269 NNPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHV 305

Transcription factor involved in differentiation of certain neurons and mesenchymal cells.

Mus musculus (taxid: 10090)

>sp|Q9UBR4|LHX3_HUMAN LIM/homeobox protein Lhx3 OS=Homo sapiens GN=LHX3 PE=1 SV=2

 Score =  120 bits (302), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 62/146 (42%), Positives = 88/146 (60%), Gaps = 15/146 (10%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 83  FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 142

Query: 671 SHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLE 730
           + Y                ++   +++ AKR RTT T +QL+ L++ +     P     E
Sbjct: 143 ADY--------------ETAKQREAEATAKRPRTTITAKQLETLKSAYNTSPKPARHVRE 188

Query: 731 RIAQITGLSKRVTQVWFQNSRARQKK 756
           +++  TGL  RV QVWFQN RA++K+
Sbjct: 189 QLSSETGLDMRVVQVWFQNRRAKEKR 214

Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with Pit-1.

Homo sapiens (taxid: 9606)

>sp|P50481|LHX3_MOUSE LIM/homeobox protein Lhx3 OS=Mus musculus GN=Lhx3 PE=1 SV=1

 Score =  120 bits (301), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 62/146 (42%), Positives = 88/146 (60%), Gaps = 15/146 (10%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 86  FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 145

Query: 671 SHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLE 730
           + Y                ++   +++ AKR RTT T +QL+ L++ +     P     E
Sbjct: 146 ADY--------------ETAKQREAEATAKRPRTTITAKQLETLKSAYNTSPKPARHVRE 191

Query: 731 RIAQITGLSKRVTQVWFQNSRARQKK 756
           +++  TGL  RV QVWFQN RA++K+
Sbjct: 192 QLSSETGLDMRVVQVWFQNRRAKEKR 217

Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with Pit-1.

Mus musculus (taxid: 10090)

>sp|O97581|LHX3_PIG LIM/homeobox protein Lhx3 (Fragment) OS=Sus scrofa GN=LHX3 PE=2 SV=1

 Score =  120 bits (301), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 62/146 (42%), Positives = 88/146 (60%), Gaps = 15/146 (10%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 68  FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 127

Query: 671 SHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLE 730
           + Y                ++   +++ AKR RTT T +QL+ L++ +     P     E
Sbjct: 128 ADY--------------ETAKQREAEATAKRPRTTITAKQLETLKSAYNTSPKPARHVRE 173

Query: 731 RIAQITGLSKRVTQVWFQNSRARQKK 756
           +++  TGL  RV QVWFQN RA++K+
Sbjct: 174 QLSSETGLDMRVVQVWFQNRRAKEKR 199

Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with Pit-1.

Sus scrofa (taxid: 9823)

>sp|P53412|LHX3_CHICK LIM/homeobox protein Lhx3 OS=Gallus gallus GN=LHX3 PE=2 SV=1

 Score =  120 bits (300), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 63/146 (43%), Positives = 88/146 (60%), Gaps = 15/146 (10%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C +GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 80  FKRFGTKCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCK 139

Query: 671 SHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLE 730
           + Y                ++   ++S AKR RTT T +QL+ L+  +     P     E
Sbjct: 140 ADY--------------ETAKQREAESTAKRPRTTITAKQLETLKNAYNNSPKPARHVRE 185

Query: 731 RIAQITGLSKRVTQVWFQNSRARQKK 756
           +++  TGL  RV QVWFQN RA++K+
Sbjct: 186 QLSSETGLDMRVVQVWFQNRRAKEKR 211

Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways. Acts in conjunction with LIM-1, ISL-1 and ISL-2.

Gallus gallus (taxid: 9031)

>sp|P50212|ISL2B_ONCTS Insulin gene enhancer protein ISL-2B (Fragment) OS=Oncorhynchus tschawytscha GN=isl2b PE=2 SV=1

 Score =  120 bits (300), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 64/165 (38%), Positives = 87/165 (52%), Gaps = 21/165 (12%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           R FG KC+KC  G  SSD V +ARD+VYH+ CF C  C RQL  G+EF+L ++ +LC++ 
Sbjct: 65  RLFGIKCAKCNIGFCSSDLVMRARDNVYHMECFRCSVCSRQLVPGDEFSLRDEELLCRAD 124

Query: 673 Y---LELVDGGTTSSDDGADSESSH------------------SKSKAKRVRTTFTEEQL 711
           +   LE    G+  S     S S H                     K  RVRT   E+QL
Sbjct: 125 HGLLLERASAGSPISPGNILSRSFHIADPVSVRQPPHRNHVHKQSEKTTRVRTVLNEKQL 184

Query: 712 QVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
             L+  +  +  PD    E++ ++TGLS RV +VWFQN R + KK
Sbjct: 185 HTLRTCYNANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 229

Binds to one of the cis-acting domain of the insulin gene enhancer. May be involved in subtype specialization of primary motoneurons.

Oncorhynchus tschawytscha (taxid: 74940)

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	768
340384014	1577	PREDICTED: hypothetical protein LOC10063	0.601	0.292	0.390	5e-94
340383257	938	PREDICTED: hypothetical protein LOC10063	0.533	0.437	0.389	1e-78
91078266	343	PREDICTED: similar to GA10520-PA [Tribol	0.197	0.443	0.882	1e-73
270004863	349	arrowhead [Tribolium castaneum]	0.197	0.435	0.882	2e-73
379698940	274	arrowhead PA [Bombyx mori] gi|346223348|	0.200	0.562	0.864	5e-72
357605400	406	hypothetical protein KGM_21596 [Danaus p	0.200	0.379	0.841	2e-70
195125467	239	GI12512 [Drosophila mojavensis] gi|19391	0.196	0.631	0.809	1e-67
195375542	239	GJ12418 [Drosophila virilis] gi|19415371	0.196	0.631	0.809	1e-67
195441498	275	GK20529 [Drosophila willistoni] gi|19416	0.213	0.596	0.754	1e-67
195016322	239	GH16430 [Drosophila grimshawi] gi|193897	0.196	0.631	0.809	2e-67

>gi|340384014|ref|XP_003390510.1| PREDICTED: hypothetical protein LOC100638826 [Amphimedon queenslandica]

 Score =  352 bits (903), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 181/464 (39%), Positives = 269/464 (57%), Gaps = 2/464 (0%)

Query: 131  PKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKV 190
            P +GY+PEP+K  L++    L+ A LLF D  V IV + +FLGGVIGN   + +++  K 
Sbjct: 1108 PLFGYFPEPSKCHLIVSESNLDNARLLFRDTGVNIVKDGKFLGGVIGNKVARDSFISSKS 1167

Query: 191  NQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVP 250
             +W   +++LS      PQ+A+ V++K+LQ EW +LQR+++ C   +  +   I  + +P
Sbjct: 1168 EKWSGYIRQLSSLCVSEPQSAYIVLSKALQYEWIYLQRIMSDCGGLFNDVTHDIAHSFLP 1227

Query: 251  SIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQ 310
            S+F   +S SE   F LP R GGL I DP  T+  ++A + +    LV+++        +
Sbjct: 1228 SLFGCGVSESERLFFSLPIRMGGLNIKDPTVTSSFSYAASRDATSYLVNAIKNNLDFESE 1287

Query: 311  EHNQCVKNAINTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSD 370
             HN CV  +  +      ++ ++  E I++   P  +R L +  +  S+ WL+V P + D
Sbjct: 1288 AHNDCVHASRLSAYNASTSQSEQLYENIMTDASPMLKRTLQKARDCLSA-WLSVPPIAKD 1346

Query: 371  NFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDEC 430
            NFDLS  +FRD LALRY   L  LP  CDGCG E SVTHAL+C+KGGLV   H+ +RD  
Sbjct: 1347 NFDLSANEFRDGLALRYGKPLLQLPPTCDGCGSEFSVTHALDCRKGGLVVQRHNEIRDMI 1406

Query: 431  IMMASYAWNGIVKEPIMRDSS-STSPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSS 489
              +AS  W  +VKEP++ DSS S +  L+AD  I GVW+   TA FD R+V+ DA SY  
Sbjct: 1407 CSLASIVWGQVVKEPVVSDSSASDTGGLVADIAIRGVWQRQATALFDVRVVDTDAKSYLR 1466

Query: 490  QTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWK 549
            Q+  ++     +EK  KY+ A      SFTPL  S DG +  E  +FL R+   L+ KW+
Sbjct: 1467 QSPQSVLATAEREKKRKYSAACTARHVSFTPLCFSVDGLMGSETKTFLDRLGDHLASKWE 1526

Query: 550  KMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGL 593
            + Y  V+ WLRV+   ++L+A  L LRGTR  ++P   +D A +
Sbjct: 1527 RPYSVVVHWLRVKMSMALLRATDLCLRGTRSKLRPMLIEDDAPI 1570

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|340383257|ref|XP_003390134.1| PREDICTED: hypothetical protein LOC100637810, partial [Amphimedon queenslandica]

 Score =  300 bits (769), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 164/421 (38%), Positives = 236/421 (56%), Gaps = 11/421 (2%)

Query: 131 PKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKKNYVKEKV 190
           P +GY+PEP+KS L++K   L  A   F    V IV   R+LGGVIGN    +++V  +V
Sbjct: 523 PLFGYFPEPSKSSLIVKDTTLPSAEQSFDGSGVSIVQCGRYLGGVIGNRAGIESFVSSRV 582

Query: 191 NQWIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFLQRVVNHCQDEYIPLREIIHSTLVP 250
           + W + V  LS  A   PQAA+  +TK LQ EW FLQRV   C D +  L + + +  +P
Sbjct: 583 SAWSNYVSLLSSIAVDQPQAAYIALTKLLQSEWIFLQRVTPDCGDLFSDLEQALCTHFLP 642

Query: 251 SIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAVTSEKCKVLVDSLLKQEQLNLQ 310
           S+  H   S +  L+ LP R GGL I DP +TA  A++ +    ++L++S++KQ   +  
Sbjct: 643 SLTSHACGSHDRFLYSLPIRMGGLNIKDPTKTADQAYSASRNAVRLLMESIIKQSPFSTT 702

Query: 311 EHNQCVKNA----INTELVRKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIP 366
           +H  CV  +    I T+  R ET ++E     LS      QR + R  +   SHWL  +P
Sbjct: 703 DHYLCVTQSRLDHIATQNERNETYFKEA----LSLFDARHQRAILRSRDSL-SHWLCALP 757

Query: 367 KSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYL 426
              DNF+LS  +FRDA+ +RY   L  LP  CDGCG   S  HAL+C+KGGLV   H+ +
Sbjct: 758 VQKDNFNLSSQEFRDAICMRYLKPLVSLPPLCDGCGAPFSTVHALDCRKGGLVSLRHNEI 817

Query: 427 RDECIMMASYAWNGIVKEPIMRDSSST--SPALIADFKINGVWEAGGTAFFDNRIVNADA 484
           RD    ++S  W+ +V+EPI+++ + T  S  L+AD    GVW+   TA FD  +V++D+
Sbjct: 818 RDLLCDLSSILWSNVVREPIIQEPNMTTNSEGLVADMAARGVWQRQCTAMFDVPVVDSDS 877

Query: 485 PSYSSQTWNTIAKRHAQEKHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVL 544
           PSY+++T   +      +K  KY  A E    SFTPL  + DG +  E  SF+ R A  L
Sbjct: 878 PSYANRTPQAVLATAENDKKRKYVAACESNHCSFTPLCLTVDGVMGSEMRSFIDRQADRL 937

Query: 545 S 545
           S
Sbjct: 938 S 938

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|91078266|ref|XP_971202.1| PREDICTED: similar to GA10520-PA [Tribolium castaneum]

 Score =  284 bits (726), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 135/153 (88%), Positives = 144/153 (94%), Gaps = 1/153 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           +SFGAKCS C RGI+SSDWVRKARDHVYHLACFAC AC RQLSTGEEFALHEDRVLCK+H
Sbjct: 138 KSFGAKCSVCSRGISSSDWVRKARDHVYHLACFACAACHRQLSTGEEFALHEDRVLCKAH 197

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE +DGGTTSSDDG D+E  H K+KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI
Sbjct: 198 YLETLDGGTTSSDDGCDAEGYH-KNKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 256

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS 765
           AQITGLSKRVTQVWFQNSRARQKKH+HTGK+K+
Sbjct: 257 AQITGLSKRVTQVWFQNSRARQKKHMHTGKIKT 289

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270004863|gb|EFA01311.1| arrowhead [Tribolium castaneum]

 Score =  283 bits (724), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 135/153 (88%), Positives = 144/153 (94%), Gaps = 1/153 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           +SFGAKCS C RGI+SSDWVRKARDHVYHLACFAC AC RQLSTGEEFALHEDRVLCK+H
Sbjct: 124 KSFGAKCSVCSRGISSSDWVRKARDHVYHLACFACAACHRQLSTGEEFALHEDRVLCKAH 183

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE +DGGTTSSDDG D+E  H K+KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI
Sbjct: 184 YLETLDGGTTSSDDGCDAEGYH-KNKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 242

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS 765
           AQITGLSKRVTQVWFQNSRARQKKH+HTGK+K+
Sbjct: 243 AQITGLSKRVTQVWFQNSRARQKKHMHTGKIKT 275

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|379698940|ref|NP_001243941.1| arrowhead PA [Bombyx mori] gi|346223348|dbj|BAK78925.1| arrowhead PA [Bombyx mori]

 Score =  279 bits (713), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 134/155 (86%), Positives = 143/155 (92%), Gaps = 1/155 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           +SFGAKCSKCCRGI+SSDWVRKAR+ VYHLACFAC+AC RQLSTGE+FALHEDRVLCK H
Sbjct: 63  KSFGAKCSKCCRGISSSDWVRKAREQVYHLACFACDACGRQLSTGEQFALHEDRVLCKPH 122

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE +DGG+ SSDDG DSE  H KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI
Sbjct: 123 YLETLDGGSISSDDGCDSEGYH-KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 181

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQ 767
           AQ+TGLSKRVTQVWFQNSRARQKKH HTGK K +Q
Sbjct: 182 AQVTGLSKRVTQVWFQNSRARQKKHQHTGKGKQNQ 216

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357605400|gb|EHJ64588.1| hypothetical protein KGM_21596 [Danaus plexippus]

 Score =  273 bits (698), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 133/158 (84%), Positives = 143/158 (90%), Gaps = 4/158 (2%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           +SFGAKCSKCCRGI+SSDWVRKAR+ VYHLACFAC+AC RQLSTGE+FALHEDRVLCK H
Sbjct: 193 KSFGAKCSKCCRGISSSDWVRKAREQVYHLACFACDACGRQLSTGEQFALHEDRVLCKPH 252

Query: 673 YLELVDGGTTSSD---DGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDL 729
           YLE +DGG+ SSD   +G DSE  H KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDL
Sbjct: 253 YLETLDGGSISSDGKCNGCDSEGYH-KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDL 311

Query: 730 ERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQ 767
           ERIAQ+TGLSKRVTQVWFQNSRARQKKH HTGK K +Q
Sbjct: 312 ERIAQVTGLSKRVTQVWFQNSRARQKKHQHTGKGKQNQ 349

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195125467|ref|XP_002007199.1| GI12512 [Drosophila mojavensis] gi|193918808|gb|EDW17675.1| GI12512 [Drosophila mojavensis]

 Score =  265 bits (676), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 123/152 (80%), Positives = 138/152 (90%), Gaps = 1/152 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           ++FGAKCSKCCRGI++SDWVR+ARD V+HLACFAC+ C RQLSTGE+FAL +DRVLCK+H
Sbjct: 27  KNFGAKCSKCCRGISASDWVRRARDLVFHLACFACDQCGRQLSTGEQFALMDDRVLCKAH 86

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE V+GGTTSSDDG D +  H KSK KRVRTTFTEEQLQVLQANFQ+DSNPDGQDLERI
Sbjct: 87  YLETVEGGTTSSDDGCDGDGYH-KSKTKRVRTTFTEEQLQVLQANFQIDSNPDGQDLERI 145

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMK 764
           A +TGLSKRVTQVWFQNSRARQKKH+H GK K
Sbjct: 146 ASVTGLSKRVTQVWFQNSRARQKKHIHAGKNK 177

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195375542|ref|XP_002046559.1| GJ12418 [Drosophila virilis] gi|194153717|gb|EDW68901.1| GJ12418 [Drosophila virilis]

 Score =  264 bits (675), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 123/152 (80%), Positives = 138/152 (90%), Gaps = 1/152 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           ++FGAKCSKCCRGI++SDWVR+ARD V+HLACFAC+ C RQLSTGE+FAL +DRVLCK+H
Sbjct: 27  KNFGAKCSKCCRGISASDWVRRARDLVFHLACFACDQCGRQLSTGEQFALMDDRVLCKAH 86

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE V+GGTTSSDDG D +  H KSK KRVRTTFTEEQLQVLQANFQ+DSNPDGQDLERI
Sbjct: 87  YLETVEGGTTSSDDGCDGDGYH-KSKTKRVRTTFTEEQLQVLQANFQIDSNPDGQDLERI 145

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMK 764
           A +TGLSKRVTQVWFQNSRARQKKH+H GK K
Sbjct: 146 ASVTGLSKRVTQVWFQNSRARQKKHIHAGKNK 177

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195441498|ref|XP_002068546.1| GK20529 [Drosophila willistoni] gi|194164631|gb|EDW79532.1| GK20529 [Drosophila willistoni]

 Score =  264 bits (674), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 129/171 (75%), Positives = 145/171 (84%), Gaps = 7/171 (4%)

Query: 595 YIRVR-ILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQ 653
           YIR R +  K   S     ++FGAKCSKCCRGI++SDWVR+ARD V+HLACFAC+ C RQ
Sbjct: 49  YIRERQVYCKADYS-----KNFGAKCSKCCRGISASDWVRRARDLVFHLACFACDQCGRQ 103

Query: 654 LSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQV 713
           LSTGE+FAL +DRVLCK+HYLE V+GGTTSSDDG D +  H KSK KRVRTTFTEEQLQV
Sbjct: 104 LSTGEQFALMDDRVLCKAHYLETVEGGTTSSDDGCDGDGYH-KSKTKRVRTTFTEEQLQV 162

Query: 714 LQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK 764
           LQANFQ+DSNPDGQDLERIA +TGLSKRVTQVWFQNSRARQKKH+H GK K
Sbjct: 163 LQANFQIDSNPDGQDLERIASVTGLSKRVTQVWFQNSRARQKKHIHAGKNK 213

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195016322|ref|XP_001984389.1| GH16430 [Drosophila grimshawi] gi|193897871|gb|EDV96737.1| GH16430 [Drosophila grimshawi]

 Score =  263 bits (672), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 123/152 (80%), Positives = 137/152 (90%), Gaps = 1/152 (0%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           +SFGAKCSKCCR I++SDWVR+ARD V+HLACFAC+ C RQLSTGE+FAL +DRVLCK+H
Sbjct: 27  KSFGAKCSKCCRSISASDWVRRARDLVFHLACFACDQCGRQLSTGEQFALMDDRVLCKAH 86

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           YLE V+GGTTSSDDG D +  H KSK KRVRTTFTEEQLQVLQANFQ+DSNPDGQDLERI
Sbjct: 87  YLETVEGGTTSSDDGCDGDGYH-KSKTKRVRTTFTEEQLQVLQANFQIDSNPDGQDLERI 145

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMK 764
           A +TGLSKRVTQVWFQNSRARQKKH+H GK K
Sbjct: 146 ASVTGLSKRVTQVWFQNSRARQKKHIHAGKNK 177

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	768
FB|FBgn0013751	275	Awh "Arrowhead" [Drosophila me	0.196	0.549	0.730	2.8e-57
WB|WBGene00002987	355	lim-4 [Caenorhabditis elegans	0.175	0.380	0.625	4.6e-43
ZFIN|ZDB-GENE-041025-1	375	lhx6 "LIM homeobox 6" [Danio r	0.195	0.4	0.531	2.7e-38
UNIPROTKB|E2REU0	379	LHX8 "Uncharacterized protein"	0.201	0.408	0.512	5.9e-38
UNIPROTKB|J9PBA6	295	LHX8 "Uncharacterized protein"	0.201	0.525	0.512	5.9e-38
UNIPROTKB|E9PGE3	346	LHX8 "LIM/homeobox protein Lhx	0.201	0.447	0.512	5.9e-38
UNIPROTKB|Q68G74	356	LHX8 "LIM/homeobox protein Lhx	0.201	0.435	0.512	5.9e-38
UNIPROTKB|C8YLT4	295	Lhx8 "LIM homeobox 8" [Sus scr	0.201	0.525	0.512	5.9e-38
UNIPROTKB|F1P4G9	347	LHX8 "Uncharacterized protein"	0.191	0.423	0.532	7.5e-38
UNIPROTKB|F1NLU0	354	F1NLU0 "Uncharacterized protei	0.194	0.420	0.528	9.7e-38

FB|FBgn0013751 Awh "Arrowhead" [Drosophila melanogaster (taxid:7227)]

 Score = 589 (212.4 bits), Expect = 2.8e-57, P = 2.8e-57
 Identities = 111/152 (73%), Positives = 125/152 (82%)

Query:   613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
             ++FGAKCSKCCRGI++SDWVR+AR+ V+HLACFAC+ C RQLSTGE+FAL +DRVLCK+H
Sbjct:    63 KNFGAKCSKCCRGISASDWVRRARELVFHLACFACDQCGRQLSTGEQFALMDDRVLCKAH 122

Query:   673 YLELVXXXXXXXXXXXXXXXXXXKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
             YLE V                  KSK KRVRTTFTEEQLQVLQANFQ+DSNPDGQDLERI
Sbjct:   123 YLETVEGGTTSSDEGCDGDGYH-KSKTKRVRTTFTEEQLQVLQANFQIDSNPDGQDLERI 181

Query:   733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMK 764
             A +TGLSKRVTQVWFQNSRARQKKH+H GK K
Sbjct:   182 ASVTGLSKRVTQVWFQNSRARQKKHIHAGKNK 213

GO:0007444 "imaginal disc development" evidence=IMP

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

WB|WBGene00002987 lim-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 459 (166.6 bits), Expect = 4.6e-43, P = 4.6e-43
 Identities = 90/144 (62%), Positives = 104/144 (72%)

Query:   613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
             R  G KC+ C R I ++DWVR+AR++VYHLACF+C  CKRQLSTGEE+AL E  +LCK H
Sbjct:   162 RELGPKCASCDRTIQATDWVRRARNYVYHLACFSCNQCKRQLSTGEEYALQEGNLLCKQH 221

Query:   673 YLELVXXXXXXXXXXXXXXXXXXKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
             +LELV                  K+K KRVRTTF E+QL VLQ  F  DSNPDG DLE+I
Sbjct:   222 FLELVEGDSGVSSQ---------KAKTKRVRTTFAEDQLSVLQTYFNRDSNPDGADLEKI 272

Query:   733 AQITGLSKRVTQVWFQNSRARQKK 756
             A +TGLSKRVTQVWFQNSRARQKK
Sbjct:   273 ASMTGLSKRVTQVWFQNSRARQKK 296

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001708 "cell fate specification" evidence=IMP

GO:0005623 "cell" evidence=IDA

ZFIN|ZDB-GENE-041025-1 lhx6 "LIM homeobox 6" [Danio rerio (taxid:7955)]

 Score = 416 (151.5 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 85/160 (53%), Positives = 104/160 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             F  FG KC++C R I +SDWVR+AR + YHLACFAC +CKRQLSTGEEF L E++VLC+ 
Sbjct:   151 FSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRI 210

Query:   672 HYLELVXXXXXXXXXXXXXXXXXX-------KSK-AKRVRTTFTEEQLQVLQANFQLDSN 723
             HY  +V                         + K AKR RT+FT EQLQV+QA F  D+N
Sbjct:   211 HYDTMVENLKRAAESGSGLTLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNN 270

Query:   724 PDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL--HTG 761
             PD Q L+++A +TGLS+RV QVWFQN RAR KKH   H G
Sbjct:   271 PDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKHTPQHNG 310

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

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E2REU0 LHX8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 413 (150.4 bits), Expect = 5.9e-38, P = 5.9e-38
 Identities = 84/164 (51%), Positives = 107/164 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct:   152 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 211

Query:   672 HY--------LELVXXXXXXXXXXXXXXXXXXKSK-AKRVRTTFTEEQLQVLQANFQLDS 722
             HY         E+                     K AKR RT+FT +QLQV+QA F  D+
Sbjct:   212 HYDCMLDNLKREVENGNGISVEGALLTEQDVNHPKPAKRARTSFTADQLQVMQAQFAQDN 271

Query:   723 NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
             NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+      S+
Sbjct:   272 NPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHVSPNHSSSA 315

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|J9PBA6 LHX8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 413 (150.4 bits), Expect = 5.9e-38, P = 5.9e-38
 Identities = 84/164 (51%), Positives = 107/164 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct:    68 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 127

Query:   672 HY--------LELVXXXXXXXXXXXXXXXXXXKSK-AKRVRTTFTEEQLQVLQANFQLDS 722
             HY         E+                     K AKR RT+FT +QLQV+QA F  D+
Sbjct:   128 HYDCMLDNLKREVENGNGISVEGALLTEQDVNHPKPAKRARTSFTADQLQVMQAQFAQDN 187

Query:   723 NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
             NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+      S+
Sbjct:   188 NPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHVSPNHSSSA 231

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|E9PGE3 LHX8 "LIM/homeobox protein Lhx8" [Homo sapiens (taxid:9606)]

 Score = 413 (150.4 bits), Expect = 5.9e-38, P = 5.9e-38
 Identities = 84/164 (51%), Positives = 107/164 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct:   119 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 178

Query:   672 HY--------LELVXXXXXXXXXXXXXXXXXXKSK-AKRVRTTFTEEQLQVLQANFQLDS 722
             HY         E+                     K AKR RT+FT +QLQV+QA F  D+
Sbjct:   179 HYDCMLDNLKREVENGNGISVEGALLTEQDVNHPKPAKRARTSFTADQLQVMQAQFAQDN 238

Query:   723 NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
             NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+      S+
Sbjct:   239 NPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHVSPNHSSST 282

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0007611 "learning or memory" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q68G74 LHX8 "LIM/homeobox protein Lhx8" [Homo sapiens (taxid:9606)]

 Score = 413 (150.4 bits), Expect = 5.9e-38, P = 5.9e-38
 Identities = 84/164 (51%), Positives = 107/164 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct:   129 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 188

Query:   672 HY--------LELVXXXXXXXXXXXXXXXXXXKSK-AKRVRTTFTEEQLQVLQANFQLDS 722
             HY         E+                     K AKR RT+FT +QLQV+QA F  D+
Sbjct:   189 HYDCMLDNLKREVENGNGISVEGALLTEQDVNHPKPAKRARTSFTADQLQVMQAQFAQDN 248

Query:   723 NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
             NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+      S+
Sbjct:   249 NPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHVSPNHSSST 292

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|C8YLT4 Lhx8 "LIM homeobox 8" [Sus scrofa (taxid:9823)]

 Score = 413 (150.4 bits), Expect = 5.9e-38, P = 5.9e-38
 Identities = 84/164 (51%), Positives = 107/164 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct:    68 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 127

Query:   672 HY--------LELVXXXXXXXXXXXXXXXXXXKSK-AKRVRTTFTEEQLQVLQANFQLDS 722
             HY         E+                     K AKR RT+FT +QLQV+QA F  D+
Sbjct:   128 HYDCMLDNLKREVENGNGISVEGALLTEQDVNHPKPAKRARTSFTADQLQVMQAQFAQDN 187

Query:   723 NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
             NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+      S+
Sbjct:   188 NPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHVSPNHSSSA 231

GO:0005634 "nucleus" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1P4G9 LHX8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 412 (150.1 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 83/156 (53%), Positives = 105/156 (67%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             FR +G +CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ 
Sbjct:   120 FRRYGTRCSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRV 179

Query:   672 HY--------LELVXXXXXXXXXXXXXXXXXXKSK-AKRVRTTFTEEQLQVLQANFQLDS 722
             HY         E+                     K AKR RT+FT +QLQV+QA F  D+
Sbjct:   180 HYDCMLDNLKREVENGNGVSMEGALLTEQDVNHPKPAKRARTSFTADQLQVMQAQFAQDN 239

Query:   723 NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL 758
             NPD Q L+++A+ TGLS+RV QVWFQN RAR KKH+
Sbjct:   240 NPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKHV 275

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

UNIPROTKB|F1NLU0 F1NLU0 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 411 (149.7 bits), Expect = 9.7e-38, P = 9.7e-38
 Identities = 84/159 (52%), Positives = 104/159 (65%)

Query:   612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
             F  FG KC++C R I +SDWVR+AR + YHLACFAC +CKRQLSTGEEF L E++VLC+ 
Sbjct:   129 FGRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRI 188

Query:   672 HYLELVXXXXXXXXXXXXXXXXXX-------KSK-AKRVRTTFTEEQLQVLQANFQLDSN 723
             HY  ++                         + K AKR RT+FT EQLQV+QA F  D+N
Sbjct:   189 HYDTMIENLKRAAENGNGITLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNN 248

Query:   724 PDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL--HT 760
             PD Q L+++A +TGLS+RV QVWFQN RAR KKH   HT
Sbjct:   249 PDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKHTPQHT 287

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0021799 "cerebral cortex radially oriented cell migration" evidence=IEA

GO:0021800 "cerebral cortex tangential migration" evidence=IEA

GO:0021853 "cerebral cortex GABAergic interneuron migration" evidence=IEA

GO:0021877 "forebrain neuron fate commitment" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0048469 "cell maturation" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8IRC7	AWH_DROME	No assigned EC number	0.7960	0.1966	0.5490	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	768
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	2e-35
cd09383	55	cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of	7e-23
cd09382	55	cd09382, LIM2_Lhx6, The second LIM domain of Lhx6	4e-22
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	5e-20
pfam00046	57	pfam00046, Homeobox, Homeobox domain	9e-20
pfam00046	57	pfam00046, Homeobox, Homeobox domain	9e-20
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	1e-19
smart00389	57	smart00389, HOX, Homeodomain	9e-18
smart00389	57	smart00389, HOX, Homeodomain	9e-18
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-17
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-17
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	5e-17
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	1e-16
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	2e-16
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	7e-16
cd09471	55	cd09471, LIM2_Isl2, The second LIM domain of Isl2	8e-16
pfam00412	58	pfam00412, LIM, LIM domain	4e-15
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	7e-15
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	1e-14
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	9e-14
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-13
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	2e-13
cd09390	55	cd09390, LIM2_dLMO, The second LIM domain of dLMO	4e-13
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	2e-11
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	4e-10
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	9e-10
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	5e-09
cd09385	56	cd09385, LIM2_LMO2, The second LIM domain of LMO2	2e-07
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	1e-06
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	2e-06
cd09451	53	cd09451, LIM_RIL, The LIM domain of RIL	9e-06
cd09352	54	cd09352, LIM1_Ajuba_like, The first LIM domain of	5e-05
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	7e-05
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	7e-05
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	1e-04
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	1e-04
cd09429	53	cd09429, LIM3_FHL1, The third LIM domain of Four a	2e-04
cd09461	54	cd09461, LIM3_Enigma_like_1, The third LIM domain	6e-04
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	7e-04
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	7e-04
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	0.001
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	0.001
cd09414	58	cd09414, LIM1_LIMPETin, The first LIM domain of pr	0.001
cd09450	53	cd09450, LIM_ALP, This family represents the LIM d	0.001
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	0.001
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	0.002
cd09365	54	cd09365, LIM2_LIMK, The second LIM domain of LIMK	0.002
cd09460	55	cd09460, LIM3_ZASP_Cypher, The third LIM domain of	0.002
cd09458	55	cd09458, LIM3_Enigma, The third LIM domain of Enig	0.002
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	0.002
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	0.002
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	0.002
cd09421	59	cd09421, LIM3_LIMPETin, The third LIM domain of pr	0.003
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	0.003
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	0.003
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	0.004
cd09431	57	cd09431, LIM3_Fhl2, The third LIM domain of Four a	0.004
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	0.004

>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH)

 Score =  127 bits (320), Expect = 2e-35
 Identities = 46/55 (83%), Positives = 52/55 (94%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C+KC R I++SDWVR+ARDHVYHLACFAC+ACKRQLSTGEEFAL EDRVLCK+HY
Sbjct: 1   CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

The second LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8

 Score = 92.0 bits (228), Expect = 7e-23
 Identities = 39/55 (70%), Positives = 48/55 (87%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           CS+C R I S+DWVR+A+ +VYHLACFAC +CKRQLSTGEEFAL E++VLC+ HY
Sbjct: 1   CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55

The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6

 Score = 89.8 bits (222), Expect = 4e-22
 Identities = 37/55 (67%), Positives = 46/55 (83%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C++C R I +SDWVR+AR + YHLACFAC +CKRQLSTGEEF L E++VLC+ HY
Sbjct: 1   CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55

The second LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family

 Score = 83.9 bits (208), Expect = 5e-20
 Identities = 23/56 (41%), Positives = 37/56 (66%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           +C++C  GI++S+ V +ARD V+HL CF C  C + L+ G+ F + +  V C+ HY
Sbjct: 4   RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59

The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

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

 Score = 82.9 bits (206), Expect = 9e-20
 Identities = 25/57 (43%), Positives = 39/57 (68%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           +R RTTFT EQL+ L+  F+ +  P  ++ E +A+  GL++R  +VWFQN RA+ K+
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 82.9 bits (206), Expect = 9e-20
 Identities = 25/57 (43%), Positives = 39/57 (68%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           +R RTTFT EQL+ L+  F+ +  P  ++ E +A+  GL++R  +VWFQN RA+ K+
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family

 Score = 82.8 bits (205), Expect = 1e-19
 Identities = 32/56 (57%), Positives = 40/56 (71%), Gaps = 1/56 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCKSHY 673
           C+ C  GI  +  VR+A+D+VYHL CFAC  CKRQL TG+EF L ED R++CK  Y
Sbjct: 1   CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56

The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 77.3 bits (191), Expect = 9e-18
 Identities = 26/56 (46%), Positives = 38/56 (67%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 116
           +R RT+FT EQL+ L+  FQ +  P  ++ E +A+  GLS+R  +VWFQN RA+ K
Sbjct: 2   RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 77.3 bits (191), Expect = 9e-18
 Identities = 26/56 (46%), Positives = 38/56 (67%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           +R RT+FT EQL+ L+  FQ +  P  ++ E +A+  GLS+R  +VWFQN RA+ K
Sbjct: 2   RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. 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 = 76.9 bits (190), Expect = 2e-17
 Identities = 23/58 (39%), Positives = 38/58 (65%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           +R RT FT EQL+ L+  F+ +  P  ++ E +A+  GL++R  ++WFQN RA+ K+ 
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

>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 = 76.9 bits (190), Expect = 2e-17
 Identities = 23/58 (39%), Positives = 38/58 (65%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           +R RT FT EQL+ L+  F+ +  P  ++ E +A+  GL++R  ++WFQN RA+ K+ 
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 29/56 (51%), Positives = 41/56 (73%), Gaps = 1/56 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEE-FALHEDRVLCKSHY 673
           C+ C +GI+ +D VR+ARD V+HL CF C  C++QLSTGEE + L E++ +CK  Y
Sbjct: 1   CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX protein family

 Score = 74.0 bits (182), Expect = 1e-16
 Identities = 25/53 (47%), Positives = 37/53 (69%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           C+KC +  + +D+V +AR  +YH+ CF C AC RQL  G+EFAL +D + CK+
Sbjct: 1   CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKA 53

The second LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b

 Score = 73.6 bits (180), Expect = 2e-16
 Identities = 33/57 (57%), Positives = 43/57 (75%), Gaps = 1/57 (1%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCKSHY 673
           KC+ C +GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK+ Y
Sbjct: 1   KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57

The second LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4

 Score = 72.0 bits (176), Expect = 7e-16
 Identities = 32/56 (57%), Positives = 40/56 (71%), Gaps = 1/56 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCKSHY 673
           C+ C +GI  +  VRKA+D VYHL CFAC  C RQL+TG+EF L ED R++CK  Y
Sbjct: 1   CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56

The second LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2

 Score = 71.9 bits (176), Expect = 8e-16
 Identities = 27/55 (49%), Positives = 37/55 (67%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C++C  G +SSD V +ARD VYH+ CF C  C RQL  G+EF L E  +LC++ +
Sbjct: 1   CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRADH 55

The second LIM domain of Isl2: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl proteins are found in the nucleus and act as transcription factors or cofactors. Isl1 and Isl2 are the two conserved members of this family. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Isl2 may be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 70.1 bits (172), Expect = 4e-15
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
           C+ C + I   + VR+A   V+H  CF C  C + L  G +F   + ++ CK  Y +L
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPG-DFFEKDGKLYCKHDYFKL 57

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and Lmx1b

 Score = 69.0 bits (169), Expect = 7e-15
 Identities = 29/55 (52%), Positives = 37/55 (67%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           CS C   IA S+ V +A ++VYHL CF C  C+RQL  G+EF L E ++LCKS Y
Sbjct: 1   CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55

The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9

 Score = 68.6 bits (167), Expect = 1e-14
 Identities = 23/56 (41%), Positives = 41/56 (73%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           +C++C  GI++S+ V +AR+ VYHL+CF C  C + L+TG+ F + ++ V C++H+
Sbjct: 4   RCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59

The second LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 65.8 bits (161), Expect = 9e-14
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 2/55 (3%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C+ C + I     + +A    +H  CF C  C + L  G+ F   + +  C+  Y
Sbjct: 1   CAGCGKPI-EGRELLRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 53

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 65.1 bits (159), Expect = 1e-13
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           KC+ C + I  ++ V +A   V+H  CF C  C + LS G+ F   + ++ CK  
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLS-GDTFFEKDGKLYCKDC 54

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2

 Score = 65.1 bits (158), Expect = 2e-13
 Identities = 24/56 (42%), Positives = 39/56 (69%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           +C++C  GI++S+ V +ARD VYHL CF C  C + L+TG+ F + ++ V C+ H+
Sbjct: 4   RCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59

The second LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx)

 Score = 64.1 bits (156), Expect = 4e-13
 Identities = 22/55 (40%), Positives = 35/55 (63%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C+ C + I + + V +AR +VYHL CFAC+ C  +   G+ F L E+++LC+  Y
Sbjct: 1   CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55

The second LIM domain of dLMO (Beaderx): dLMO is a nuclear protein that plays important roles in transcriptional regulation and development. In Drosophila dLMO modulates the activity of LIM-homeodomain protein Apterous (Ap), which regulates the formation of the dorsal-ventral axis of the Drosophila wing. Biochemical analysis shows that dLMO protein influences the activity of Apterous by binding of its cofactor Chip. Further studies shown that dLMO proteins might function in an evolutionarily conserved mechanism involved in patterning the appendages. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 58.9 bits (142), Expect = 2e-11
 Identities = 21/55 (38%), Positives = 36/55 (65%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C+ C + I + + V +A+D+VYHL CFAC+ C ++   G++F L  + +LC+  Y
Sbjct: 1   CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55

The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 58.6 bits (142), Expect = 4e-10
 Identities = 28/126 (22%), Positives = 53/126 (42%), Gaps = 12/126 (9%)

Query: 9   SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFT 68
           S  +++R+    T +  +  +     DS               +   S  K+KR RTT  
Sbjct: 10  SALESQRMPQIRTIKTTKNKREVEAADSEMKLER--------KQDGSSPPKSKRRRTT-- 59

Query: 69  EEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK--S 126
           +EQL VL+  F+++  P      +++ +  +  +  Q+WFQN RA++KK       +   
Sbjct: 60  DEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPG 119

Query: 127 SQNRPK 132
            +    
Sbjct: 120 EEEADL 125

Length = 156

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

 Score = 57.8 bits (140), Expect = 9e-10
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 690 SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 749
            +   S  K+KR RTT  +EQL VL+  F+++  P      +++ +  +  +  Q+WFQN
Sbjct: 44  KQDGSSPPKSKRRRTT--DEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQN 101

Query: 750 SRARQKKHLHTGKMK 764
            RA++KK       +
Sbjct: 102 KRAKEKKKRSGKVEQ 116

Length = 156

>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only protein 4)

 Score = 52.5 bits (126), Expect = 5e-09
 Identities = 20/51 (39%), Positives = 28/51 (54%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
           CS C + I +S+ V +A+ +VYHL CF C  C  QL  G+ F      + C
Sbjct: 1   CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51

The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only protein 2)

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK 670
           C+ C + I + +   + +D VYHL CF C AC++    G+ + L    ++C+
Sbjct: 1   CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCE 52

The second LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 46.8 bits (111), Expect = 1e-06
 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C  C + ++ +    +A  H++H+ CF C  C++QL  G++F   E +  C+  Y
Sbjct: 34  CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQ-GQQFYSLEGKPYCEECY 87

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 87

>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule interacting with CasL) like family

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 638 HVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
            ++H +CF C  C + L  G  +A  E ++ CK H+
Sbjct: 19  KLFHKSCFRCSHCNKTLRLG-NYASLEGKLYCKPHF 53

The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL

 Score = 43.4 bits (102), Expect = 9e-06
 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C++C  GI  +  + KARD +YH  CF C+ C   L     F + ++++ C++H
Sbjct: 1   CTRCGNGIVGT--IVKARDKLYHPECFMCDDCGLNLKQRGYFFI-DEQLYCETH 51

The LIM domain of RIL: RIL contains an N-terminal PDZ domain, a LIM domain, and a short consensus C-terminal region. It is the smallest molecule in the ALP LIM domain containing protein family. RIL was identified in rat fibroblasts and in human lymphocytes. The LIM domain interacts with the AMPA glutamate receptor in dendritic spines. The consensus C-terminus interacts with PTP-BL, a submembranous protein tyrosine phosphatase and the PDZ domain is responsible to interact with alpha-actinin molecules. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like proteins

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C KC +G+  +    +A  ++YH  CF C +C R L  G+ F     +V C+  Y
Sbjct: 1   CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLR-GKAFYNVNGKVYCEEDY 54

The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C++C + +  ++ V    D  +H ACF CE CK  L+    +  ++ +  C +HY
Sbjct: 1   CARCGKIVYPTEKV-NCLDKTWHKACFHCEVCKMTLNM-NNYKGYQKKPYCNAHY 53

The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 635 ARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           A    +H +CF CE C  +LS G   +LH  R+ CK H+
Sbjct: 16  ADKQNFHKSCFRCEHCNSKLSLGNYASLH-GRIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 635 ARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           A   +YH +CF C  C  +LS G   +LH   + CK H+
Sbjct: 16  ANQQIYHNSCFRCSYCNTKLSLGTYASLH-GNIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin): Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C  C + I  +     A +  +H  CF C  C +    G  F  HE    C++HY
Sbjct: 1   CGGCNKPILEN--YISALNTQWHPECFVCRECHKPFINGSFFE-HEGLPYCETHY 52

The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C KC + I S       +D  +H  CF C +C ++L+ G+ F   ED+  C   Y
Sbjct: 1   CVKCNKPITSGGV--TYQDQPWHSECFVCSSCSKKLA-GQRFTAVEDQYYCVDCY 52

The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma subfamily with unknown function

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 619 CSKCCRGIASSD-WVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C  C   I + D WV +A ++ YH  CF C  C   L  G+ F     R  CK H
Sbjct: 1   CVSCGFPIEAGDRWV-EALNNNYHSQCFNCTRCNVNLE-GQSFYAKGGRPFCKLH 53

The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 6/57 (10%)

Query: 617 AKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
            KC K C+G      V + +D  +H+ CF C+ C   L+ G  F   E    C   Y
Sbjct: 2   YKCGKKCKGE-----VLRVQDKYFHIKCFTCKVCGCDLAQGGFFV-KEGEYYCTDDY 52

The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1 (CRP1)

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           KC  C + +  ++ V +     +H +CF C  CK+ L +    A+H + + CKS Y
Sbjct: 2   KCGVCQKTVYFAEEV-QCEGRSFHKSCFLCMVCKKNLDS-TTVAVHGEEIYCKSCY 55

The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH) family

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C  C   I + D   +A  H +H  CF C  C   L  G+ F   +D+ LCK H
Sbjct: 1   CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLE-GQTFFSKKDKPLCKKH 53

The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C +C   +        A D V+H+ CF C  C  +L  G+ F   E +  C+  Y
Sbjct: 1   CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLR-GQPFYAVEKKAYCEPCY 54

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 619 CSKCCRGIASSD---WVRKARDHV-YHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C  C   +   +      K  + + +H ACF C  C+ +L     + +H+D++ C+ HY
Sbjct: 1   CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCE-ELLVDLTYCVHDDQIYCERHY 58

The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP, actinin-associated LIM protein

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C KC  GI  +  V KARD   H  CF C  C   L     F + E ++ C++H
Sbjct: 1   CDKCGSGIVGT--VVKARDKYRHPECFVCSDCNLNLKQKGYFFV-EGQLYCEAH 51

This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C KC   +        A D VYH++CF C  C+  L  G+ F   + +  C+  Y
Sbjct: 1   CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQ-GKPFYALDGKPYCEEDY 54

The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C++C  G+  ++ +    D  +H ACF CE CK  L T   F  H+ +  C++H
Sbjct: 1   CARCGYGVYPAEKI-NCIDQTWHKACFHCEVCKMML-TVNNFVSHQKKPYCQAH 52

The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain Kinase )

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 13/30 (43%), Positives = 19/30 (63%)

Query: 635 ARDHVYHLACFACEACKRQLSTGEEFALHE 664
           A DH +H  CF+C +CK  +  G+ +AL E
Sbjct: 15  AGDHKFHPECFSCSSCKAFIGDGDSYALVE 44

The second LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher family

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C  C   + + D   +A  H +H  CF C  C   L  G+ F   +D+ LCK H
Sbjct: 1   CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDKPLCKKH 53

The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C  C   I + D   +A    +H  CF C  C+  L  G+ F   +D+ LCKSH
Sbjct: 1   CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLE-GKTFYSKKDKPLCKSH 53

The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           KC  C R +  ++ V +     +H  CF C  C++ L +    A+H+  + CKS Y
Sbjct: 1   KCGACGRTVYHAEEV-QCDGRSFHKCCFLCMVCRKNLDS-TTVAIHDQEIYCKSCY 54

The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 2/55 (3%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           C KC  G A       A    YH+  F C  C       + +  HE ++ C  HY
Sbjct: 1   CFKC--GGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like family

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C  C   I + D   +A  H +H  CF C  C   L  G+ F   +D+ LCK+H
Sbjct: 1   CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLE-GQTFYSKKDKPLCKNH 53

The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 615 FGAKCSKCCR--GIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           F  +C +C +  GI S D   K  D  +H ACF C  CK  L   + F    DR+ C + 
Sbjct: 1   FANQCEECSKIIGIDSKDLSYK--DKHWHEACFLCSKCKISL-VDKPFGSKADRIYCGNC 57

Query: 673 Y 673
           Y
Sbjct: 58  Y 58

The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)

Query: 640 YHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           +H  C  CE CK+ L+ G + + HE +  C   Y
Sbjct: 21  WHKPCLRCEKCKKTLTPG-QHSEHEGKPYCNKCY 53

The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated LIM protein) family

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
           C KC  GI     V KARD   H  CF C  C   L     F + ED + C++H
Sbjct: 1   CDKCGNGIVGV--VVKARDKNRHPECFVCADCGLNLKNKGYFFI-EDELYCETH 51

This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
           C+KC + I S       RD  +H  CF C  CK+QL+ G+ F   ++   C
Sbjct: 1   CAKCKKAITSGGVTY--RDQPWHKECFVCTGCKKQLA-GQRFTSRDEYPYC 48

The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
           C +C + I +       RD  +H  CF C  CK+QLS G+ F   +D   C + +  L
Sbjct: 1   CVQCKKPITTGGVTY--RDQPWHKECFVCTGCKKQLS-GQRFTSRDDFAYCLNCFCNL 55

The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. Length = 57

>gnl|CDD|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 634 KARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
            A  H+YH  CF C+ C +QL   + +  HE  + CK H+
Sbjct: 15  IAEKHIYHKNCFRCKDCNKQLKV-DNYQSHEGNLYCKVHF 53

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	768
KOG4577|consensus	383		100.0
KOG1701|consensus	468		99.75
KOG0484|consensus	125		99.67
KOG2272|consensus	332		99.67
KOG0494|consensus	332		99.66
KOG1701|consensus	468		99.62
KOG0488|consensus	309		99.58
KOG0489|consensus	261		99.56
KOG0484|consensus	125		99.55
KOG2251|consensus	228		99.55
KOG0850|consensus	245		99.51
KOG0485|consensus	268		99.51
KOG0850|consensus	245		99.5
KOG0843|consensus	197		99.49
KOG0843|consensus	197		99.48
KOG0842|consensus	307		99.48
KOG0487|consensus	308		99.47
KOG0488|consensus	309		99.47
KOG0842|consensus	307		99.46
KOG0485|consensus	268		99.45
KOG0489|consensus	261		99.45
KOG0486|consensus	351		99.44
KOG0494|consensus	332		99.44
KOG0490|consensus	235		99.43
KOG1044|consensus	670		99.43
KOG0490|consensus	235		99.43
KOG0492|consensus	246		99.42
KOG0491|consensus	194		99.4
KOG1703|consensus	479		99.4
KOG0487|consensus	308		99.39
KOG2251|consensus	228		99.39
KOG0848|consensus	317		99.39
KOG0493|consensus	342		99.36
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.35
KOG0844|consensus	408		99.33
KOG0848|consensus	317		99.33
KOG1703|consensus	479		99.31
KOG0492|consensus	246		99.3
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.3
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.26
KOG0844|consensus	408		99.19
KOG2272|consensus	332		99.18
KOG0493|consensus	342		99.18
KOG4577|consensus	383		99.17
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.15
COG5576	156	Homeodomain-containing transcription factor [Trans	99.15
KOG3802|consensus	398		99.15
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.13
KOG0486|consensus	351		99.13
KOG0483|consensus	198		99.12
COG5576	156	Homeodomain-containing transcription factor [Trans	99.1
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.1
KOG0847|consensus	288		99.07
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.05
KOG0491|consensus	194		99.04
KOG0847|consensus	288		99.03
KOG0483|consensus	198		99.02
KOG3802|consensus	398		99.02
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.02
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.98
KOG0849|consensus	354		98.97
KOG1044|consensus	670		98.75
KOG0775|consensus	304		98.63
KOG1168|consensus	385		98.63
KOG0849|consensus	354		98.55
KOG0775|consensus	304		98.49
KOG1168|consensus	385		98.49
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.17
KOG1700|consensus	200		97.89
KOG0774|consensus	334		97.74
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	97.51
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.43
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.42
KOG0774|consensus	334		97.24
KOG2252|consensus	558		97.24
KOG2252|consensus	558		97.18
KOG1146|consensus	1406		96.19
KOG1146|consensus	1406		95.22
KOG1702|consensus	264		94.69
KOG1700|consensus	200		93.81
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	92.08
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	91.46
KOG0773|consensus	342		89.06
KOG3623|consensus	1007		88.69
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	87.02
KOG3623|consensus	1007		85.19
KOG0773|consensus	342		84.46
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	83.58

>KOG4577|consensus

Probab=100.00  E-value=1.8e-36  Score=303.54  Aligned_cols=197  Identities=34%  Similarity=0.503  Sum_probs=171.4

Q ss_pred             cchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchhh
Q psy17256        531 LEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLI  610 (768)
Q Consensus       531 ~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~  610 (768)
                      |.|..|.+.|.++.+.|...     ..||..|+.|+.|...+.                  ..||.+++..|    |..|
T Consensus        34 p~CagC~q~IlDrFilKvl~-----R~wHs~CLkCs~C~~qL~------------------drCFsR~~s~y----Cked   86 (383)
T KOG4577|consen   34 PICAGCDQHILDRFILKVLD-----RHWHSSCLKCSDCHDQLA------------------DRCFSREGSVY----CKED   86 (383)
T ss_pred             ccccchHHHHHHHHHHHHHh-----hhhhhhhcchhhhhhHHH------------------HHHhhcCCcee----ehHH
Confidence            45999999999999887743     299999999999985433                  35788888885    4589


Q ss_pred             hhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeec-CcccccccccccccCCcccCCCCCC
Q psy17256        611 CFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHE-DRVLCKSHYLELVDGGTTSSDDGAD  689 (768)
Q Consensus       611 y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~-g~~~C~~~y~e~~~~~~~s~~~g~~  689 (768)
                      |+++||++|.+|..+|.+...|.+|.+.+||..||.|..|+++|..|++|++.+ .++.|+.+|++.........     
T Consensus        87 FfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l-----  161 (383)
T KOG4577|consen   87 FFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNEL-----  161 (383)
T ss_pred             HHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcccccc-----
Confidence            999999999999999999878888999999999999999999999999999775 78999999998765432211     


Q ss_pred             cccccCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        690 SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       690 ~~~~~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                          .+....||+||.||+.|++.|+..|...+.|....|++|+..+||..++|||||||||||.||.++..+.
T Consensus       162 ----~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T KOG4577|consen  162 ----EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T ss_pred             ----ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence                1123468999999999999999999999999999999999999999999999999999999998877654

>KOG1701|consensus

Probab=99.75  E-value=7.9e-19  Score=186.73  Aligned_cols=135  Identities=20%  Similarity=0.256  Sum_probs=112.8

Q ss_pred             ccccccccccccccccccccccCCccccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccc
Q psy17256        504 HLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVK  583 (768)
Q Consensus       504 ~~ky~~~c~~~~~~F~Pl~~s~~G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~  583 (768)
                      ++.|++.|+.+.              ...|..|.+.|.++++.+.|+      .||+.||+|.+|..   ||        
T Consensus       322 ~k~~CE~cyq~t--------------lekC~~Cg~~I~d~iLrA~Gk------ayHp~CF~Cv~C~r---~l--------  370 (468)
T KOG1701|consen  322 GKPYCEGCYQDT--------------LEKCNKCGEPIMDRILRALGK------AYHPGCFTCVVCAR---CL--------  370 (468)
T ss_pred             CcccchHHHHHH--------------HHHHhhhhhHHHHHHHHhccc------ccCCCceEEEEecc---cc--------
Confidence            456888887762              345999999999999999999      99999999999983   32        


Q ss_pred             cccccCCCCcceeecccccccccchhhhhhhcccccccCCCCCCCCc-----ceeeecCceecccCccccccccccC---
Q psy17256        584 PYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSD-----WVRKARDHVYHLACFACEACKRQLS---  655 (768)
Q Consensus       584 ~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~~C~~C~~~I~~~e-----~~~~a~~~~~H~~CF~C~~C~~~L~---  655 (768)
                           ||.++....++++    ||+.||+++|++||+.|+++|.+.|     .-+.++|+.||++|++|..|+.+|.   
T Consensus       371 -----dgipFtvd~~n~v----~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~  441 (468)
T KOG1701|consen  371 -----DGIPFTVDSQNNV----YCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEE  441 (468)
T ss_pred             -----CCccccccCCCce----eeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccC
Confidence                 3445556666788    6789999999999999999998744     2367899999999999999999996   


Q ss_pred             CCCceEeecCccccccccccccc
Q psy17256        656 TGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       656 ~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      +|+.++..+|+++|+.|+...+.
T Consensus       442 e~qgCyPld~HllCk~Ch~~Rl~  464 (468)
T KOG1701|consen  442 EGQGCYPLDGHLLCKTCHLKRLQ  464 (468)
T ss_pred             CCCcceeccCceeechhhhhhhc
Confidence            56678999999999999876543

>KOG0484|consensus

Probab=99.67  E-value=9.6e-18  Score=145.02  Aligned_cols=68  Identities=40%  Similarity=0.532  Sum_probs=64.0

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      ...+|.||.||+||..||.+||+.|..++||++.+|++||.++.|++.+|||||||||+|.+|+.+..
T Consensus        12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            44678899999999999999999999999999999999999999999999999999999999987754

>KOG2272|consensus

Probab=99.67  E-value=1.2e-17  Score=165.80  Aligned_cols=132  Identities=20%  Similarity=0.344  Sum_probs=118.2

Q ss_pred             hhcccccccccccccccccccccccCCccccc-hhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccc
Q psy17256        501 QEKHLKYNTAAEDLRASFTPLVCSTDGALHLE-FHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTR  579 (768)
Q Consensus       501 ~eK~~ky~~~c~~~~~~F~Pl~~s~~G~~g~~-C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r  579 (768)
                      +-|..+|+-+|.+.              ||.+ |..|.++|-++.+.++|+      +||.++|+|+.|-.+++   |.|
T Consensus       179 evk~eLyClrChD~--------------mgipiCgaC~rpIeervi~amgK------hWHveHFvCa~CekPFl---GHr  235 (332)
T KOG2272|consen  179 EVKGELYCLRCHDK--------------MGIPICGACRRPIEERVIFAMGK------HWHVEHFVCAKCEKPFL---GHR  235 (332)
T ss_pred             hhccceeccccccc--------------cCCcccccccCchHHHHHHHhcc------ccchhheeehhcCCccc---chh
Confidence            34778888888876              4544 999999999999999999      99999999999997766   454


Q ss_pred             cccccccccCCCCcceeecccccccccchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCc
Q psy17256        580 QIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEE  659 (768)
Q Consensus       580 ~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~  659 (768)
                      +              |++.+..    ||+.+|+++||..|..|+..|.++  ++.|+++.|-++||.|+.|.+.|.-.++
T Consensus       236 H--------------YEkkGla----YCe~h~~qLfG~~CF~C~~~i~G~--vv~al~KawCv~cf~Cs~Cdkkl~~K~K  295 (332)
T KOG2272|consen  236 H--------------YEKKGLA----YCETHYHQLFGNLCFICNRVIGGD--VVSALNKAWCVECFSCSTCDKKLTQKNK  295 (332)
T ss_pred             h--------------hhhcCch----hHHHHHHHHhhhhheecCCccCcc--HHHHhhhhhccccccccccccccccccc
Confidence            4              8888999    456899999999999999999988  8999999999999999999999998999


Q ss_pred             eEeecCcccccccccc
Q psy17256        660 FALHEDRVLCKSHYLE  675 (768)
Q Consensus       660 f~~~~g~~~C~~~y~e  675 (768)
                      |+..|.+|.|+.||..
T Consensus       296 f~E~DmkP~CKkCy~r  311 (332)
T KOG2272|consen  296 FYEFDMKPVCKKCYDR  311 (332)
T ss_pred             eeeeccchHHHHHHhh
Confidence            9999999999999963

>KOG0494|consensus

Probab=99.66  E-value=7.5e-17  Score=160.76  Aligned_cols=88  Identities=32%  Similarity=0.396  Sum_probs=72.1

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCCCCCCCCCCCCC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQNRPKYGYYP  137 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~~~~~p~~g~~p  137 (768)
                      +|+|+-||+||.-|+++||+.|...+||+...|+.||.++.|+|.+|||||||||+||||.++.|....  ....||.+.
T Consensus       139 ~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT--~maeyglyG  216 (332)
T KOG0494|consen  139 KKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGST--IMAEYGLYG  216 (332)
T ss_pred             cccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcch--hhhhhcccc
Confidence            344445999999999999999999999999999999999999999999999999999999999998643  334455555


Q ss_pred             CCCCCccccC
Q psy17256        138 EPNKSFLVIK  147 (768)
Q Consensus       138 ~p~~s~l~~~  147 (768)
                      ..+..+++..
T Consensus       217 amvrhslplp  226 (332)
T KOG0494|consen  217 AMVRHSLPLP  226 (332)
T ss_pred             hhhcccCCch
Confidence            4444444433

>KOG1701|consensus

Probab=99.62  E-value=1.9e-17  Score=176.24  Aligned_cols=161  Identities=17%  Similarity=0.210  Sum_probs=123.0

Q ss_pred             chhhhhhhhhhH--HHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        532 EFHSFLKRIALV--LSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       532 ~C~~c~k~Ia~~--~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      .|..|+|.|...  -..++++      .||.+||+|..|+..   |+|+              .+|..|+++||    +.
T Consensus       276 iC~~C~K~V~g~~~ac~Am~~------~fHv~CFtC~~C~r~---L~Gq--------------~FY~v~~k~~C----E~  328 (468)
T KOG1701|consen  276 ICAFCHKTVSGQGLAVEAMDQ------LFHVQCFTCRTCRRQ---LAGQ--------------SFYQVDGKPYC----EG  328 (468)
T ss_pred             hhhhcCCcccCcchHHHHhhh------hhcccceehHhhhhh---hccc--------------cccccCCcccc----hH
Confidence            599999999764  4578888      899999999999954   4555              34777888854    57


Q ss_pred             hhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEee-cCcccccccccccccCCc-ccCCCC
Q psy17256        610 ICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALH-EDRVLCKSHYLELVDGGT-TSSDDG  687 (768)
Q Consensus       610 ~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~-~g~~~C~~~y~e~~~~~~-~s~~~g  687 (768)
                      ||.. -..||..|+++|.  |++++|+|+.||+.||+|.+|++.| +|..|.+. ++++||..||+..+..-- +.+..-
T Consensus       329 cyq~-tlekC~~Cg~~I~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI  404 (468)
T KOG1701|consen  329 CYQD-TLEKCNKCGEPIM--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPI  404 (468)
T ss_pred             HHHH-HHHHHhhhhhHHH--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCcchhhccCCc
Confidence            7765 3469999999999  6699999999999999999999999 89999876 478999999998876422 111111


Q ss_pred             CCcccccCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHH
Q psy17256        688 ADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQI  735 (768)
Q Consensus       688 ~~~~~~~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~  735 (768)
                         ....  ++.--.       .+..|.+.|+.+.|-+...+..|+.+
T Consensus       405 ---~P~~--G~~etv-------Rvvamdr~fHv~CY~CEDCg~~LS~e  440 (468)
T KOG1701|consen  405 ---LPRD--GKDETV-------RVVAMDRDFHVNCYKCEDCGLLLSSE  440 (468)
T ss_pred             ---cCCC--CCcceE-------EEEEccccccccceehhhcCcccccc
Confidence               1111  111111       14678999999999999999888743

>KOG0488|consensus

Probab=99.58  E-value=1.5e-15  Score=162.70  Aligned_cols=76  Identities=26%  Similarity=0.381  Sum_probs=68.4

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCCCCCC
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQNR  130 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~~~~~  130 (768)
                      ..++|+|+.||.||..||.+||+.|+++.|++.++|.+||..|||+..||++||||||+||||+...+.......+
T Consensus       167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~  242 (309)
T KOG0488|consen  167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAG  242 (309)
T ss_pred             CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccccccc
Confidence            4458899999999999999999999999999999999999999999999999999999999999877655444443

>KOG0489|consensus

Probab=99.56  E-value=2.4e-15  Score=158.46  Aligned_cols=69  Identities=32%  Similarity=0.448  Sum_probs=64.4

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCC
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK  125 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~  125 (768)
                      .++.||.||.||..|+.+||++|+.|+|++...|.|||..|.|+|+||+||||||||||||..+.....
T Consensus       156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            356789999999999999999999999999999999999999999999999999999999987776655

>KOG0484|consensus

Probab=99.55  E-value=6.6e-16  Score=133.70  Aligned_cols=66  Identities=41%  Similarity=0.547  Sum_probs=63.0

Q ss_pred             CCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .++|++|.||.||..|+..||+.|...+||+...|++||.++.|++..|||||||||||.||+++.
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~   78 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA   78 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence            467889999999999999999999999999999999999999999999999999999999999764

>KOG2251|consensus

Probab=99.55  E-value=9.1e-15  Score=144.36  Aligned_cols=68  Identities=37%  Similarity=0.507  Sum_probs=64.8

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      ..++|.||.||+|+..|+++||..|.+++|||+..|++||.+|+|++.+|||||.|||+|+|++.+..
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            56789999999999999999999999999999999999999999999999999999999999987764

>KOG0850|consensus

Probab=99.51  E-value=9.8e-15  Score=144.60  Aligned_cols=70  Identities=29%  Similarity=0.419  Sum_probs=65.4

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      .+.+|.|++||+++.-||..|.+.|++++|+..++|.+||..|||+.+||+|||||||.|.||..+.+..
T Consensus       117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            4567888999999999999999999999999999999999999999999999999999999998885554

>KOG0485|consensus

Probab=99.51  E-value=1.6e-14  Score=141.09  Aligned_cols=71  Identities=23%  Similarity=0.419  Sum_probs=65.0

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  126 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~  126 (768)
                      ...++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|+||+|||||||.||||+.....+..
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~  170 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAA  170 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence            34578889999999999999999999999999999999999999999999999999999999877665543

>KOG0850|consensus

Probab=99.50  E-value=1.2e-14  Score=144.10  Aligned_cols=72  Identities=28%  Similarity=0.409  Sum_probs=66.8

Q ss_pred             ccCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccC
Q psy17256        693 SHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK  764 (768)
Q Consensus       693 ~~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~  764 (768)
                      ....+|.|++||.++.-||+.|++.|++.+|+-..+|.+||..|||+.+||||||||||.|.||.++.|+.-
T Consensus       116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~  187 (245)
T KOG0850|consen  116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP  187 (245)
T ss_pred             CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence            344677788899999999999999999999999999999999999999999999999999999999977754

>KOG0843|consensus

Probab=99.49  E-value=1.6e-14  Score=137.79  Aligned_cols=64  Identities=36%  Similarity=0.570  Sum_probs=60.7

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      +.||.||.||.+||..||.+|+.++|....+|+.||+.|+|++.||+|||||||.|.||.....
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            7888999999999999999999999999999999999999999999999999999999876553

>KOG0843|consensus

Probab=99.48  E-value=1.6e-14  Score=137.89  Aligned_cols=65  Identities=37%  Similarity=0.578  Sum_probs=61.9

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +.||.||.|+.+|+..||..|..++|....+|+.||..|+|++.||+|||||||+|.||++..++
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~k  165 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQEDK  165 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHhh
Confidence            67889999999999999999999999999999999999999999999999999999999877743

>KOG0842|consensus

Probab=99.48  E-value=4.5e-14  Score=148.48  Aligned_cols=71  Identities=23%  Similarity=0.426  Sum_probs=64.7

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  126 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~  126 (768)
                      ...++||.|..||..|.-+||+.|..++|++.++|++||..|.||++||||||||||-|.||+.+......
T Consensus       149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            35677888999999999999999999999999999999999999999999999999999999877665433

>KOG0487|consensus

Probab=99.47  E-value=3.7e-14  Score=149.22  Aligned_cols=69  Identities=22%  Similarity=0.431  Sum_probs=63.0

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      ..+..|++|..+|..|+.+||++|..|.|.+...|.+|++.|+|+++||+|||||||||.||..+....
T Consensus       231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~  299 (308)
T KOG0487|consen  231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRL  299 (308)
T ss_pred             cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhc
Confidence            346678889999999999999999999999999999999999999999999999999999998864443

>KOG0488|consensus

Probab=99.47  E-value=2.5e-14  Score=153.25  Aligned_cols=67  Identities=28%  Similarity=0.458  Sum_probs=63.4

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++|+|+.||.||..|+..||+.|++.+|.+..+|..||.+|||+..||++||||||+||||+...+.
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~  235 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG  235 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence            4777888999999999999999999999999999999999999999999999999999999977754

>KOG0842|consensus

Probab=99.46  E-value=4.5e-14  Score=148.51  Aligned_cols=72  Identities=22%  Similarity=0.418  Sum_probs=66.2

Q ss_pred             cCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccCC
Q psy17256        694 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  765 (768)
Q Consensus       694 ~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~~  765 (768)
                      ....++|+.|..||..|+.+||+.|.+.+|++..+|+.||..|.|+++||||||||||-|.||+++.+.+..
T Consensus       148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            345677778999999999999999999999999999999999999999999999999999999988877653

>KOG0485|consensus

Probab=99.45  E-value=3.4e-14  Score=138.74  Aligned_cols=65  Identities=25%  Similarity=0.472  Sum_probs=61.3

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      +.++|+.||+|+..|+..||..|+...|.+..+|..||.+|.|++.||||||||||.||||+...
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            45678889999999999999999999999999999999999999999999999999999998653

>KOG0489|consensus

Probab=99.45  E-value=2e-14  Score=151.47  Aligned_cols=68  Identities=32%  Similarity=0.460  Sum_probs=64.0

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccC
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK  764 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~  764 (768)
                      ++.||.||.||..|+.+||+.|+.|+|.++..|-+||..|.|+++||||||||||+||||..+.+...
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            45788999999999999999999999999999999999999999999999999999999998877654

>KOG0486|consensus

Probab=99.44  E-value=7.6e-14  Score=143.66  Aligned_cols=65  Identities=42%  Similarity=0.595  Sum_probs=62.8

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      |+||.||.||.+|+.+||..|++|+||+...|++||.+++|+|.+|+|||.|||+||+|.++...
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            78999999999999999999999999999999999999999999999999999999999888765

>KOG0494|consensus

Probab=99.44  E-value=6.1e-14  Score=140.20  Aligned_cols=66  Identities=36%  Similarity=0.450  Sum_probs=60.6

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +++|+-||.||..|+..||..|...+||+...|+.||.++.|.+..|+||||||||||||.++.-.
T Consensus       139 ~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg  204 (332)
T KOG0494|consen  139 KKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG  204 (332)
T ss_pred             cccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence            344445999999999999999999999999999999999999999999999999999999987644

>KOG0490|consensus

Probab=99.43  E-value=8.9e-14  Score=144.62  Aligned_cols=198  Identities=30%  Similarity=0.420  Sum_probs=155.7

Q ss_pred             hhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchhhhhh--
Q psy17256        536 FLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFR--  613 (768)
Q Consensus       536 c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~--  613 (768)
                      |...|.+++......     ..||..|+.|..|...+.               .+. .+|.+++..+    |..||.+  
T Consensus         2 ~~~~~~~~~~l~~~~-----~~~~~~~~~~~~~~~~~~---------------~~~-~~~~~~g~~~----~~~d~~~~~   56 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLD-----RYWHASCLKCAECDNPLG---------------VGD-TCFSKDGSIY----CKRDYQREF   56 (235)
T ss_pred             CCccccchHHhhccc-----HHHHHHHHhhhhhcchhc---------------cCC-CcccCCCccc----ccccchhhh
Confidence            566777777665542     499999999999984322               111 2344466774    5589998  


Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecC-ccccccccccc--ccCCcccC-CC---
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCKSHYLEL--VDGGTTSS-DD---  686 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g-~~~C~~~y~e~--~~~~~~s~-~~---  686 (768)
                      .+..+|.+|...|...|.++++..++ |..||.|..|...+..++++.+.++ ...|..++.+.  ...+.... ..   
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~  135 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTA  135 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCC
Confidence            88999999999999889999999998 9999999999999999999999987 88898888654  22111111 11   


Q ss_pred             -----CCCcccccCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        687 -----GADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       687 -----g~~~~~~~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                           ...........+.++.|+.+...|+..+...|...++|+...+..|+..+|++++.|++||||+|++.++...
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  136 PPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence                 0111122345677888999999999999999999999999999999999999999999999999999998654

>KOG1044|consensus

Probab=99.43  E-value=5.3e-14  Score=154.73  Aligned_cols=115  Identities=21%  Similarity=0.295  Sum_probs=97.8

Q ss_pred             ccccc-hhhhhhhhhhH-HHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccc
Q psy17256        528 ALHLE-FHSFLKRIALV-LSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGR  605 (768)
Q Consensus       528 ~~g~~-C~~c~k~Ia~~-~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~  605 (768)
                      ..++. |++|...|... .++++++      +||.-||.|..|.+.+.                  +-++.+++.+    
T Consensus       130 ~~~ps~cagc~~~lk~gq~llald~------qwhv~cfkc~~c~~vL~------------------gey~skdg~p----  181 (670)
T KOG1044|consen  130 SYGPSTCAGCGEELKNGQALLALDK------QWHVSCFKCKSCSAVLN------------------GEYMSKDGVP----  181 (670)
T ss_pred             ccCCccccchhhhhhccceeeeecc------ceeeeeeehhhhccccc------------------ceeeccCCCc----
Confidence            34555 99999999875 4678888      99999999999996544                  3456678888    


Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcc---ccccc
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRV---LCKSH  672 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~---~C~~~  672 (768)
                      ||+.||+.+||.+|..|.+.|.+.  |+.|.|+.||+.|-+|+.|+++|.+|++.++.+..+   -|+.-
T Consensus       182 yce~dy~~~fgvkc~~c~~fisgk--vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa  249 (670)
T KOG1044|consen  182 YCEKDYQAKFGVKCEECEKFISGK--VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQA  249 (670)
T ss_pred             chhhhhhhhcCeehHHhhhhhhhh--hhhccCcccCcchhhhhhhccccccchheeeccccccCCccccc
Confidence            566999999999999999999988  999999999999999999999999999999998654   55543

>KOG0490|consensus

Probab=99.43  E-value=3.9e-14  Score=147.35  Aligned_cols=120  Identities=28%  Similarity=0.464  Sum_probs=103.2

Q ss_pred             cCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccCCcccCCCCCCcccccCCCccc
Q psy17256        621 KCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAK  700 (768)
Q Consensus       621 ~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~~~~s~~~g~~~~~~~~~~k~r  700 (768)
                      +|+..|.+. ....+.+..||..|..|..|...|..+...+..+|..||..+|..                  ....+++
T Consensus         1 ~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~------------------~~~~~~r   61 (235)
T KOG0490|consen    1 GCGRQILDR-YLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQR------------------EFKFSKR   61 (235)
T ss_pred             CCCccccch-HHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchh------------------hhhcccc
Confidence            477777753 445666889999999999999999544555555999999999975                  1135678


Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      +.|+.|+..|+..|++.|.+.+||+...++.||..+++++..|+|||||||+||+++++
T Consensus        62 r~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   62 CARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             ccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            89999999999999999999999999999999999999999999999999999999874

>KOG0492|consensus

Probab=99.42  E-value=6.3e-14  Score=136.21  Aligned_cols=72  Identities=24%  Similarity=0.361  Sum_probs=65.0

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCC
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  126 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~  126 (768)
                      .+.+..|++||.||.+||..||+.|...+|+++.+|.+++..|.|+++||+|||||||+|.||.+....++.
T Consensus       139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~  210 (246)
T KOG0492|consen  139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKL  210 (246)
T ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHh
Confidence            456778889999999999999999999999999999999999999999999999999999999766554443

>KOG0491|consensus

Probab=99.40  E-value=7.5e-14  Score=130.95  Aligned_cols=71  Identities=27%  Similarity=0.473  Sum_probs=64.9

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCCCC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSSQ  128 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~~~  128 (768)
                      -++++-||+|+..|+..||+.|+.++|++.++|.|||..|+|+++||+.||||||||.||+.+..+.+.+.
T Consensus        98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~  168 (194)
T KOG0491|consen   98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSN  168 (194)
T ss_pred             HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCC
Confidence            35677899999999999999999999999999999999999999999999999999999998887754433

>KOG1703|consensus

Probab=99.40  E-value=8.9e-14  Score=159.14  Aligned_cols=130  Identities=15%  Similarity=0.169  Sum_probs=111.1

Q ss_pred             cccccccccccccccccccccccCCccccchhhhhhhhhhHHHHHhhcccccccccccceEEEecccccccccccccccc
Q psy17256        503 KHLKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIV  582 (768)
Q Consensus       503 K~~ky~~~c~~~~~~F~Pl~~s~~G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~  582 (768)
                      ....|+..|....             ..+.|..|.++|.++.+.+.++      .||+.||.|+.|.+.+..        
T Consensus       349 ~g~~~c~~~~~~~-------------~~p~C~~C~~~i~~~~v~a~~~------~wH~~cf~C~~C~~~~~~--------  401 (479)
T KOG1703|consen  349 DGKILCHECFHAP-------------FRPNCKRCLLPILEEGVCALGR------LWHPECFVCADCGKPLKN--------  401 (479)
T ss_pred             CCCccHHHHHHHh-------------hCccccccCCchHHhHhhhccC------eechhceeeecccCCCCC--------
Confidence            4555666665542             4677999999999999999988      999999999999754432        


Q ss_pred             ccccccCCCCcceeecccccccccchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEe
Q psy17256        583 KPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFAL  662 (768)
Q Consensus       583 ~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~  662 (768)
                               ..+|..++.+    ||+.||+++|+++|..|.++|...+..+++++..||..||+|..|.+.| .+..|+.
T Consensus       402 ---------~~~~~~~~~p----yce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l-~~~~~~~  467 (479)
T KOG1703|consen  402 ---------SSFFESDGEP----YCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKL-TKKTFFE  467 (479)
T ss_pred             ---------CcccccCCcc----chhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhccc-cCCceee
Confidence                     4567777888    5669999999999999999999877899999999999999999999999 6778999


Q ss_pred             ecCcccccccc
Q psy17256        663 HEDRVLCKSHY  673 (768)
Q Consensus       663 ~~g~~~C~~~y  673 (768)
                      ..++++|..|+
T Consensus       468 ~~~~p~c~~~~  478 (479)
T KOG1703|consen  468 TLDKPLCQKHF  478 (479)
T ss_pred             cCCccccccCC
Confidence            99999999886

>KOG0487|consensus

Probab=99.39  E-value=2e-13  Score=143.73  Aligned_cols=67  Identities=21%  Similarity=0.434  Sum_probs=61.3

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                      +..|++|..+|..|+.+||+.|..|.|.+...|.+|++.|+|+++||||||||||+|.||..++...
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~  299 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRL  299 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhc
Confidence            4556678899999999999999999999999999999999999999999999999999998865443

>KOG2251|consensus

Probab=99.39  E-value=2.1e-13  Score=134.88  Aligned_cols=68  Identities=37%  Similarity=0.507  Sum_probs=64.6

Q ss_pred             cCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        694 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       694 ~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      ..++|.+|.||.|+-.|+++||..|.+..||+...|++||.+++|.+.+|||||.|||+|+|++++..
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            45788999999999999999999999999999999999999999999999999999999999998764

>KOG0848|consensus

Probab=99.39  E-value=1.1e-13  Score=139.16  Aligned_cols=68  Identities=25%  Similarity=0.434  Sum_probs=62.5

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      +.+++-+-|.++|..|..+||++|.-++|..+..+.|||..|||+|+||+|||||||+|+||..+...
T Consensus       195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            44566677999999999999999999999999999999999999999999999999999999877764

>KOG0493|consensus

Probab=99.36  E-value=5.8e-13  Score=133.27  Aligned_cols=63  Identities=43%  Similarity=0.579  Sum_probs=58.8

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      +.-||+||.||.+||..|...|+.|+|+....|++||.+|+|.|.||+|||||+|+|.||..-
T Consensus       244 ~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  244 KEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             chhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            345789999999999999999999999999999999999999999999999999999998543

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.35  E-value=4.6e-13  Score=108.03  Aligned_cols=57  Identities=46%  Similarity=0.735  Sum_probs=55.1

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ||+|+.||.+|+..|+..|..++||+..+++.||..+||++.+|++||+|||+++|+
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            578999999999999999999999999999999999999999999999999999886

; 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 ....

>KOG0844|consensus

Probab=99.33  E-value=6.3e-13  Score=135.63  Aligned_cols=65  Identities=28%  Similarity=0.456  Sum_probs=60.7

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ....-||-||.||.+|+..||+.|-+..|-+.+.|.|||..|+|+|.+|+|||||||+|+||+.-
T Consensus       177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            34567889999999999999999999999999999999999999999999999999999999754

>KOG0848|consensus

Probab=99.33  E-value=2.3e-13  Score=136.94  Aligned_cols=67  Identities=25%  Similarity=0.453  Sum_probs=61.5

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                      +.+-+.|.++|..|+.+||++|+-++|.....+.+||..|||++|||||||||||||+||..+.+..
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~  263 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRL  263 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHH
Confidence            3445569999999999999999999999999999999999999999999999999999999887743

>KOG1703|consensus

Probab=99.31  E-value=3.4e-13  Score=154.43  Aligned_cols=161  Identities=19%  Similarity=0.270  Sum_probs=123.9

Q ss_pred             ccchhhhhhhhhh-HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIAL-VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~-~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .+.|..|...|.+ ......++      .||+.+|.|+.|...+.-               +  .+...++..    ||.
T Consensus       303 ~p~c~~c~~~i~~~~~i~~~~~------~~h~~~~~c~~~~~~~~~---------------~--~~~~~~g~~----~c~  355 (479)
T KOG1703|consen  303 RPLCLSCNQKIRSVKVIVALGK------EWHPEHFSCEVCAIVILD---------------G--GPRELDGKI----LCH  355 (479)
T ss_pred             cccccccccCcccceeEeeccc------cccccceeeccccccccC---------------C--CccccCCCc----cHH
Confidence            3457778888888 88888888      999999999999854431               1  224555666    556


Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccCCcccCCCCC
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGA  688 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~~~~s~~~g~  688 (768)
                      .||+..++++|.+|+++|.+.  +|.|++..||++||+|..|+.+| ....|+..++.+||+.||+++......      
T Consensus       356 ~~~~~~~~p~C~~C~~~i~~~--~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~~~~~------  426 (479)
T KOG1703|consen  356 ECFHAPFRPNCKRCLLPILEE--GVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFTTKCD------  426 (479)
T ss_pred             HHHHHhhCccccccCCchHHh--HhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhccccch------
Confidence            899999999999999999965  89999999999999999999998 566789999999999999987751100      


Q ss_pred             CcccccCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHh
Q psy17256        689 DSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQIT  736 (768)
Q Consensus       689 ~~~~~~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~l  736 (768)
                               ..+. -..+-..+++.+...|+...|-+..+...|..+.
T Consensus       427 ---------~~~~-p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~  464 (479)
T KOG1703|consen  427 ---------YCKK-PVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKT  464 (479)
T ss_pred             ---------hccc-hhHhhhhHhhccCccccccceehhhhhccccCCc
Confidence                     0011 1223356788888888888888877776665444

>KOG0492|consensus

Probab=99.30  E-value=1.1e-12  Score=127.60  Aligned_cols=64  Identities=25%  Similarity=0.419  Sum_probs=59.9

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      .+..|.+||.||..|+..||+.|...+|.+..+|.+++..|.|++.||+|||||||||.||.+.
T Consensus       141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            4556788999999999999999999999999999999999999999999999999999998754

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.30  E-value=2.5e-12  Score=102.90  Aligned_cols=53  Identities=25%  Similarity=0.431  Sum_probs=50.7

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCC----CCHHHHHHHHHHcCCCcccccccccccH
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSN----PDGQDLERIAQITGLSKRVTQVWFQNSR  112 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~----p~~~~r~~la~~l~l~~~~vqvWFqNrR  112 (768)
                      +||.||.||.+|+..||..|+.++|    |+...+++||..+||++++|+|||||.+
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            3789999999999999999999999    9999999999999999999999999964

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.

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.26  E-value=1.4e-12  Score=105.23  Aligned_cols=57  Identities=46%  Similarity=0.735  Sum_probs=55.0

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      ++.|+.||.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|+++||
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            567999999999999999999999999999999999999999999999999999986

; 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 ....

>KOG0844|consensus

Probab=99.19  E-value=7.9e-12  Score=127.75  Aligned_cols=66  Identities=27%  Similarity=0.453  Sum_probs=61.5

Q ss_pred             CCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .....||.||.||.+|+..||+.|-+..|.+...|-+||..|+|++..|||||||||+|+|||...
T Consensus       177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            345679999999999999999999999999999999999999999999999999999999997543

>KOG2272|consensus

Probab=99.18  E-value=1.8e-12  Score=129.34  Aligned_cols=116  Identities=16%  Similarity=0.214  Sum_probs=97.6

Q ss_pred             hhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchhhhh
Q psy17256        533 FHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICF  612 (768)
Q Consensus       533 C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~  612 (768)
                      |.+|+..|.+..+...+.      .||+-+|.|+.|+..+..              |.   -.++ +.+    ||..|+.
T Consensus       140 C~KCh~~iD~~~l~fr~d------~yH~yHFkCt~C~keL~s--------------da---Revk-~eL----yClrChD  191 (332)
T KOG2272|consen  140 CQKCHAHIDEQPLTFRGD------PYHPYHFKCTTCGKELTS--------------DA---REVK-GEL----YCLRCHD  191 (332)
T ss_pred             hhhhhhhcccccccccCC------CCCccceecccccccccc--------------hh---hhhc-cce----ecccccc
Confidence            999999999988888888      799999999999965432              11   1222 345    4557788


Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      ++.-+.|..|.+||.  |.++.|+|+.||++.|+|+.|.+|+ -|.+-+.+.|.+||+.||.++++.
T Consensus       192 ~mgipiCgaC~rpIe--ervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG~  255 (332)
T KOG2272|consen  192 KMGIPICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFGN  255 (332)
T ss_pred             ccCCcccccccCchH--HHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhhh
Confidence            888889999999999  5699999999999999999999999 688888999999999999998864

>KOG0493|consensus

Probab=99.18  E-value=7.3e-12  Score=125.52  Aligned_cols=62  Identities=44%  Similarity=0.589  Sum_probs=58.6

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      -||+||.||.+|++.|+..|+.+.|.....|.+||.+|+|.+.||+|||||+|+|.||-...
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs  307 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS  307 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence            47899999999999999999999999999999999999999999999999999999986543

>KOG4577|consensus

Probab=99.17  E-value=1.7e-11  Score=124.40  Aligned_cols=65  Identities=38%  Similarity=0.607  Sum_probs=60.4

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ....||+||++|..||+.|..+|...+.|....|+.|+.++||..++|||||||||||.||-.+.
T Consensus       164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            44568899999999999999999999999999999999999999999999999999999986554

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.15  E-value=2.7e-11  Score=97.01  Aligned_cols=52  Identities=25%  Similarity=0.442  Sum_probs=50.5

Q ss_pred             ccccccccHHHHHHHhhccccCCC----CCHHHHHHHHHHhCCCCCccccccccch
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSN----PDGQDLERIAQITGLSKRVTQVWFQNSR  751 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~----p~~~~r~~LA~~lgls~~~V~vWFQNrR  751 (768)
                      +|.||.||.+|+..|+..|..+.|    |+...+.+||..+||++++|+|||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            788999999999999999999999    9999999999999999999999999975

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.

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.15  E-value=3.9e-11  Score=115.92  Aligned_cols=66  Identities=30%  Similarity=0.509  Sum_probs=59.2

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ...+++|++.|..|+.+|++.|+.++||+..+|.+|+..++|+++.|||||||||++.|+......
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            345666777899999999999999999999999999999999999999999999999998765543

>KOG3802|consensus

Probab=99.15  E-value=5.7e-11  Score=127.42  Aligned_cols=63  Identities=29%  Similarity=0.502  Sum_probs=60.0

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .|+||+||.|+......||+.|.+|+.|+..+...||.+|+|...+|+|||+|||.|.||...
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            378889999999999999999999999999999999999999999999999999999999655

>smart00389 HOX Homeodomain

Probab=99.13  E-value=3.1e-11  Score=96.85  Aligned_cols=56  Identities=46%  Similarity=0.734  Sum_probs=52.5

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      ++.|+.|+..|+..|++.|..++||+..++..||..+||+..+|+.||+|||++.+
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            35678899999999999999999999999999999999999999999999998754

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>KOG0486|consensus

Probab=99.13  E-value=2.5e-11  Score=125.29  Aligned_cols=66  Identities=42%  Similarity=0.597  Sum_probs=62.4

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +|++|.||.|+..|++.||..|+++.||+..+|++||..++|++..|+|||.|||+||||++....
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            378899999999999999999999999999999999999999999999999999999999976544

>KOG0483|consensus

Probab=99.12  E-value=2.1e-11  Score=121.78  Aligned_cols=62  Identities=31%  Similarity=0.489  Sum_probs=57.1

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      .+++.+++.+|+..||..|+.+.+.....+..||.+|||.++||.|||||||||||.++...
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~  112 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK  112 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence            44456799999999999999999999999999999999999999999999999999987654

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.10  E-value=7e-11  Score=114.17  Aligned_cols=67  Identities=30%  Similarity=0.502  Sum_probs=61.0

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      .+..++.|++-+.+|+.+|++.|..++||+...|..|+..++|+++.||+||||||++.|+....+.
T Consensus        48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            3556777888999999999999999999999999999999999999999999999999999766544

>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=99.10  E-value=6.2e-11  Score=95.98  Aligned_cols=57  Identities=40%  Similarity=0.711  Sum_probs=54.0

Q ss_pred             CCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         62 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        62 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      +.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||.+.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            467889999999999999999999999999999999999999999999999998763

>KOG0847|consensus

Probab=99.07  E-value=4.5e-11  Score=117.11  Aligned_cols=66  Identities=29%  Similarity=0.466  Sum_probs=61.4

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      +.++++..|.+|+..|+..||..|+..+|+..++|.+||..+||++.+|+|||||||.||||+...
T Consensus       163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            457778889999999999999999999999999999999999999999999999999999996543

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.05  E-value=8.2e-11  Score=95.11  Aligned_cols=57  Identities=30%  Similarity=0.736  Sum_probs=51.7

Q ss_pred             cccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccc
Q psy17256        619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL  676 (768)
Q Consensus       619 C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~  676 (768)
                      |.+|+++|.+.+.++.+.|+.||.+||+|..|+++|..+. |+..++++||+.||.++
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~~   57 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQKR   57 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHHH
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhhh
Confidence            8899999999888888999999999999999999996554 99999999999999754

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>KOG0491|consensus

Probab=99.04  E-value=3.5e-11  Score=113.21  Aligned_cols=65  Identities=26%  Similarity=0.492  Sum_probs=60.6

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++++.||+|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||+|.||+++...
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            34667999999999999999999999999999999999999999999999999999999877654

>KOG0847|consensus

Probab=99.03  E-value=6.6e-11  Score=115.95  Aligned_cols=63  Identities=30%  Similarity=0.492  Sum_probs=58.4

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ++++..|..|+..|+..|+..|.+.+|+-..++.+||..+||++.+|+|||||||+||||+..
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            445666889999999999999999999999999999999999999999999999999999743

>KOG0483|consensus

Probab=99.02  E-value=1.1e-10  Score=116.75  Aligned_cols=56  Identities=32%  Similarity=0.529  Sum_probs=52.9

Q ss_pred             ccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         65 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        65 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .+|+.+|...||..|+.+.++.+..+..||..|||.++||.||||||||+||.+..
T Consensus        55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql  110 (198)
T KOG0483|consen   55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL  110 (198)
T ss_pred             ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence            35999999999999999999999999999999999999999999999999998644

>KOG3802|consensus

Probab=99.02  E-value=1.8e-10  Score=123.68  Aligned_cols=64  Identities=28%  Similarity=0.502  Sum_probs=60.5

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ..++|++||.|.......||..|.+|+.|+..+...||.+|+|+..+|+|||+|||.|.||...
T Consensus       291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            3467888999999999999999999999999999999999999999999999999999999876

>smart00389 HOX Homeodomain

Probab=99.02  E-value=1.1e-10  Score=93.66  Aligned_cols=55  Identities=47%  Similarity=0.731  Sum_probs=51.9

Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      +.|+.++.+|+..|+..|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            4577899999999999999999999999999999999999999999999998854

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>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=98.98  E-value=1.9e-10  Score=93.04  Aligned_cols=57  Identities=40%  Similarity=0.711  Sum_probs=53.9

Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      +.|+.++..++..|+..|..++||+..++..||..+||+..+|++||+|||++.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            457889999999999999999999999999999999999999999999999998864

>KOG0849|consensus

Probab=98.97  E-value=6.5e-10  Score=122.08  Aligned_cols=69  Identities=35%  Similarity=0.516  Sum_probs=63.5

Q ss_pred             CCCCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         53 SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        53 ~~~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .....++.+|.||+|+..|+..||+.|++++||++..|++||.++++++.+|+|||+|||++++|+...
T Consensus       169 ~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  169 GYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            334567788889999999999999999999999999999999999999999999999999999998743

>KOG1044|consensus

Probab=98.75  E-value=2.5e-09  Score=118.52  Aligned_cols=116  Identities=16%  Similarity=0.266  Sum_probs=84.8

Q ss_pred             hhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchhhhh-
Q psy17256        534 HSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICF-  612 (768)
Q Consensus       534 ~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~-  612 (768)
                      ..|..-|.+....++|+      .+|..||+|++|+.+...               |....+. +....    |+.|-. 
T Consensus        69 ~~c~~~~~gevvsa~gk------tyh~~cf~cs~ck~pf~~---------------g~~vt~~-gk~~~----c~~c~~~  122 (670)
T KOG1044|consen   69 DDCRAFVEGEVVSTLGK------TYHPKCFSCSTCKSPFKS---------------GDKVTFS-GKECL----CQTCSQP  122 (670)
T ss_pred             cchhhhccceeEecccc------eeccccceecccCCCCCC---------------CCeeeec-chhhh----hhhhcCc
Confidence            45666677778888898      999999999999976442               2221111 11222    233321 


Q ss_pred             -------hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 -------RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 -------~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                             ..+-.-|++|++.|..+ .++.|+++.||+.||.|..|...| .| +|..++|.+||+.||.+.+.
T Consensus       123 ~~~~p~~~~~ps~cagc~~~lk~g-q~llald~qwhv~cfkc~~c~~vL-~g-ey~skdg~pyce~dy~~~fg  192 (670)
T KOG1044|consen  123 MPVSPAESYGPSTCAGCGEELKNG-QALLALDKQWHVSCFKCKSCSAVL-NG-EYMSKDGVPYCEKDYQAKFG  192 (670)
T ss_pred             ccCCcccccCCccccchhhhhhcc-ceeeeeccceeeeeeehhhhcccc-cc-eeeccCCCcchhhhhhhhcC
Confidence                   12334899999999875 577899999999999999999999 45 48889999999999987653

>KOG0775|consensus

Probab=98.63  E-value=1.2e-08  Score=103.85  Aligned_cols=123  Identities=23%  Similarity=0.327  Sum_probs=90.1

Q ss_pred             cceeeecCce-ecccCccccccccccCCCCceEee----cCcccccccccccccCCcccCCCCCCcccccCCCccccccc
Q psy17256        630 DWVRKARDHV-YHLACFACEACKRQLSTGEEFALH----EDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRT  704 (768)
Q Consensus       630 e~~~~a~~~~-~H~~CF~C~~C~~~L~~G~~f~~~----~g~~~C~~~y~e~~~~~~~s~~~g~~~~~~~~~~k~rr~Rt  704 (768)
                      |.|++|...+ ||..-|.=-.   .|.+...|...    --.++-+.||.|...   ..+.+-+.+....-++|-.-+||
T Consensus        99 EsvLkArA~vafH~gnf~eLY---~iLE~h~Fs~~~h~~LQ~lWl~AhY~EAek---~RGR~LgaV~KYRvRrKfPlPrT  172 (304)
T KOG0775|consen   99 ESVLKARAVVAFHSGNFRELY---HILENHKFSPHNHPKLQALWLKAHYKEAEK---LRGRPLGAVDKYRVRRKFPLPRT  172 (304)
T ss_pred             HHHHHHHHHHHHhcccHHHHH---HHHHhccCChhhhHHHHHHHHHHHHHHHHH---hcCCcCCccccceeeccCCCCCc
Confidence            5567776544 7877763110   00122223222    124677888876543   45566666777777888888999


Q ss_pred             cccHHH---------HHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        705 TFTEEQ---------LQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       705 ~~s~~Q---------l~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      .+.++|         ...|+.+|..++||+..++.+||+.+||+..||-+||+|||+|+|-..
T Consensus       173 IWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~  235 (304)
T KOG0775|consen  173 IWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA  235 (304)
T ss_pred             cccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence            999987         457999999999999999999999999999999999999999999443

>KOG1168|consensus

Probab=98.63  E-value=1.1e-08  Score=104.43  Aligned_cols=63  Identities=33%  Similarity=0.582  Sum_probs=58.5

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..+||+||.+..-....||++|..++.|+......||++|+|...+|+|||+|.|+|.||...
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            456788999999999999999999999999999999999999999999999999999998544

>KOG0849|consensus

Probab=98.55  E-value=4.8e-08  Score=107.42  Aligned_cols=66  Identities=36%  Similarity=0.547  Sum_probs=62.1

Q ss_pred             cCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        694 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       694 ~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ...++.+|.||.|+..|+..|+..|+.++||+...|+.||.++++++..|+|||+|||+||+|+..
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            456777888999999999999999999999999999999999999999999999999999999873

>KOG0775|consensus

Probab=98.49  E-value=1.4e-07  Score=96.22  Aligned_cols=105  Identities=18%  Similarity=0.257  Sum_probs=77.6

Q ss_pred             cCCHHHHHHhhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCHHH---------HHHHHHhhhhCCCCCHHH
Q psy17256         19 TFTEEQLQVLQANFQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQ---------LQVLQANFQLDSNPDGQD   89 (768)
Q Consensus        19 ~~~~~q~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~Q---------l~~Le~~F~~~~~p~~~~   89 (768)
                      .|+......||.++-...|-+.....+..-+....-.-++|-.-+||+...+|         ...|...|..++||+..+
T Consensus       126 ~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~e  205 (304)
T KOG0775|consen  126 KFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPRE  205 (304)
T ss_pred             cCChhhhHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHH
Confidence            46666677777766666665544444444444344344555566688766655         577999999999999999


Q ss_pred             HHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         90 LERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        90 r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      +.+||+.+||+..||-.||.|||+++|-......
T Consensus       206 KReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~  239 (304)
T KOG0775|consen  206 KRELAEATGLTITQVSNWFKNRRQRDRAAAAKNS  239 (304)
T ss_pred             HHHHHHHhCCchhhhhhhhhhhhhhhhhcccccc
Confidence            9999999999999999999999999995544433

>KOG1168|consensus

Probab=98.49  E-value=5.7e-08  Score=99.24  Aligned_cols=64  Identities=33%  Similarity=0.580  Sum_probs=59.6

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ..+||+||.|..-+...||.+|...+.|+.+....||.+|+|...+|+|||+|.|+|.||....
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S  370 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS  370 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence            4578899999999999999999999999999999999999999999999999999999986543

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=98.17  E-value=9.7e-07  Score=64.82  Aligned_cols=37  Identities=35%  Similarity=0.845  Sum_probs=34.2

Q ss_pred             ccccCCCCCCCCcceeeecCceecccCcccccccccc
Q psy17256        618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQL  654 (768)
Q Consensus       618 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L  654 (768)
                      +|.+|+++|.+.+.++.+.++.||..||+|..|+++|
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L   37 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL   37 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence            6899999999866788899999999999999999998

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>KOG1700|consensus

Probab=97.89  E-value=4.8e-06  Score=84.58  Aligned_cols=60  Identities=28%  Similarity=0.707  Sum_probs=47.7

Q ss_pred             ccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       618 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      .|..|.+.+.+.|. +.+.+..||..||.|..|+..|..+ .+...++.+||..++..+..+
T Consensus       110 ~c~~c~k~vy~~Ek-~~~~~~~~hk~cfrc~~~~~~ls~~-~~~~~~g~l~~~~~~~~~~~~  169 (200)
T KOG1700|consen  110 KCARCQKTVYPLEK-VTGNGLEFHKSCFRCTHCGKKLSPK-NYAALEGVLYCKHHFAQLFKG  169 (200)
T ss_pred             ccccccceeeehHH-HhhhhhhhhhhheeecccccccCCc-chhhcCCccccchhhheeecC
Confidence            68888888876544 3356788999999999999999654 578888999999988775543

>KOG0774|consensus

Probab=97.74  E-value=4.5e-05  Score=77.45  Aligned_cols=62  Identities=26%  Similarity=0.484  Sum_probs=56.0

Q ss_pred             CCCCCccCCHHHHHHHHHhhh---hCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQ---LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .||+|..|+..-.++|..+|.   .|+||+..++++||.+.+++..||-.||.|.|-++||..-.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k  252 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK  252 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence            466788899999999999995   78999999999999999999999999999999998886443

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.51  E-value=1.3e-05  Score=64.54  Aligned_cols=56  Identities=16%  Similarity=-0.069  Sum_probs=42.1

Q ss_pred             hhhhhhhhhhHHHH--HhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchhh
Q psy17256        533 FHSFLKRIALVLSE--KWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLI  610 (768)
Q Consensus       533 C~~c~k~Ia~~~~~--~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~  610 (768)
                      |..|.+.|.+....  +.|+      .||+.||.|+.|+..+.               ++  .++..++.+|    |..|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~------~~H~~Cf~C~~C~~~l~---------------~~--~~~~~~~~~~----C~~c   53 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGK------FWHPECFKCSKCGKPLN---------------DG--DFYEKDGKPY----CKDC   53 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTE------EEETTTSBETTTTCBTT---------------TS--SEEEETTEEE----EHHH
T ss_pred             CCCCCCCccCcEEEEEeCCc------EEEccccccCCCCCccC---------------CC--eeEeECCEEE----CHHH
Confidence            67788888865444  6676      99999999999996543               12  2678888885    5589


Q ss_pred             hhhhc
Q psy17256        611 CFRSF  615 (768)
Q Consensus       611 y~~~f  615 (768)
                      |.++|
T Consensus        54 ~~~~f   58 (58)
T PF00412_consen   54 YQKRF   58 (58)
T ss_dssp             HHHHT
T ss_pred             HhhhC
Confidence            98876

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>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=97.43  E-value=3.7e-05  Score=57.20  Aligned_cols=34  Identities=35%  Similarity=0.657  Sum_probs=28.9

Q ss_pred             hCCCCCHHHHHHHHHHcCCCcccccccccccHHH
Q psy17256         81 LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR  114 (768)
Q Consensus        81 ~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak  114 (768)
                      .+|||+..++++||..+||+..||..||-|.|.+
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            4799999999999999999999999999998864

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>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=97.42  E-value=3e-05  Score=57.67  Aligned_cols=34  Identities=35%  Similarity=0.657  Sum_probs=28.9

Q ss_pred             cCCCCCHHHHHHHHHHhCCCCCccccccccchhH
Q psy17256        720 LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR  753 (768)
Q Consensus       720 ~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak  753 (768)
                      .++||+..++..||.++||+..||..||-|.|.|
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            4789999999999999999999999999998865

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>KOG0774|consensus

Probab=97.24  E-value=0.00016  Score=73.55  Aligned_cols=59  Identities=25%  Similarity=0.502  Sum_probs=54.5

Q ss_pred             ccccccccHHHHHHHhhccc---cCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQ---LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      +|+|..|+..-.++|..+|.   .++||+...+++||++.+++..||-.||.|+|-++||..
T Consensus       189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence            67788899999999999985   488999999999999999999999999999999998864

>KOG2252|consensus

Probab=97.24  E-value=0.00056  Score=77.01  Aligned_cols=58  Identities=31%  Similarity=0.390  Sum_probs=53.8

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHH
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ  115 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~  115 (768)
                      ...||+|.+||..|...|...|+.+++|+....+.|+.+|+|..++|.+||-|-|.+.
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            4556779999999999999999999999999999999999999999999999987764

>KOG2252|consensus

Probab=97.18  E-value=0.00024  Score=79.90  Aligned_cols=58  Identities=31%  Similarity=0.390  Sum_probs=54.0

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHH
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ  754 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~  754 (768)
                      -..|++|.+||..|...|...|+.+++|+......|+.+|+|....|.+||.|-|.|.
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            3457779999999999999999999999999999999999999999999999988774

>KOG1146|consensus

Probab=96.19  E-value=0.015  Score=71.67  Aligned_cols=65  Identities=37%  Similarity=0.574  Sum_probs=59.2

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      -.+|+.||.++..||..+...|....||...+-+.|-..++++.+.|+|||||-|+|.++..-+.
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            35677899999999999999999999999999999999999999999999999999999865533

>KOG1146|consensus

Probab=95.22  E-value=0.011  Score=72.96  Aligned_cols=64  Identities=38%  Similarity=0.590  Sum_probs=59.2

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      -+++.|+.++..|+..+...|....+|...+.+.|...++++.++|+|||||-|+|.||....+
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            3577899999999999999999999999999999999999999999999999999999976544

>KOG1702|consensus

Probab=94.69  E-value=0.0057  Score=60.57  Aligned_cols=58  Identities=26%  Similarity=0.575  Sum_probs=44.5

Q ss_pred             ccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccc
Q psy17256        618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       618 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      -|..|++.+.+-|. ++.+++.||..||.|..|+..|. =..+-.-+-++||..||...+
T Consensus         6 n~~~cgk~vYPvE~-v~cldk~whk~cfkce~c~mtln-mKnyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen    6 NREDCGKTVYPVEE-VKCLDKVWHKQCFKCEVCGMTLN-MKNYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             hhhhhccccccHHH-HhhHHHHHHHHhheeeeccCChh-hhhccccccCCCcCcccccce
Confidence            46678888877544 56789999999999999999883 233444567899999997543

>KOG1700|consensus

Probab=93.81  E-value=0.021  Score=58.25  Aligned_cols=59  Identities=27%  Similarity=0.594  Sum_probs=47.6

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL  676 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~  676 (768)
                      +.+|..|++.+.-.+.+. ..+..||..||.|..|...|.. ..+..+++.+||+.+|-..
T Consensus         7 ~~kc~~c~k~vy~~e~~~-~~g~~~hk~c~~c~~~~k~l~~-~~~~~~e~~~yc~~~~~~~   65 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEKVQ-KDGVDFHKECFKCEKCKKTLTL-SGYSEHEGVPYCKNCHVAQ   65 (200)
T ss_pred             cchhhhccCcchHHHHHh-ccCcchhhhHHhcccccccccc-ccccccccccccccchHhh
Confidence            358999999998765544 7788999999999999999954 4466689999999965433

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=92.08  E-value=0.019  Score=41.61  Aligned_cols=33  Identities=15%  Similarity=-0.022  Sum_probs=25.7

Q ss_pred             hhhhhhhhhh--HHHHHhhcccccccccccceEEEeccccc
Q psy17256        533 FHSFLKRIAL--VLSEKWKKMYGHVLSWLRVRTEFSILKAV  571 (768)
Q Consensus       533 C~~c~k~Ia~--~~~~~~~~~~s~~~~wh~~~~~c~~c~~~  571 (768)
                      |..|.+.|.+  ..+...++      .||+.||.|..|+..
T Consensus         2 C~~C~~~i~~~~~~~~~~~~------~~H~~Cf~C~~C~~~   36 (39)
T smart00132        2 CAGCGKPIRGGELVLRALGK------VWHPECFKCSKCGKP   36 (39)
T ss_pred             ccccCCcccCCcEEEEeCCc------cccccCCCCcccCCc
Confidence            6778888877  34445555      999999999999854

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A

Probab=91.46  E-value=0.066  Score=42.68  Aligned_cols=41  Identities=17%  Similarity=0.373  Sum_probs=31.1

Q ss_pred             HHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccH
Q psy17256         72 LQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR  112 (768)
Q Consensus        72 l~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrR  112 (768)
                      +..|++.|...+++.......|..+.+|+..+|+.||.-|+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            45699999999999999999999999999999999997654

>KOG0773|consensus

Probab=89.06  E-value=0.19  Score=55.65  Aligned_cols=58  Identities=28%  Similarity=0.385  Sum_probs=48.2

Q ss_pred             cccccccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      .+|++..+......+|+.+...   .+||+..++..||.++||+..||.+||-|.|-|..+
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~  299 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK  299 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence            4555667888888888876433   579999999999999999999999999999887554

>KOG3623|consensus

Probab=88.69  E-value=0.61  Score=54.57  Aligned_cols=49  Identities=29%  Similarity=0.533  Sum_probs=45.2

Q ss_pred             HHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         72 LQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        72 l~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      +..|...|..|..|+..+...+|.+.|++.+.|++||++++++.....+
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r  616 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER  616 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence            7788999999999999999999999999999999999999998876544

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A

Probab=87.02  E-value=0.16  Score=40.49  Aligned_cols=41  Identities=17%  Similarity=0.373  Sum_probs=30.7

Q ss_pred             HHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccch
Q psy17256        711 LQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR  751 (768)
Q Consensus       711 l~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrR  751 (768)
                      ++-|+++|....++.......|..+.+|+..||+.||--|+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            45699999999999999999999999999999999996543

>KOG3623|consensus

Probab=85.19  E-value=0.52  Score=55.15  Aligned_cols=51  Identities=27%  Similarity=0.512  Sum_probs=46.1

Q ss_pred             HHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        711 LQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       711 l~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      ...|..+|..|.+|+..+...+|.+.|++-+.|++||++++++...-+..-
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsp  618 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSP  618 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCc
Confidence            788999999999999999999999999999999999999999877655433

>KOG0773|consensus

Probab=84.46  E-value=0.81  Score=50.64  Aligned_cols=57  Identities=28%  Similarity=0.437  Sum_probs=46.9

Q ss_pred             CCCCCccCCHHHHHHHHHhh-h--hCCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         60 AKRVRTTFTEEQLQVLQANF-Q--LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F-~--~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      ..|++..+......+|+... +  ..+||+...+..||.++||+..||-.||-|.|-+..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w  298 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW  298 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence            44556688888888888663 2  357999999999999999999999999999887544

>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=83.58  E-value=1.1  Score=35.57  Aligned_cols=47  Identities=21%  Similarity=0.257  Sum_probs=36.0

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccH
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR  112 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrR  112 (768)
                      ||+|..+|-++-..+-..++.+.     ...+||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46788999999888888888775     578899999999999999998843

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	768
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		5e-14
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		9e-14
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		1e-13
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		6e-13
2da3_A	80	Solution Structure Of The Third Homeobox Domain Of		5e-12
1bw5_A	66	The Nmr Solution Structure Of The Homeodomain Of Th		5e-08
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		8e-07
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-06
2l6y_B	96	Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid Length =		3e-06
2lxd_A	125	Backbone 1h, 13c, And 15n Chemical Shift Assignment		4e-06
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		4e-06
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		4e-06
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		6e-06
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		6e-06
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		1e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		1e-05
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		2e-05
2da2_A	70	Solution Structure Of The Second Homeobox Domain Of		8e-05
2da2_A	70	Solution Structure Of The Second Homeobox Domain Of		8e-05
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		8e-05
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		8e-05
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		9e-05
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		1e-04
2da1_A	70	Solution Structure Of The First Homeobox Domain Of		1e-04
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		2e-04
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		4e-04

>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex Length = 182

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 46/63 (73%), Gaps = 1/63 (1%)
Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 115 FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 174
Query: 671 SHY 673
           + Y
Sbjct: 175 ADY 177

>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The Binding Domain Of Isl1 Length = 169

Iteration: 1
 Score = 75.9 bits (185), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 46/63 (73%), Gaps = 1/63 (1%)
Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 61  FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 120
Query: 671 SHY 673
           + Y
Sbjct: 121 ADY 123

>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of Transcription Factors, The Lim-Homeodomain Proteins, In Neural Cell Type Specification Length = 169

Iteration: 1
 Score = 75.5 bits (184), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 45/63 (71%), Gaps = 1/63 (1%)
Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C +GI  +  VRKA+D VYHL CFAC  C RQL+TG+EF L ED R++CK
Sbjct: 61  FKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCK 120
Query: 671 SHY 673
             Y
Sbjct: 121 EDY 123

>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX Protein Lhx9 Length = 80

Iteration: 1
 Score = 73.2 bits (178), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/62 (50%), Positives = 49/62 (79%)
Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           S  KR+RT+F   QL+ +++ F ++ NPD +DL+++AQ TGL+KRV QVWFQN+RA+ ++
Sbjct: 5   SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
Query: 757 HL 758
           +L
Sbjct: 65  NL 66

>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 80

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 43/59 (72%)
Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           + KR+RTT T EQL++L   + LDSNP  + L+ IA   GL KRV QVWFQN+RAR++K
Sbjct: 16  RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74

>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat Insulin Gene Enhancer Protein Isl-1, 50 Structures Length = 66

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 36/60 (60%)
Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           K  RVRT   E+QL  L+  +  +  PD    E++ ++TGLS RV +VWFQN R + KK 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4, Northeast Structural Genomics Consortium (Nesg) Target Hr4490c Length = 75

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 41/69 (59%)
Query: 696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           K K +R RTTFT  QL+ L+  FQ    PD    E++A  T L++   QVWFQN RA+ +
Sbjct: 6   KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWR 65
Query: 756 KHLHTGKMK 764
           K    G+M+
Sbjct: 66  KRERFGQMQ 74

>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A Dna Oligonucleotide Length = 81

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           K K +R RTTF+  QL  L+  F+    PD    E +AQ T L++   QVWFQN RAR +
Sbjct: 15  KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
Query: 756 KHLHTG 761
           K  HT 
Sbjct: 75  KQ-HTS 79

>pdb|2L6Y|B Chain B, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 612 FRSFGAK--CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
            R FG    C+ C + I + +   + +D VYHL CF C AC++  S G+ + L    ++C
Sbjct: 2   LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 61
Query: 670 KSHYLE 675
           +    E
Sbjct: 62  EQDIYE 67

>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For Lmo2(Lim2)- Ldb1(Lid) Length = 125

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 612 FRSFGAK--CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
            R FG    C+ C + I + +   + +D VYHL CF C AC++  S G+ + L    ++C
Sbjct: 4   LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 63
Query: 670 KSHYLE 675
           +    E
Sbjct: 64  EQDIYE 69

>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid Domain Length = 188

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 613 RSFG--AKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK 670
           R FG    CS C + I +S+ V +A+ +VYHL CF C  C+ +L  G+ F      + C+
Sbjct: 64  RLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCE 123

>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim Domains 1 And 2 With The Lim Interacting Domain Of Ldb1 Length = 195

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 613 RSFG--AKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK 670
           R FG    CS C + I +S+ V +A+ +VYHL CF C  C+ +L  G+ F      + C+
Sbjct: 62  RLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCE 121

>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant Length = 68

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           +R RT FT +QLQ L+A FQ +  PD    E IA  T L++   +VWF+N RA+ +K
Sbjct: 4   RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain Length = 68

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           +R RT FT +QLQ L+A FQ +  PD    E IA  T L++   +VWF+N RA+ +K 
Sbjct: 4   RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna Length = 61

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 34/58 (58%)
Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           +R RTTFT EQL+ L+  F+    PD    E +AQ   L++   QVWF N RAR +K 
Sbjct: 3   RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 35/62 (56%)
Query: 696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           K K +R RTTFT  QL+ L+  F     PD    E +A   GL++   QVWFQN RA+ +
Sbjct: 3   KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 756 KH 757
           K 
Sbjct: 63  KQ 64

>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21 Crystal Form Length = 131

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 612 FRSFGAK--CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
            R FG    C+ C + I + +   + +D VYHL CF C AC++    G+ + L    ++C
Sbjct: 60  LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 119
Query: 670 KSHYLE 675
           +    E
Sbjct: 120 EQDIYE 125

>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 70

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 33/53 (62%)
Query: 65  TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           T FT+ QL+VLQ  F  ++ P   + E+++ +  L  RV  VWFQN+R + +K
Sbjct: 12  TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64

>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 70

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 33/53 (62%)
Query: 704 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           T FT+ QL+VLQ  F  ++ P   + E+++ +  L  RV  VWFQN+R + +K
Sbjct: 12  TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64

>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 32/57 (56%)
Query: 62  RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           R RTTFT  QL+ L+  F     PD    E +A   GL++   QVWFQN RA+ +K 
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 32/57 (56%)
Query: 701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           R RTTFT  QL+ L+  F     PD    E +A   GL++   QVWFQN RA+ +K 
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L Length = 67

Iteration: 1
 Score = 45.8 bits (107), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
            +R RT FT+ Q++VL+  F+++  P    LE +AQ   L     Q+WFQN RA+ K+
Sbjct: 1   GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58

>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 36/60 (60%)
Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           S  +R RT FT+EQL+ L+  FQ    PD    E++A+   L +   +VWF+N RA+ ++
Sbjct: 5   SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 70

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 37/54 (68%)
Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNS 750
           S  KR RT  T++QL+VL+  F ++++P  + ++ +A  +GL ++V + WF+N+
Sbjct: 5   SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNT 58

>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human Paired Box Protein Pax-6 Length = 80

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           S  +R RT+FT+EQ++ L+  F+    PD    ER+A    L +   QVWF N RA+ ++
Sbjct: 5   SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64
Query: 757 H 757
Sbjct: 65  E 65

>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Otx2 Length = 80

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 31/57 (54%)
Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 753
           S  +R RTTFT  QL VL+A F     PD    E +A    L +   QVWF+N RA+
Sbjct: 5   SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	768
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	1e-29
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	4e-28
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	9e-28
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-27
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-27
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-26
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	5e-08
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-25
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-25
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	5e-25
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-08
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	7e-25
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	4e-08
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	8e-25
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-07
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-23
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-23
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	5e-23
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	5e-23
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	6e-23
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	6e-23
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-22
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-22
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-20
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-20
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	6e-20
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-19
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	3e-19
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-19
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-19
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	6e-18
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	7e-18
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	7e-18
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-17
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	7e-17
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	6e-17
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	8e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	7e-17
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	2e-16
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-16
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-16
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-16
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	9e-16
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	5e-16
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-15
1e3o_C	160	Octamer-binding transcription factor 1; transcript	8e-16
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-15
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	3e-15
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	7e-15
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-15
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-12
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	5e-15
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	9e-15
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-14
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-14
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-14
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-14
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-14
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	4e-14
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	1e-13
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	5e-14
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	5e-14
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	6e-14
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-13
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-13
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-13
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-13
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-13
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-13
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	5e-13
2e19_A	64	Transcription factor 8; homeobox domain, structura	5e-13
2e19_A	64	Transcription factor 8; homeobox domain, structura	5e-13
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	1e-12
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	1e-12
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	2e-12
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	2e-12
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-12
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	3e-12
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	9e-12
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	9e-12
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-11
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	2e-11
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	2e-11
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	2e-11
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-11
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-11
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	2e-11
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	6e-11
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	6e-11
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	7e-11
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	1e-10
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-10
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	2e-10
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	2e-10
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-10
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-10
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-10
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	9e-09
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	2e-10
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	4e-10
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	5e-10
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	8e-10
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	9e-10
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-09
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-08
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-09
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-09
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-09
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	6e-09
2co8_A	82	NEDD9 interacting protein with calponin homology a	1e-08
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	2e-08
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	5e-08
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	4e-08
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-08
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	5e-08
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	3e-07
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	5e-08
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-07
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-07
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-07
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	3e-07
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-07
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	4e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	6e-06
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	6e-07
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	6e-07
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	6e-07
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	6e-07
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	7e-07
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	7e-07
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	8e-07
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	8e-07
1lfb_A	99	Liver transcription factor (LFB1); transcription r	8e-07
1lfb_A	99	Liver transcription factor (LFB1); transcription r	8e-07
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	1e-06
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	7e-06
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	1e-06
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	1e-05
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-06
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	5e-06
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-06
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-06
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	3e-06
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	3e-06
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-06
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-06
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	6e-06
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	6e-06
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	8e-06
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	8e-06
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	9e-06
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	9e-06
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-05
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	5e-05
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	1e-05
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	1e-04
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-05
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-05
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	2e-05
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	2e-05
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-05
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-05
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	3e-05
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	3e-05
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	4e-05
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	4e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	5e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	5e-05
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	1e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	1e-04
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-04
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-04
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	3e-04
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	3e-04
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	3e-04
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	3e-04
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	3e-04
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	3e-04
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	6e-04
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	6e-04

>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 =  107 bits (268), Expect = 4e-28
 Identities = 34/74 (45%), Positives = 46/74 (62%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVT 104
           S+  +         + KR+RTT T EQL++L   + LDSNP  + L+ IA   GL KRV 
Sbjct: 2   SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVV 61

Query: 105 QVWFQNSRARQKKH 118
           QVWFQN+RAR++K 
Sbjct: 62  QVWFQNTRARERKS 75

>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 =  106 bits (265), Expect = 9e-28
 Identities = 34/74 (45%), Positives = 45/74 (60%)

Query: 684 SDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVT 743
           S   +         + KR+RTT T EQL++L   + LDSNP  + L+ IA   GL KRV 
Sbjct: 2   SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVV 61

Query: 744 QVWFQNSRARQKKH 757
           QVWFQN+RAR++K 
Sbjct: 62  QVWFQNTRARERKS 75

>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 =  104 bits (262), Expect = 2e-27
 Identities = 20/63 (31%), Positives = 42/63 (66%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  KR RT  T++QL+VL+  F ++++P  + ++ +A  +GL ++V + WF+N+  ++
Sbjct: 3   SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62

Query: 116 KKH 118
           ++ 
Sbjct: 63  RQS 65

>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 =  104 bits (262), Expect = 2e-27
 Identities = 20/63 (31%), Positives = 42/63 (66%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  KR RT  T++QL+VL+  F ++++P  + ++ +A  +GL ++V + WF+N+  ++
Sbjct: 3   SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62

Query: 755 KKH 757
           ++ 
Sbjct: 63  RQS 65

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score =  105 bits (264), Expect = 2e-26
 Identities = 25/111 (22%), Positives = 41/111 (36%), Gaps = 15/111 (13%)

Query: 617 AKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
             CS C + I +S+ V +A+ +VYHL CF C  C+ +L  G+ F      + C+      
Sbjct: 70  GACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTA 129

Query: 677 VDGGTTSSDDGADSE---------------SSHSKSKAKRVRTTFTEEQLQ 712
           +  G  +S     S                      + +R+ T     Q  
Sbjct: 130 LINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFD 180

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score = 52.7 bits (126), Expect = 5e-08
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 615 FGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHY 673
              +C+ C   I +  ++  A D  +H  C  C +C+ QL   G         +LC++ Y
Sbjct: 4   SWKRCAGCGGKI-ADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 62

Query: 674 LEL 676
           + L
Sbjct: 63  IRL 65

>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 = 98.3 bits (245), Expect = 4e-25
 Identities = 32/74 (43%), Positives = 51/74 (68%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  KR+RT+F   QL+ +++ F ++ NPD +DL+++AQ TGL+KRV QVWFQN+RA+ 
Sbjct: 3   SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62

Query: 116 KKHLHTGKMKSSQN 129
           +++L   +      
Sbjct: 63  RRNLLRQENGGVSG 76

>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 = 98.3 bits (245), Expect = 4e-25
 Identities = 32/74 (43%), Positives = 51/74 (68%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  KR+RT+F   QL+ +++ F ++ NPD +DL+++AQ TGL+KRV QVWFQN+RA+ 
Sbjct: 3   SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62

Query: 755 KKHLHTGKMKSSQN 768
           +++L   +      
Sbjct: 63  RRNLLRQENGGVSG 76

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score =  101 bits (254), Expect = 5e-25
 Identities = 36/63 (57%), Positives = 46/63 (73%), Gaps = 1/63 (1%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 115 FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 174

Query: 671 SHY 673
           + Y
Sbjct: 175 ADY 177

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score = 53.8 bits (129), Expect = 2e-08
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 3/66 (4%)

Query: 611 CFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK 670
                   C+ C + I    ++ KA D  +H  C  C  C   L   E      + V CK
Sbjct: 55  GGTPEIPMCAGCDQHILDR-FILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCK 111

Query: 671 SHYLEL 676
             + + 
Sbjct: 112 DDFFKR 117

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 99.4 bits (248), Expect = 7e-25
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 612 FRSFGAK--CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
            R FG    C+ C + I + +   + +D VYHL CF C AC++    G+ + L    ++C
Sbjct: 60  LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 119

Query: 670 KSHYLELV 677
           +    E  
Sbjct: 120 EQDIYEWT 127

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 51.7 bits (124), Expect = 4e-08
 Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHYLEL 676
            C  C + I    +  KA D  +H  C +C+ C  +L   G        R LC+  YL L
Sbjct: 4   TCGGCQQNI-GDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 62

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score =  100 bits (251), Expect = 8e-25
 Identities = 40/88 (45%), Positives = 52/88 (59%), Gaps = 1/88 (1%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           F+ FG KC+ C  GI  +  VR+A+D VYHL CFAC  CKRQL+TG+EF L ED R++CK
Sbjct: 61  FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 120

Query: 671 SHYLELVDGGTTSSDDGADSESSHSKSK 698
           + Y     GG+  S          + S 
Sbjct: 121 ADYETAKQGGSGGSGGSGGGTPMVAASP 148

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 50.6 bits (121), Expect = 2e-07
 Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
            C+ C + I    ++ KA D  +H  C  C  C   L   E      + V CK  + + 
Sbjct: 8   MCAGCDQHILDR-FILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDFFKR 63

>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 = 92.8 bits (231), Expect = 3e-23
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  +  RT FT+ QL+VLQ  F  ++ P   + E+++ +  L  RV  VWFQN+R + 
Sbjct: 3   SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKA 62

Query: 116 KKH 118
           +K 
Sbjct: 63  RKS 65

>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 = 92.8 bits (231), Expect = 3e-23
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  +  RT FT+ QL+VLQ  F  ++ P   + E+++ +  L  RV  VWFQN+R + 
Sbjct: 3   SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKA 62

Query: 755 KKH 757
           +K 
Sbjct: 63  RKS 65

>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 = 92.2 bits (229), Expect = 5e-23
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 114
           S S   R RT  + E L +LQ+    +   PD + +  ++    L K     +FQN R  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62

Query: 115 QKKH 118
            K  
Sbjct: 63  VKHS 66

>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 = 92.2 bits (229), Expect = 5e-23
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 753
           S S   R RT  + E L +LQ+    +   PD + +  ++    L K     +FQN R  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62

Query: 754 QKKH 757
            K  
Sbjct: 63  VKHS 66

>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 = 91.6 bits (228), Expect = 6e-23
 Identities = 26/60 (43%), Positives = 36/60 (60%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           K  RVRT   E+QL  L+  +  +  PD    E++ ++TGLS RV +VWFQN R + KK 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 = 91.6 bits (228), Expect = 6e-23
 Identities = 26/60 (43%), Positives = 36/60 (60%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           K  RVRT   E+QL  L+  +  +  PD    E++ ++TGLS RV +VWFQN R + KK 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 90.2 bits (224), Expect = 3e-22
 Identities = 20/74 (27%), Positives = 34/74 (45%)

Query: 54  SHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRA 113
           S   S A   +   + EQL  L+ +F  +  P   ++E + ++TGLS R  + WF + R 
Sbjct: 2   SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61

Query: 114 RQKKHLHTGKMKSS 127
             +    +    SS
Sbjct: 62  HCRNLKGSRSGPSS 75

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 90.2 bits (224), Expect = 3e-22
 Identities = 20/74 (27%), Positives = 34/74 (45%)

Query: 693 SHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRA 752
           S   S A   +   + EQL  L+ +F  +  P   ++E + ++TGLS R  + WF + R 
Sbjct: 2   SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61

Query: 753 RQKKHLHTGKMKSS 766
             +    +    SS
Sbjct: 62  HCRNLKGSRSGPSS 75

>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 = 84.1 bits (208), Expect = 3e-20
 Identities = 16/61 (26%), Positives = 32/61 (52%)

Query: 58  SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           +         T+EQ+  L+A+F     PD  ++ R+ ++TGL++   + WF + R R ++
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 118 H 118
            
Sbjct: 62  G 62

>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 = 84.1 bits (208), Expect = 3e-20
 Identities = 16/61 (26%), Positives = 32/61 (52%)

Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           +         T+EQ+  L+A+F     PD  ++ R+ ++TGL++   + WF + R R ++
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 757 H 757
            
Sbjct: 62  G 62

>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 = 86.2 bits (213), Expect = 6e-20
 Identities = 23/88 (26%), Positives = 39/88 (44%)

Query: 669 CKSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQD 728
           CK   +               +E   +  + ++ RTT +      L+ +F   S P  Q+
Sbjct: 57  CKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQE 116

Query: 729 LERIAQITGLSKRVTQVWFQNSRARQKK 756
           + R+A+   L K V +VWF N R R+K+
Sbjct: 117 IMRMAEELNLEKEVVRVWFCNRRQREKR 144

>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 = 84.7 bits (209), Expect = 2e-19
 Identities = 22/86 (25%), Positives = 40/86 (46%)

Query: 32  FQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLE 91
            +   +     A+      +E   +  + ++ RTT +      L+ +F   S P  Q++ 
Sbjct: 59  LKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIM 118

Query: 92  RIAQITGLSKRVTQVWFQNSRARQKK 117
           R+A+   L K V +VWF N R R+K+
Sbjct: 119 RMAEELNLEKEVVRVWFCNRRQREKR 144

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 81.8 bits (202), Expect = 3e-19
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHED-RVLCK 670
           +  FG  C  C   +  +     A +  YH  CFAC +CK  +  G+ +AL +   + C 
Sbjct: 11  WGKFGEFCHGCSLLM--TGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCG 68

Query: 671 SHYLELV 677
             + E+V
Sbjct: 69  KCHNEVV 75

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73

 Score = 80.9 bits (200), Expect = 5e-19
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 60  AKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           + +  +  TE+Q+++L+ NF  ++ +PD   L  IA   GL++  TQ WF+   A  ++ 
Sbjct: 2   SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73

 Score = 80.9 bits (200), Expect = 5e-19
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 699 AKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           + +  +  TE+Q+++L+ NF  ++ +PD   L  IA   GL++  TQ WF+   A  ++ 
Sbjct: 2   SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 77.9 bits (192), Expect = 6e-18
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
            R +G +C  C + I     V  A    YH  CF C  C+     G+    +    +C+ 
Sbjct: 11  QRLYGTRCFSCDQFI--EGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68

Query: 672 HYLELVDGGTTS 683
             L +   G +S
Sbjct: 69  CSLPVSVSGPSS 80

>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 = 77.8 bits (192), Expect = 7e-18
 Identities = 26/74 (35%), Positives = 35/74 (47%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  +R RTTFT  QL VL+A F     PD    E +A    L +   QVWF+N RA+ 
Sbjct: 3   SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62

Query: 116 KKHLHTGKMKSSQN 129
           ++     +      
Sbjct: 63  RQQQQQQQNGGQSG 76

>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 = 77.8 bits (192), Expect = 7e-18
 Identities = 26/74 (35%), Positives = 35/74 (47%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  +R RTTFT  QL VL+A F     PD    E +A    L +   QVWF+N RA+ 
Sbjct: 3   SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62

Query: 755 KKHLHTGKMKSSQN 768
           ++     +      
Sbjct: 63  RQQQQQQQNGGQSG 76

>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 = 77.3 bits (190), Expect = 2e-17
 Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 8/95 (8%)

Query: 42  GADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSK 101
           G+  +     + +  K K K      T+ Q+++L+ +F   S P   +L+R+   T LS+
Sbjct: 1   GSSGSSGAYPDFAPQKFKEK------TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSR 54

Query: 102 RVTQVWFQNSRARQKKH--LHTGKMKSSQNRPKYG 134
           R    WF   R  +          M S ++ P  G
Sbjct: 55  REIDSWFSERRKLRDSMEQAVLDSMGSGKSGPSSG 89

>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 = 75.4 bits (185), Expect = 7e-17
 Identities = 18/71 (25%), Positives = 31/71 (43%)

Query: 687 GADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVW 746
           G+   S      A +     T+ Q+++L+ +F   S P   +L+R+   T LS+R    W
Sbjct: 1   GSSGSSGAYPDFAPQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSW 60

Query: 747 FQNSRARQKKH 757
           F   R  +   
Sbjct: 61  FSERRKLRDSM 71

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 76.7 bits (189), Expect = 6e-17
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 4/66 (6%)

Query: 611 CF-RSFGAKCSKCCRGIASSDWVRKARDHVYHLA--CFACEACKRQLSTGEEFALHEDRV 667
           C+ ++    C  C   I          +  +H +  CF C  C + L  G++F   E  V
Sbjct: 57  CYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMV 115

Query: 668 LCKSHY 673
            C    
Sbjct: 116 FCSVEC 121

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 56.3 bits (136), Expect = 8e-10
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
           +C+ C   I  S+   +A +  +HL  F C  C   L  GE + +  D+ +CK  Y++ 
Sbjct: 5   RCAGCDELI-FSNEYTQAENQNWHLKHFCCFDCDSIL-AGEIYVMVNDKPVCKPCYVKN 61

>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 = 75.4 bits (185), Expect = 7e-17
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVT 104
           S+  +  + +  K K K      T EQL+VLQA+F   S    ++L R+   T L++R  
Sbjct: 2   SSGSSGPDFTPQKFKEK------TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREI 55

Query: 105 QVWFQNSRARQKKHLHTGKMKSSQ 128
             WF   +  +       ++  S 
Sbjct: 56  DAWFTEKKKSKALKEEKMEIDESN 79

>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 = 73.9 bits (181), Expect = 2e-16
 Identities = 18/61 (29%), Positives = 29/61 (47%)

Query: 707 TEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
           T EQL+VLQA+F   S    ++L R+   T L++R    WF   +  +       ++  S
Sbjct: 19  TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDES 78

Query: 767 Q 767
            
Sbjct: 79  N 79

>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 = 74.2 bits (182), Expect = 1e-16
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 51  SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 110
           S  S   +K K        EQL+ L+++F  +  P  ++L+R+   T +++R    WF  
Sbjct: 2   SSGSSGPTKYKE----RAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSE 57

Query: 111 SRARQKKH 118
            R +    
Sbjct: 58  RRKKVNAE 65

>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 = 74.2 bits (182), Expect = 1e-16
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 690 SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 749
           S  S   +K K        EQL+ L+++F  +  P  ++L+R+   T +++R    WF  
Sbjct: 2   SSGSSGPTKYKE----RAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSE 57

Query: 750 SRARQKKH 757
            R +    
Sbjct: 58  RRKKVNAE 65

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 76.6 bits (188), Expect = 2e-16
 Identities = 29/142 (20%), Positives = 55/142 (38%), Gaps = 11/142 (7%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKR---QLSTGEEFALHEDRVLCKSHYL 674
           K  +   G   +D V  A   +Y         C+    QLS      L       K    
Sbjct: 23  KQRRIKLGFTQAD-VGLALGTLYGNVFSQTTICRFEALQLSFKNMCKL-------KPLLN 74

Query: 675 ELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQ 734
           + ++   +SS    + +   ++ + ++ RT+        L+++F     P   ++  +A 
Sbjct: 75  KWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLAD 134

Query: 735 ITGLSKRVTQVWFQNSRARQKK 756
              L K V +VWF N R ++K+
Sbjct: 135 SLQLEKEVVRVWFCNRRQKEKR 156

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 74.7 bits (183), Expect = 9e-16
 Identities = 16/71 (22%), Positives = 34/71 (47%)

Query: 47  DHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV 106
             T+ +   ++ + ++ RT+        L+++F     P   ++  +A    L K V +V
Sbjct: 86  SPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRV 145

Query: 107 WFQNSRARQKK 117
           WF N R ++K+
Sbjct: 146 WFCNRRQKEKR 156

>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 = 75.1 bits (184), Expect = 5e-16
 Identities = 23/85 (27%), Positives = 33/85 (38%)

Query: 33  QLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER 92
            L+   +    +      S+S       KR RT+        L+  F     P  Q +  
Sbjct: 69  LLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITH 128

Query: 93  IAQITGLSKRVTQVWFQNSRARQKK 117
           IA   GL K V +VWF N R + K+
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGKR 153

>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 = 73.6 bits (180), Expect = 2e-15
 Identities = 22/72 (30%), Positives = 30/72 (41%)

Query: 685 DDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQ 744
           +    S+S       KR RT+        L+  F     P  Q +  IA   GL K V +
Sbjct: 82  NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141

Query: 745 VWFQNSRARQKK 756
           VWF N R + K+
Sbjct: 142 VWFSNRRQKGKR 153

>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 = 74.6 bits (183), Expect = 8e-16
 Identities = 20/76 (26%), Positives = 37/76 (48%)

Query: 681 TTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSK 740
           + SS    +S      S+ ++ RT+        L+ +F  +  P  +D+  IA+   + K
Sbjct: 83  SLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEK 142

Query: 741 RVTQVWFQNSRARQKK 756
            V +VWF N R ++K+
Sbjct: 143 EVIRVWFSNRRQKEKR 158

>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 = 73.1 bits (179), Expect = 2e-15
 Identities = 19/74 (25%), Positives = 35/74 (47%)

Query: 44  DSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRV 103
            S    +S      S+ ++ RT+        L+ +F  +  P  +D+  IA+   + K V
Sbjct: 85  SSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEV 144

Query: 104 TQVWFQNSRARQKK 117
            +VWF N R ++K+
Sbjct: 145 IRVWFSNRRQKEKR 158

>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 = 70.5 bits (173), Expect = 3e-15
 Identities = 30/75 (40%), Positives = 39/75 (52%)

Query: 44  DSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRV 103
           D +D         K K +R RTTF+  QL  L+  F+    PD    E +AQ T L++  
Sbjct: 2   DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61

Query: 104 TQVWFQNSRARQKKH 118
            QVWFQN RAR +K 
Sbjct: 62  IQVWFQNRRARLRKQ 76

>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 = 69.3 bits (170), Expect = 7e-15
 Identities = 32/76 (42%), Positives = 42/76 (55%), Gaps = 3/76 (3%)

Query: 685 DDGADSESSHS---KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKR 741
           +D +D ES      K K +R RTTF+  QL  L+  F+    PD    E +AQ T L++ 
Sbjct: 1   EDISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEA 60

Query: 742 VTQVWFQNSRARQKKH 757
             QVWFQN RAR +K 
Sbjct: 61  RIQVWFQNRRARLRKQ 76

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 73.0 bits (178), Expect = 3e-15
 Identities = 27/148 (18%), Positives = 48/148 (32%), Gaps = 14/148 (9%)

Query: 610 ICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
           I    F  +     +G   SD +R  +                +L +G E      + L 
Sbjct: 22  IPQAIFAQRVLCRSQG-TLSDLLRNPKPW-------------SKLKSGRETFRRMWKWLQ 67

Query: 670 KSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDL 729
           +  +  +      +             +  K+ R  FT+ Q + L A F+ +  P  +  
Sbjct: 68  EPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQ 127

Query: 730 ERIAQITGLSKRVTQVWFQNSRARQKKH 757
             I+Q  GL       +F N+R R    
Sbjct: 128 ITISQQLGLELSTVSNFFMNARRRSLDK 155

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 65.7 bits (159), Expect = 1e-12
 Identities = 17/75 (22%), Positives = 27/75 (36%)

Query: 44  DSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRV 103
                         +  K+ R  FT+ Q + L A F+ +  P  +    I+Q  GL    
Sbjct: 81  ACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELST 140

Query: 104 TQVWFQNSRARQKKH 118
              +F N+R R    
Sbjct: 141 VSNFFMNARRRSLDK 155

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 69.4 bits (170), Expect = 5e-15
 Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
            C  C   +        A D V+H+ CF C  C+ QL  G+ F   E R  C+  Y+  
Sbjct: 7   GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVERRAYCEGCYVAT 64

>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 = 71.2 bits (174), Expect = 9e-15
 Identities = 20/83 (24%), Positives = 38/83 (45%)

Query: 35  DSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIA 94
            +  +    +   +         SK ++ RT+FT + ++ L A F+ +  P GQ++  +A
Sbjct: 68  LNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMA 127

Query: 95  QITGLSKRVTQVWFQNSRARQKK 117
           +     + V +VWF N R   K 
Sbjct: 128 KELNYDREVVRVWFSNRRQTLKN 150

>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 = 71.2 bits (174), Expect = 1e-14
 Identities = 21/84 (25%), Positives = 37/84 (44%)

Query: 673 YLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERI 732
           +L   +                  SK ++ RT+FT + ++ L A F+ +  P GQ++  +
Sbjct: 67  WLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEM 126

Query: 733 AQITGLSKRVTQVWFQNSRARQKK 756
           A+     + V +VWF N R   K 
Sbjct: 127 AKELNYDREVVRVWFSNRRQTLKN 150

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 77

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 611 CF-RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
                  A C +C  G A ++ +  +   +YH  CF C  C +Q   G  F   E R  C
Sbjct: 5   MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYC 63

Query: 670 KSHYLEL 676
           +  +  L
Sbjct: 64  EHDFQML 70

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 67.4 bits (165), Expect = 3e-14
 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSH 672
            S  A C +C  G A ++ +  +   +YH  CF C  C +Q   G  F   E R  C+  
Sbjct: 8   GSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHD 66

Query: 673 YLEL 676
           +  L
Sbjct: 67  FQML 70

>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 = 67.0 bits (164), Expect = 3e-14
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 60  AKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
                 T TE+Q+++L+ NF  ++ +PD   L  IA   GL++  TQ WF+   A  ++ 
Sbjct: 1   GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 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 = 67.0 bits (164), Expect = 3e-14
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 699 AKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
                 T TE+Q+++L+ NF  ++ +PD   L  IA   GL++  TQ WF+   A  ++ 
Sbjct: 1   GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 67.9 bits (165), Expect = 4e-14
 Identities = 18/75 (24%), Positives = 34/75 (45%)

Query: 682 TSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKR 741
            SS      +    KS +       T EQL +L++ F     P  ++ +++A+ +GL++ 
Sbjct: 8   HSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLART 67

Query: 742 VTQVWFQNSRARQKK 756
               WF ++R   K 
Sbjct: 68  DIVSWFGDTRYAWKN 82

>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 = 66.4 bits (161), Expect = 1e-13
 Identities = 17/74 (22%), Positives = 33/74 (44%)

Query: 44  DSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRV 103
            S      +    KS +       T EQL +L++ F     P  ++ +++A+ +GL++  
Sbjct: 9   SSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTD 68

Query: 104 TQVWFQNSRARQKK 117
              WF ++R   K 
Sbjct: 69  IVSWFGDTRYAWKN 82

>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 = 66.2 bits (162), Expect = 5e-14
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  +R RT FT+EQL+ L+  FQ    PD    E++A+   L +   +VWF+N RA+ 
Sbjct: 3   SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKW 62

Query: 116 KKH 118
           ++ 
Sbjct: 63  RRS 65

>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 = 66.2 bits (162), Expect = 5e-14
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  +R RT FT+EQL+ L+  FQ    PD    E++A+   L +   +VWF+N RA+ 
Sbjct: 3   SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKW 62

Query: 755 KKH 757
           ++ 
Sbjct: 63  RRS 65

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 66.4 bits (162), Expect = 6e-14
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 5/70 (7%)

Query: 611 CF-RSFGAKCSKCCRGI---ASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDR 666
           C+      KC+ C   I        V       +H  CF C+ C   L+  + F  H+++
Sbjct: 9   CYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQ 67

Query: 667 VLCKSHYLEL 676
           V C     +L
Sbjct: 68  VYCPDCAKKL 77

>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 = 65.4 bits (160), Expect = 1e-13
 Identities = 23/64 (35%), Positives = 36/64 (56%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH 120
           +R RT FT+ Q++VL+  F+++  P    LE +AQ   L     Q+WFQN RA+ K+   
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 121 TGKM 124
             + 
Sbjct: 62  ESQF 65

>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 = 65.4 bits (160), Expect = 1e-13
 Identities = 23/64 (35%), Positives = 36/64 (56%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH 759
           +R RT FT+ Q++VL+  F+++  P    LE +AQ   L     Q+WFQN RA+ K+   
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 760 TGKM 763
             + 
Sbjct: 62  ESQF 65

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 24/74 (32%), Positives = 37/74 (50%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  +R RT+FT+EQ++ L+  F+    PD    ER+A    L +   QVWF N RA+ 
Sbjct: 3   SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKW 62

Query: 116 KKHLHTGKMKSSQN 129
           ++       +    
Sbjct: 63  RREEKLRNQRRQSG 76

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 24/74 (32%), Positives = 37/74 (50%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  +R RT+FT+EQ++ L+  F+    PD    ER+A    L +   QVWF N RA+ 
Sbjct: 3   SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKW 62

Query: 755 KKHLHTGKMKSSQN 768
           ++       +    
Sbjct: 63  RREEKLRNQRRQSG 76

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 26/60 (43%), Positives = 36/60 (60%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
             +R RT FT +QLQ L+A FQ +  PD    E IA  T L++   +VWF+N RA+ +K 
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 26/60 (43%), Positives = 36/60 (60%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
             +R RT FT +QLQ L+A FQ +  PD    E IA  T L++   +VWF+N RA+ +K 
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 91

 Score = 64.5 bits (157), Expect = 5e-13
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
            C +C + +   + +  A   V+H++CF C  C  +LS G  +A    R+ CK H+ +L
Sbjct: 17  TCVECQKTVYPMERL-LANQQVFHISCFRCSYCNNKLSLG-TYASLHGRIYCKPHFNQL 73

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 63.5 bits (154), Expect = 5e-13
 Identities = 14/49 (28%), Positives = 26/49 (53%)

Query: 69  EEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           +  L +L+A + L++ P  ++L +IA    L   V + WF+  +A Q  
Sbjct: 12  KNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 63.5 bits (154), Expect = 5e-13
 Identities = 14/49 (28%), Positives = 26/49 (53%)

Query: 708 EEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           +  L +L+A + L++ P  ++L +IA    L   V + WF+  +A Q  
Sbjct: 12  KNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 611 CF-RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
           C  R    KC  C + I + D   + +  V+H  CF C  CK+ + TG  F    +   C
Sbjct: 9   CTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTG-SFFPKGEDFYC 67

Query: 670 KSHYLEL 676
            + +   
Sbjct: 68  VTCHETK 74

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           S  + C +C + I       + +   +H  CF C  C++ + T   F   +++  C   Y
Sbjct: 3   SGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTK-SFIPKDNQNFCVPCY 61

Query: 674 LEL 676
            + 
Sbjct: 62  EKQ 64

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 63.2 bits (154), Expect = 2e-12
 Identities = 10/39 (25%), Positives = 17/39 (43%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEAC 650
            R    KC  C + I + D   + +  V+H  CF+  + 
Sbjct: 62  TREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 63.2 bits (154), Expect = 2e-12
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           S  + C +C + I +       ++  +H  CF C  C   L+  E F   ++++LC    
Sbjct: 3   SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCT 61

Query: 674 LEL 676
              
Sbjct: 62  TRE 64

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 62.4 bits (152), Expect = 2e-12
 Identities = 19/65 (29%), Positives = 24/65 (36%), Gaps = 3/65 (4%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
              F  KC  C R +  +     A D V+H  CF C  C    S    F   + R  C+ 
Sbjct: 11  LAMFSPKCGGCNRPVLEN--YLSAMDTVWHPECFVCGDCFTSFS-TGSFFELDGRPFCEL 67

Query: 672 HYLEL 676
           HY   
Sbjct: 68  HYHHR 72

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 1/63 (1%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           S  + CS C   +       +     +H  CF C  C++ L +   F   +    C   Y
Sbjct: 3   SGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSR-SFVPDKGAHYCVPCY 61

Query: 674 LEL 676
              
Sbjct: 62  ENK 64

>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 = 59.9 bits (146), Expect = 9e-12
 Identities = 14/60 (23%), Positives = 32/60 (53%)

Query: 57  KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 116
           K K+ + +++ + +    L+  F+   + + ++ E +A+  G++    +VWF N R R K
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>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 = 59.9 bits (146), Expect = 9e-12
 Identities = 14/60 (23%), Positives = 32/60 (53%)

Query: 696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           K K+ + +++ + +    L+  F+   + + ++ E +A+  G++    +VWF N R R K
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 611 CF-RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
           C+  +F   C++C + I          D  +H  CF C  C+R L+  E F   +  +LC
Sbjct: 9   CYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTCQDSELLC 67

Query: 670 KSHYLEL 676
              Y   
Sbjct: 68  NDCYCSA 74

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 69

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           S  + C KC + I +S  +   +D  +H  CF C  C ++L+ G+ F   ED+  C   Y
Sbjct: 3   SGSSGCVKCNKAI-TSGGIT-YQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCY 59

Query: 674 LEL 676
              
Sbjct: 60  KNF 62

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 22/55 (40%), Positives = 29/55 (52%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
             TFT  QL+ L+  F     PD    E +A   GL++   QVWFQN RA+ +K 
Sbjct: 3   HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 22/55 (40%), Positives = 29/55 (52%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
             TFT  QL+ L+  F     PD    E +A   GL++   QVWFQN RA+ +K 
Sbjct: 3   HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 59.1 bits (143), Expect = 2e-11
 Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 3/65 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVR--KARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           S  + C+ C   I+     +     +  +H  CF C+ C   L  G  F    D +LC  
Sbjct: 3   SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPD 61

Query: 672 HYLEL 676
              ++
Sbjct: 62  CGKDI 66

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 611 CF-RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
           C+   F  +C++C + +         RD  +H  C  C  C+  L  G++F   ++   C
Sbjct: 9   CYENKFAPRCARCSKTLTQG--GVTYRDQPWHRECLVCTGCQTPL-AGQQFTSRDEDPYC 65

Query: 670 KSHYLEL 676
            + + EL
Sbjct: 66  VACFGEL 72

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
           S  + C +C + I ++  V   R+  +H  CF C AC++QLS G+ F   +D   C + +
Sbjct: 3   SGSSGCVQCKKPI-TTGGVT-YREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCF 59

Query: 674 LEL 676
            +L
Sbjct: 60  CDL 62

>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 = 58.9 bits (142), Expect = 6e-11
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 15/78 (19%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIA---------------QITGLS 100
           S S  +  R T+ +E L V+++ F  +  PD    E IA                +  ++
Sbjct: 3   SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62

Query: 101 KRVTQVWFQNSRARQKKH 118
                 WF N R   K+ 
Sbjct: 63  SLKVYNWFANRRKEIKRR 80

>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 = 58.9 bits (142), Expect = 6e-11
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 15/78 (19%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIA---------------QITGLS 739
           S S  +  R T+ +E L V+++ F  +  PD    E IA                +  ++
Sbjct: 3   SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62

Query: 740 KRVTQVWFQNSRARQKKH 757
                 WF N R   K+ 
Sbjct: 63  SLKVYNWFANRRKEIKRR 80

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B Length = 66

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
                C  C R I     V  A    +H+  F C  C++    G      +    C++HY
Sbjct: 3   MGVPICGACRRPIEGR--VVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHY 59

Query: 674 LEL 676
            +L
Sbjct: 60  NQL 62

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 57.2 bits (138), Expect = 1e-10
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVR--KARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           S  + C  C + I+     +    +D  +H  CF C  C   L  G+ F      + C+ 
Sbjct: 3   SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNKEIFCQK 61

Query: 672 HYLELVDGGTTSS 684
               +    +  S
Sbjct: 62  CGSGMDTDISGPS 74

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A Length = 81

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLE 675
           G KC  C R +  ++ V +     +H  CF C  C++ L +    A+H+  V CKS Y +
Sbjct: 7   GNKCGACGRTVYHAEEV-QCDGRSFHRCCFLCMVCRKNLDST-TVAIHDAEVYCKSCYGK 64

Query: 676 L 676
            
Sbjct: 65  K 65

>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} Length = 71

 Score = 56.7 bits (136), Expect = 2e-10
 Identities = 12/59 (20%), Positives = 29/59 (49%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG 122
                ++ + VL+A + ++  P+  +L +I+   GL +   + WF+  +  Q  +  +G
Sbjct: 9   PINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNSRSG 67

>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} Length = 71

 Score = 56.7 bits (136), Expect = 2e-10
 Identities = 12/59 (20%), Positives = 29/59 (49%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG 761
                ++ + VL+A + ++  P+  +L +I+   GL +   + WF+  +  Q  +  +G
Sbjct: 9   PINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNSRSG 67

>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 = 56.6 bits (136), Expect = 2e-10
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 62  RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
                 T+EQL +L++ F        +D +++ QITGL +     WF ++R   K  
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61

>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 = 56.6 bits (136), Expect = 2e-10
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
                 T+EQL +L++ F        +D +++ QITGL +     WF ++R   K  
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 59.6 bits (144), Expect = 2e-10
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 607 SVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDR 666
           S +         C +C + + +++ V       +H +CF C  C + L      A  +  
Sbjct: 106 SRMAQKVGGSDGCPRCGQAVYAAEKV-IGAGKSWHKSCFRCAKCGKSL-ESTTLADKDGE 163

Query: 667 VLCKSHYLEL 676
           + CK  Y + 
Sbjct: 164 IYCKGCYAKN 173

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 55.0 bits (132), Expect = 9e-09
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLE 675
           G KC  C + +  ++ V +     +H +CF C  CK+ L +    A+H D + CKS Y +
Sbjct: 7   GKKCGVCQKAVYFAEEV-QCEGSSFHKSCFLCMVCKKNLDST-TVAVHGDEIYCKSCYGK 64

Query: 676 L 676
            
Sbjct: 65  K 65

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 611 CFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFAL-HEDRVLC 669
           C+ +   KC+ C + I   D + +A    YH  CF C  C R L  G  F +    ++ C
Sbjct: 10  CYVATLEKCATCSQPIL--DRILRAMGKAYHPGCFTCVVCHRGL-DGIPFTVDATSQIHC 66

Query: 670 KSHYLEL 676
              +   
Sbjct: 67  IEDFHRK 73

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 56.3 bits (136), Expect = 4e-10
 Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
            C KC  GI     V KARD   H  CF C  C   L     +   E  + C++H    
Sbjct: 27  LCDKCGSGI--VGAVVKARDKYRHPECFVCADCNLNLKQK-GYFFVEGELYCETHARAR 82

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 18/63 (28%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
                C KC  GI       K RD   H  C+ C  C   L   +     ED++ C+ H 
Sbjct: 13  QKLPMCDKCGTGI--VGVFVKLRDRHRHPECYVCTDCGTNLK-QKGHFFVEDQIYCEKHA 69

Query: 674 LEL 676
            E 
Sbjct: 70  RER 72

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 54.8 bits (132), Expect = 8e-10
 Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 611 CFRSFGA-KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
             +  G   C+ C   I     +  A D  +H++CF C+ C   L+   E+   +    C
Sbjct: 9   PIKIRGPSHCAGCKEEIKHGQSL-LALDKQWHVSCFKCQTCSVILT--GEYISKDGVPYC 65

Query: 670 KSHYLEL 676
           +S Y   
Sbjct: 66  ESDYHAQ 72

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 54.4 bits (131), Expect = 9e-10
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLEL 676
            C +C   I     V KA ++ +H  CF C+ C+  L+    F  +  R LC+  +   
Sbjct: 7   GCHQCGEFIIGR--VIKAMNNSWHPECFRCDLCQEVLADI-GFVKNAGRHLCRPCHNRE 62

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 682 TSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKR 741
           TS+++    +      K ++ RT F+  QL VL   FQ       Q ++ ++ I  LS +
Sbjct: 5   TSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYK 64

Query: 742 VTQVWFQNSRARQKK 756
             + WFQN R + K+
Sbjct: 65  QVKTWFQNQRMKSKR 79

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 20/75 (26%), Positives = 34/75 (45%)

Query: 43  ADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKR 102
             + +    +      K ++ RT F+  QL VL   FQ       Q ++ ++ I  LS +
Sbjct: 5   TSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYK 64

Query: 103 VTQVWFQNSRARQKK 117
             + WFQN R + K+
Sbjct: 65  QVKTWFQNQRMKSKR 79

>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 = 53.6 bits (129), Expect = 2e-09
 Identities = 24/73 (32%), Positives = 34/73 (46%)

Query: 684 SDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVT 743
           S   +  E      K +R RT FTE QL  L+  F+        D   +A+  GLS+   
Sbjct: 2   SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61

Query: 744 QVWFQNSRARQKK 756
           + W+QN R + KK
Sbjct: 62  KTWYQNRRMKWKK 74

>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 = 52.9 bits (127), Expect = 4e-09
 Identities = 24/73 (32%), Positives = 35/73 (47%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVT 104
           S+  +  E      K +R RT FTE QL  L+  F+        D   +A+  GLS+   
Sbjct: 2   SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61

Query: 105 QVWFQNSRARQKK 117
           + W+QN R + KK
Sbjct: 62  KTWYQNRRMKWKK 74

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 90

 Score = 53.6 bits (129), Expect = 3e-09
 Identities = 12/63 (19%), Positives = 20/63 (31%), Gaps = 3/63 (4%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHY 673
                C+ C + I        A    +H   F C  CK  +     F   +  + C+  Y
Sbjct: 23  KRTPMCAHCNQVIRGP--FLVALGKSWHPEEFNCAHCKNTM-AYIGFVEEKGALYCELCY 79

Query: 674 LEL 676
            + 
Sbjct: 80  EKF 82

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC-K 670
                +KC KC + +  ++ V  +    +H  C  CE C + L+ G   A H+ +  C K
Sbjct: 5   SSGMASKCPKCDKTVYFAEKV-SSLGKDWHKFCLKCERCSKTLTPG-GHAEHDGKPFCHK 62

Query: 671 SHYLEL 676
             Y  L
Sbjct: 63  PCYATL 68

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGE-EFALHEDRVLCKSHYLEL 676
            C+ C   +   + +     H +H +CF C  C+  L  G  E    +    C  H  + 
Sbjct: 17  LCALCGEHLYVLERL-CVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQT 75

Query: 677 VDGGTT 682
             G ++
Sbjct: 76  DSGPSS 81

>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 Length = 194

 Score = 54.1 bits (129), Expect = 2e-08
 Identities = 16/125 (12%), Positives = 35/125 (28%), Gaps = 21/125 (16%)

Query: 652 RQLSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAKRVRTTFTEEQL 711
             + T +  AL+   V  +    +              +       K +R R  +     
Sbjct: 68  TPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQ 127

Query: 712 QVLQANFQLDSNPDGQDLERIAQI---------------------TGLSKRVTQVWFQNS 750
           Q+L   ++   NP  ++ E + +                        +++     WF N 
Sbjct: 128 QILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANR 187

Query: 751 RARQK 755
           R  + 
Sbjct: 188 RKEEA 192

>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 Length = 194

 Score = 53.0 bits (126), Expect = 5e-08
 Identities = 13/105 (12%), Positives = 29/105 (27%), Gaps = 21/105 (20%)

Query: 33  QLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER 92
           ++       G        +       K +R R  +     Q+L   ++   NP  ++ E 
Sbjct: 88  EVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERET 147

Query: 93  IAQI---------------------TGLSKRVTQVWFQNSRARQK 116
           + +                        +++     WF N R  + 
Sbjct: 148 LVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA 192

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 51.1 bits (122), Expect = 4e-08
 Identities = 10/75 (13%), Positives = 19/75 (25%), Gaps = 15/75 (20%)

Query: 612 FRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
            R FG   +    G                 +             G EF   ++R++ + 
Sbjct: 63  IRLFGNSGAGGSGGH--------------MGSGGDVMVVGEPTLMGGEFGDEDERLITRL 108

Query: 672 HYLELVDGGTTSSDD 686
              +  D      D+
Sbjct: 109 ENTQF-DAANGIDDE 122

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 50.4 bits (120), Expect = 8e-08
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 2/62 (3%)

Query: 616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHYL 674
             +C+ C   IA   ++  A D  +H  C  C +C+ QL   G         +LC++ Y+
Sbjct: 5   WKRCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 675 EL 676
            L
Sbjct: 64  RL 65

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 50.0 bits (118), Expect = 5e-08
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 10/85 (11%)

Query: 54  SHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDG----QDLERIAQITGLSKRVTQVWFQ 109
           S   S A + RT F++  L  L+  +       G    + +E +A    +   + + W  
Sbjct: 2   SSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIG 61

Query: 110 NSRARQKKHLHTGKMKSSQNRPKYG 134
           N R + +       M    + P  G
Sbjct: 62  NRRRKYR------LMGIEVSGPSSG 80

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 47.6 bits (112), Expect = 3e-07
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 693 SHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDG----QDLERIAQITGLSKRVTQVWFQ 748
           S   S A + RT F++  L  L+  +       G    + +E +A    +   + + W  
Sbjct: 2   SSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIG 61

Query: 749 NSRARQKK 756
           N R + + 
Sbjct: 62  NRRRKYRL 69

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKS 671
           S  + C  C + I  +  V +A +  YH +C  C  C +  + GEE  L    +   +
Sbjct: 3   SGSSGCDSCEKYI--TGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPA 58

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 49.7 bits (119), Expect = 6e-08
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK-SHYLEL 676
           KC KC + +  ++ V  +    +H  C  CE C + L++G   A HE +  C    Y  +
Sbjct: 2   KCPKCDKEVYFAERV-TSLGKDWHRPCLKCEKCGKTLTSG-GHAEHEGKPYCNHPCYSAM 59

>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 = 55.2 bits (132), Expect = 7e-08
 Identities = 82/604 (13%), Positives = 176/604 (29%), Gaps = 199/604 (32%)

Query: 118 HLHTGKMKSSQNRPKYGYYPEPNKSFLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIG 177
           H H   M       +Y Y         V +  F++       +   + V +      ++ 
Sbjct: 1   HHHHHHMDFETGEHQYQY----KDILSVFEDAFVD-------NFDCKDVQD--MPKSILS 47

Query: 178 NGDEKKNYVKEK--VNQ-----WIDCVKKLSEAAKKSPQAAFSVVTKSLQCEWAFL-QRV 229
             +E  + +  K  V+      W    K+  E  +K     F  V + L+  + FL   +
Sbjct: 48  K-EEIDHIIMSKDAVSGTLRLFWTLLSKQ-EEMVQK-----F--VEEVLRINYKFLMSPI 98

Query: 230 VNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHAFAV 289
               +               PS+           L+           ND    A++   V
Sbjct: 99  KTEQRQ--------------PSMMTRMYIEQRDRLY-----------NDNQVFAKYN--V 131

Query: 290 TSEKCKVLVDSLLKQEQLNLQEHNQCV--------KNAINTELVRKETEYQEKQERILSS 341
           +  +   L    L+Q  L L+     +        K  +  ++            ++   
Sbjct: 132 SRLQ-PYLK---LRQALLELRPAKNVLIDGVLGSGKTWVALDVCL--------SYKVQCK 179

Query: 342 LPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPVQFRDALALRYNHGLKGLPTYCDGC 401
           +         +I       WLN+   +S    L  +Q    L  + +      P +    
Sbjct: 180 MD-------FKI------FWLNLKNCNSPETVLEMLQ---KLLYQID------PNWTSRS 217

Query: 402 GGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSSTSPALIADF 461
               ++   ++  +          LR   +    Y  N ++   ++ +        + + 
Sbjct: 218 DHSSNIKLRIHSIQ--------AELRR-LLKSKPYE-NCLL---VLLN--------VQNA 256

Query: 462 KINGVWEAGGTAFFDNR--------------IVNADAPSYSSQTWNTIAKRHAQEKHL-- 505
           K    W A     F+                 ++A   ++ S   +++     + K L  
Sbjct: 257 KA---WNA-----FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308

Query: 506 KY-NTAAEDLRA---SFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRV 561
           KY +   +DL     +  P   S            L        + WK    HV    ++
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAES---IRDGLATW-----DNWK----HVNCD-KL 355

Query: 562 RTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKG------RLSVL------ 609
            T   I+++ SL       +++P  +      M+ R+ +           LS++      
Sbjct: 356 TT---IIES-SL------NVLEPAEYRK----MFDRLSVFPPSAHIPTILLSLIWFDVIK 401

Query: 610 ICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLC 669
                   K  K    +      +++   +  +        + ++    E+ALH   ++ 
Sbjct: 402 SDVMVVVNKLHK--YSLVEKQP-KESTISIPSI------YLELKVKLENEYALH-RSIV- 450

Query: 670 KSHY 673
             HY
Sbjct: 451 -DHY 453

>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 = 48.7 bits (115), Expect = 7e-06
 Identities = 61/394 (15%), Positives = 118/394 (29%), Gaps = 112/394 (28%)

Query: 419 VKHGHDYLRDECIMMASYAWNGIVKEP-----------IMRDSSSTSPALIADF-----K 462
            K   D  +    +++    + I+               +         ++  F     +
Sbjct: 35  CKDVQDMPKS---ILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEE---MVQKFVEEVLR 88

Query: 463 INGVWEAGGTAF-FDNRIVNADAPSYSSQ---TWNT---IAKRHA--QEKHLKYNTAAED 513
           IN  +    +    + R  +     Y  Q    +N     AK +    + +LK   A  +
Sbjct: 89  INYKFLM--SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146

Query: 514 LRASFTPLVCSTDGA----LHLEFHSFLKRIALVLSEK--WKKMYGHVLSWL---RVRTE 564
           LR +   L+    G+    +             V        KM   +  WL      + 
Sbjct: 147 LRPAKNVLIDGVLGSGKTWV----------ALDVCLSYKVQCKMDFKIF-WLNLKNCNSP 195

Query: 565 FSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRI-LLKGRLSVLICFRSFGAKCSKCC 623
            ++L+ +   L    QI   +          I++RI  ++  L  L+  + +     + C
Sbjct: 196 ETVLEMLQKLLY---QIDPNWT-SRSDHSSNIKLRIHSIQAELRRLLKSKPY-----ENC 246

Query: 624 RGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGTTS 683
             +           +V +   +              F L      CK     L+   TT 
Sbjct: 247 LLVL---------LNVQNAKAW------------NAFNLS-----CKI----LL---TTR 273

Query: 684 SDDGADSESSHSKSK--AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER---------I 732
                D  S+ + +         T T ++++ L   + LD  P  QDL R         +
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY-LDCRP--QDLPREVLTTNPRRL 330

Query: 733 AQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 766
           + I    +     W  N +      L T  ++SS
Sbjct: 331 SIIAESIRDGLATW-DNWKHVNCDKLTT-IIESS 362

>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 = 44.1 bits (103), Expect = 2e-04
 Identities = 72/429 (16%), Positives = 131/429 (30%), Gaps = 105/429 (24%)

Query: 21  TEEQLQVLQA-NFQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQ----LQVL 75
            E  L++LQ   +Q+D N        +DH+ +      S    +R     +     L V 
Sbjct: 195 PETVLEMLQKLLYQIDPN----WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV- 249

Query: 76  QANFQLDSNPDGQDLERIAQ--------ITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS 127
                L    + Q+ +            +T   K+VT        A    H+       S
Sbjct: 250 -----LL---NVQNAKAWNAFNLSCKILLTTRFKQVTDF----LSAATTTHI-------S 290

Query: 128 QNRPKYGYYPEPNKS----FLVIKPQFLEEASLLFHDLHVQIVTEKRFLGGVIGNGDEKK 183
            +       P+  KS    +L  +PQ L    L  +   + I+ E   +   +   D  K
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE--SIRDGLATWDNWK 348

Query: 184 NYVKEKVNQWID-CVKKLSEAAKKSPQAAFSV----V---TKSLQCEWAFL-----QRVV 230
           +   +K+   I+  +  L  A  +      SV        T  L   W  +       VV
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV 408

Query: 231 NHCQD------EYIPLREIIHSTLVPSIFEHEISSSEH----ELFHLPTRFGGLGINDPV 280
           N          +       I S  +    + E   + H    + +++P  F    +  P 
Sbjct: 409 NKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPY 468

Query: 281 E-------TAQHAFAVT-SEKC----KVLVD-SLLKQEQLNLQEHNQCVKNAINTEL--V 325
                      H   +   E+      V +D   L+Q ++           +I   L  +
Sbjct: 469 LDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQ-KIRHDSTAWNASGSILNTLQQL 527

Query: 326 RKETEYQEKQERILSSLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSP----VQFRD 381
           +    Y    +       P  +R++  I        L+ +PK  +N   S     ++   
Sbjct: 528 KFYKPYICDND-------PKYERLVNAI--------LDFLPKIEENLICSKYTDLLR--- 569

Query: 382 ALALRYNHG 390
            +AL     
Sbjct: 570 -IALMAEDE 577

>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 = 42.5 bits (99), Expect = 6e-04
 Identities = 72/530 (13%), Positives = 133/530 (25%), Gaps = 184/530 (34%)

Query: 227 QRVVNHCQDEYIPLREIIHSTLVPSIFEHEISSSEHELFHLPTRFGGLGINDPVETAQHA 286
           + +++  +D ++   +      V  + +  +S  E +  H+      +   D V      
Sbjct: 19  KDILSVFEDAFVDNFDCKD---VQDMPKSILSKEEID--HI------IMSKDAVSGTLRL 67

Query: 287 FAVTSEK----CKVLVDSLLKQEQLNLQE--HNQCVKNAINTELVRKETEYQEKQERILS 340
           F     K     +  V+ +L+     L      +  + ++ T        Y E+++R+ +
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR------MYIEQRDRLYN 121

Query: 341 SLPPAKQRVLTRIVEGQSSHWLNVIPKSSDNFDLSPV-QFRDAL-ALRYN-----HGLKG 393
                 +  ++R+                      P  + R AL  LR        G+ G
Sbjct: 122 DNQVFAKYNVSRL---------------------QPYLKLRQALLELRPAKNVLIDGVLG 160

Query: 394 LPTYCDGCGGEMSVTHALNCKKGGLVKHGHDYLRDECIMMASYAWNGIVKEPIMRDSSST 453
                   G            K  +     D      +                      
Sbjct: 161 -------SG------------KTWVAL---DVCLSYKV---------------------- 176

Query: 454 SPALIADFKINGVWEAGGTAFFDNRIVNADAPSYSSQTWNTIAKRHAQEKHLKYNTAAED 513
                                 D +I       +    W  +   ++ E  L+     + 
Sbjct: 177 ------------------QCKMDFKI-------F----WLNLKNCNSPETVLE---MLQK 204

Query: 514 LRASFTPLVCS---TDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLR-VRTEFSILK 569
           L     P   S       + L  HS    +  +L  K    Y + L  L  V+       
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK---PYENCLLVLLNVQNA-KAWN 260

Query: 570 AVSLR---LRGTRQI-VKPYGFDDGAGLMYIRVRI--LLKG-----RLSVLICFRSFGAK 618
           A +L    L  TR   V     D  +      + +             S+L        K
Sbjct: 261 AFNLSCKILLTTRFKQV----TDFLSAATTTHISLDHHSMTLTPDEVKSLL-------LK 309

Query: 619 CSKC---------CRG-------IASSDWVRKAR-DHVYHLACF----ACEACKRQLSTG 657
              C                   IA S     A  D+  H+ C       E+    L   
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369

Query: 658 E------EFALHEDRVLCKSHYLELVDGGTTSSDDGADSESSHSKSKAKR 701
           E        ++        +  L L+      SD        H  S  ++
Sbjct: 370 EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLD---SNPDGQDLERIAQITGLSKRVTQVWFQNSR 112
           S S  ++ RT ++  QL  LQ  FQ     + P+  +L   A   GL++   ++WFQN R
Sbjct: 3   SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAEL---AASLGLTQTQVKIWFQNKR 59

Query: 113 ARQKK 117
           ++ KK
Sbjct: 60  SKIKK 64

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLD---SNPDGQDLERIAQITGLSKRVTQVWFQNSR 751
           S S  ++ RT ++  QL  LQ  FQ     + P+  +L   A   GL++   ++WFQN R
Sbjct: 3   SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAEL---AASLGLTQTQVKIWFQNKR 59

Query: 752 ARQKK 756
           ++ KK
Sbjct: 60  SKIKK 64

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 51.9 bits (123), Expect = 2e-07
 Identities = 14/98 (14%), Positives = 29/98 (29%), Gaps = 21/98 (21%)

Query: 679 GGTTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQI--- 735
             +       D+ S  +  K +R R  +     Q+L   +    NP  ++ E + +    
Sbjct: 122 QQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNR 181

Query: 736 ------------------TGLSKRVTQVWFQNSRARQK 755
                               +++     WF N R  + 
Sbjct: 182 AECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA 219

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 51.9 bits (123), Expect = 2e-07
 Identities = 15/105 (14%), Positives = 29/105 (27%), Gaps = 21/105 (20%)

Query: 33  QLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER 92
            L               D+ S  +  K +R R  +     Q+L   +    NP  ++ E 
Sbjct: 115 FLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREA 174

Query: 93  IAQI---------------------TGLSKRVTQVWFQNSRARQK 116
           + +                        +++     WF N R  + 
Sbjct: 175 LVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA 219

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens} Length = 123

 Score = 49.3 bits (117), Expect = 3e-07
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHYLEL 676
           +C+ C   IA   ++  A D  +H  C  C +C+ QL   G         +LC++ Y+ L
Sbjct: 63  RCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 121

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 19/57 (33%), Positives = 33/57 (57%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           KR RT F+ EQL  L+  F  +     +  ++++   GL++   ++WF+N RA+ KK
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 19/57 (33%), Positives = 33/57 (57%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           KR RT F+ EQL  L+  F  +     +  ++++   GL++   ++WF+N RA+ KK
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 48.1 bits (114), Expect = 4e-07
 Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 618 KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHYLEL 676
            C  C + I    +  KA D  +H  C +C+ C  +L   G        R LC+  YL L
Sbjct: 5   TCGGCQQNIGDR-YFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 63

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 45.0 bits (106), Expect = 6e-06
 Identities = 11/91 (12%), Positives = 23/91 (25%), Gaps = 21/91 (23%)

Query: 611 CFRSFGAKCSKCCRGIAS---------------SDWVRKARDHVYHLACFACEACKRQLS 655
           C       C  C   +                  D++R      +  +            
Sbjct: 30  CL-----SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGEPTL 84

Query: 656 TGEEFALHEDRVLCKSHYLELVDGGTTSSDD 686
            G EF   ++R++ +    +  D      D+
Sbjct: 85  MGGEFGDEDERLITRLENTQF-DAANGIDDE 114

>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 = 46.7 bits (111), Expect = 6e-07
 Identities = 17/75 (22%), Positives = 33/75 (44%)

Query: 53  SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 112
           S    +K ++ R  FT+ Q   L+  F+        + E +A +  L+    ++WFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 113 ARQKKHLHTGKMKSS 127
            + K+  +    +  
Sbjct: 62  YKTKRAQNEKGYEGH 76

>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 = 46.7 bits (111), Expect = 6e-07
 Identities = 17/75 (22%), Positives = 33/75 (44%)

Query: 692 SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 751
           S    +K ++ R  FT+ Q   L+  F+        + E +A +  L+    ++WFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 752 ARQKKHLHTGKMKSS 766
            + K+  +    +  
Sbjct: 62  YKTKRAQNEKGYEGH 76

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
             +++RT F++ QL  L+  FQ       Q ++ ++ I  LS +  + WFQN R + K+
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
             +++RT F++ QL  L+  FQ       Q ++ ++ I  LS +  + WFQN R + K+
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

>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 = 46.3 bits (110), Expect = 7e-07
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  K  +  F+ +Q   L+  F+        + +R+A++  LS+R  + WFQN RA+ 
Sbjct: 3   SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKW 62

Query: 116 KK 117
           ++
Sbjct: 63  RR 64

>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 = 46.3 bits (110), Expect = 7e-07
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  K  +  F+ +Q   L+  F+        + +R+A++  LS+R  + WFQN RA+ 
Sbjct: 3   SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKW 62

Query: 755 KK 756
           ++
Sbjct: 63  RR 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 = 8e-07
 Identities = 16/78 (20%), Positives = 32/78 (41%)

Query: 51  SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 110
              + +  K K+ RT+FT  Q+  L+  F         +   +A+   ++    + WFQN
Sbjct: 8   PYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQN 67

Query: 111 SRARQKKHLHTGKMKSSQ 128
            R + ++     +    Q
Sbjct: 68  RRTKWRRQTAEEREAERQ 85

>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 = 8e-07
 Identities = 16/78 (20%), Positives = 32/78 (41%)

Query: 690 SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 749
              + +  K K+ RT+FT  Q+  L+  F         +   +A+   ++    + WFQN
Sbjct: 8   PYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQN 67

Query: 750 SRARQKKHLHTGKMKSSQ 767
            R + ++     +    Q
Sbjct: 68  RRTKWRRQTAEEREAERQ 85

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99

 Score = 47.1 bits (111), Expect = 8e-07
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 21/81 (25%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQI---------------------T 97
           K +R R  +     Q+L   ++   NP  ++ E + +                       
Sbjct: 8   KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67

Query: 98  GLSKRVTQVWFQNSRARQKKH 118
            +++     WF N R  +   
Sbjct: 68  LVTEVRVYNWFANRRKEEAFR 88

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99

 Score = 47.1 bits (111), Expect = 8e-07
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 21/81 (25%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQI---------------------T 736
           K +R R  +     Q+L   ++   NP  ++ E + +                       
Sbjct: 8   KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67

Query: 737 GLSKRVTQVWFQNSRARQKKH 757
            +++     WF N R  +   
Sbjct: 68  LVTEVRVYNWFANRRKEEAFR 88

>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 Length = 80

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 684 SDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQ----LDSNPDGQDLERIAQITGLS 739
           S   + S +       KR RT FT EQ + + A  +         D + ++R  Q TG+ 
Sbjct: 2   SSGSSGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVP 61

Query: 740 KRVTQVWFQNSRARQKK 756
           ++V +VW  N++     
Sbjct: 62  RQVLKVWLHNNKHSGPS 78

>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 Length = 80

 Score = 43.8 bits (103), Expect = 7e-06
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQ----LDSNPDGQDLERIAQITGLS 100
           S+  + S +       KR RT FT EQ + + A  +         D + ++R  Q TG+ 
Sbjct: 2   SSGSSGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVP 61

Query: 101 KRVTQVWFQNSRARQKK 117
           ++V +VW  N++     
Sbjct: 62  RQVLKVWLHNNKHSGPS 78

>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 Length = 87

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 32  FQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSN---PDGQ 88
            Q + + DG   +         S    +  R    FT+E +++L++ F  +      D +
Sbjct: 3   TQKNKSADGLVFNVVTQDMINKSTKPYRGHR----FTKENVRILESWFAKNIENPYLDTK 58

Query: 89  DLERIAQITGLSKRVTQV--WFQNSRARQK 116
            LE + + T LS+   Q+  W  N R ++K
Sbjct: 59  GLENLMKNTSLSR--IQIKNWVSNRRRKEK 86

>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 Length = 87

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 681 TTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSN---PDGQDLERIAQITG 737
                    ++   +KS        FT+E +++L++ F  +      D + LE + + T 
Sbjct: 9   ADGLVFNVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTS 68

Query: 738 LSKRVTQV--WFQNSRARQK 755
           LS+   Q+  W  N R ++K
Sbjct: 69  LSR--IQIKNWVSNRRRKEK 86

>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 = 45.7 bits (108), Expect = 2e-06
 Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 10/78 (12%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGL 99
           +   T   S         +RT FT  QL  L+  F  +     + L R     IA    L
Sbjct: 19  NPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFN-----KYLSRARRVEIAATLEL 73

Query: 100 SKRVTQVWFQNSRARQKK 117
           ++   ++WFQN R +QKK
Sbjct: 74  NETQVKIWFQNRRMKQKK 91

>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 = 44.9 bits (106), Expect = 5e-06
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 681 TTSSDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQI 735
              +       S         +RT FT  QL  L+  F  +     + L R     IA  
Sbjct: 16  VKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFN-----KYLSRARRVEIAAT 70

Query: 736 TGLSKRVTQVWFQNSRARQKK 756
             L++   ++WFQN R +QKK
Sbjct: 71  LELNETQVKIWFQNRRMKQKK 91

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV--WFQNSRARQKK 117
           ++ RT FT  QL  L+  F+        +    +    L++  TQV  WFQN RA+ K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTE--TQVKIWFQNRRAKAKR 57

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV--WFQNSRARQKK 756
           ++ RT FT  QL  L+  F+        +    +    L++  TQV  WFQN RA+ K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTE--TQVKIWFQNRRAKAKR 57

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 19/66 (28%), Positives = 29/66 (43%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH 120
           +R RTTFT  Q+  L+ +F          L  ++    L     ++WF+N R R K    
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 121 TGKMKS 126
             K +S
Sbjct: 63  QHKDQS 68

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 19/66 (28%), Positives = 29/66 (43%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH 759
           +R RTTFT  Q+  L+ +F          L  ++    L     ++WF+N R R K    
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 760 TGKMKS 765
             K +S
Sbjct: 63  QHKDQS 68

>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 = 43.5 bits (103), Expect = 5e-06
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 10/62 (16%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQVWFQNSRARQ 115
           +R RT FT +QL  L+  F  +       + R     +A    L +   +VWFQN R + 
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKE-----NYVSRPRRCELAAQLNLPESTIKVWFQNRRMKD 56

Query: 116 KK 117
           K+
Sbjct: 57  KR 58

>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 = 43.5 bits (103), Expect = 5e-06
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 10/62 (16%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQVWFQNSRARQ 754
           +R RT FT +QL  L+  F  +       + R     +A    L +   +VWFQN R + 
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKE-----NYVSRPRRCELAAQLNLPESTIKVWFQNRRMKD 56

Query: 755 KK 756
           K+
Sbjct: 57  KR 58

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV--WFQNSRARQKKH 118
           ++ R  F++ Q+  L+  F+        + E +A +  L+   TQV  WFQN R + K+ 
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTP--TQVKIWFQNHRYKMKRQ 60

Query: 119 LHTGKMK 125
                 +
Sbjct: 61  AKDKAAQ 67

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV--WFQNSRARQKKH 757
           ++ R  F++ Q+  L+  F+        + E +A +  L+   TQV  WFQN R + K+ 
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTP--TQVKIWFQNHRYKMKRQ 60

Query: 758 LHTGKMK 764
                 +
Sbjct: 61  AKDKAAQ 67

>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 = 43.2 bits (102), Expect = 8e-06
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 54  SHSKSKAKRVRTTFTEEQLQVLQANFQLDS-NPDGQDLERIAQITGLSKRVTQVWFQNSR 112
           S   S   +       E    L+  F   +  PD + L+ +++    S R  Q WF++ R
Sbjct: 2   SSGSSGGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61

Query: 113 ARQKK 117
            + K 
Sbjct: 62  NQDKP 66

>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 = 43.2 bits (102), Expect = 8e-06
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 693 SHSKSKAKRVRTTFTEEQLQVLQANFQLDS-NPDGQDLERIAQITGLSKRVTQVWFQNSR 751
           S   S   +       E    L+  F   +  PD + L+ +++    S R  Q WF++ R
Sbjct: 2   SSGSSGGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61

Query: 752 ARQKK 756
            + K 
Sbjct: 62  NQDKP 66

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73

 Score = 43.3 bits (102), Expect = 9e-06
 Identities = 20/71 (28%), Positives = 36/71 (50%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
              + ++ R  +T+ QL+ L+  +  +         RI+  T LS+R   +WFQN R ++
Sbjct: 3   HMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKE 62

Query: 116 KKHLHTGKMKS 126
           KK ++  K  S
Sbjct: 63  KKVINKLKTTS 73

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73

 Score = 43.3 bits (102), Expect = 9e-06
 Identities = 20/71 (28%), Positives = 36/71 (50%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
              + ++ R  +T+ QL+ L+  +  +         RI+  T LS+R   +WFQN R ++
Sbjct: 3   HMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKE 62

Query: 755 KKHLHTGKMKS 765
           KK ++  K  S
Sbjct: 63  KKVINKLKTTS 73

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 48  HTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKR 102
           H  + + ++  + KR RT++T  Q   L+  F  +     + L R     IA    L++R
Sbjct: 16  HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFN-----RYLTRRRRIEIAHALSLTER 70

Query: 103 VTQVWFQNSRARQKK 117
             ++WFQN R + KK
Sbjct: 71  QIKIWFQNRRMKWKK 85

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88

 Score = 41.8 bits (98), Expect = 5e-05
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 10/72 (13%)

Query: 690 SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQ 744
           + + ++  + KR RT++T  Q   L+  F  +     + L R     IA    L++R  +
Sbjct: 19  TSTVNANGETKRQRTSYTRYQTLELEKEFHFN-----RYLTRRRRIEIAHALSLTERQIK 73

Query: 745 VWFQNSRARQKK 756
           +WFQN R + KK
Sbjct: 74  IWFQNRRMKWKK 85

>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 Length = 80

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 684 SDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQ----LDSNPDGQDLERIAQITGLS 739
           S   + S  S S    KR RT FT EQ + + A  +         D   +E+    TG+ 
Sbjct: 2   SSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVR 61

Query: 740 KRVTQVWFQNSRARQKK 756
           ++V ++W  N++     
Sbjct: 62  RQVLKIWMHNNKNSGPS 78

>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 Length = 80

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQ----LDSNPDGQDLERIAQITGLS 100
           S+  + S  S S    KR RT FT EQ + + A  +         D   +E+    TG+ 
Sbjct: 2   SSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVR 61

Query: 101 KRVTQVWFQNSRARQKK 117
           ++V ++W  N++     
Sbjct: 62  RQVLKIWMHNNKNSGPS 78

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 11/67 (16%), Positives = 27/67 (40%)

Query: 58  SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
                  +  +  Q+  L+  F         +   +A+   L++   ++WFQN R + K+
Sbjct: 2   GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 118 HLHTGKM 124
              + ++
Sbjct: 62  KQLSSEL 68

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 11/67 (16%), Positives = 27/67 (40%)

Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
                  +  +  Q+  L+  F         +   +A+   L++   ++WFQN R + K+
Sbjct: 2   GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 757 HLHTGKM 763
              + ++
Sbjct: 62  KQLSSEL 68

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 10/70 (14%)

Query: 53  SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQVW 107
            + +    +R R T+T  Q   L+  F  +       L R     +A    L++R  ++W
Sbjct: 13  IAGTNGLRRRGRQTYTRYQTLELEKEFHTN-----HYLTRRRRIEMAHALSLTERQIKIW 67

Query: 108 FQNSRARQKK 117
           FQN R + KK
Sbjct: 68  FQNRRMKLKK 77

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 10/70 (14%)

Query: 692 SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQVW 746
            + +    +R R T+T  Q   L+  F  +       L R     +A    L++R  ++W
Sbjct: 13  IAGTNGLRRRGRQTYTRYQTLELEKEFHTN-----HYLTRRRRIEMAHALSLTERQIKIW 67

Query: 747 FQNSRARQKK 756
           FQN R + KK
Sbjct: 68  FQNRRMKLKK 77

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV--WFQNSRARQK 116
           ++ R  F++ Q+  L+  F+        + +++A +  L+   TQV  WFQN R + K
Sbjct: 3   RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTS--TQVKIWFQNRRYKSK 58

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQV--WFQNSRARQK 755
           ++ R  F++ Q+  L+  F+        + +++A +  L+   TQV  WFQN R + K
Sbjct: 3   RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTS--TQVKIWFQNRRYKSK 58

>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 = 41.4 bits (97), Expect = 3e-05
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  ++ R  +++ QL+ L+  +  +         +I+  T LS+R   +WFQN R ++
Sbjct: 3   SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62

Query: 116 KK 117
           KK
Sbjct: 63  KK 64

>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 = 41.4 bits (97), Expect = 3e-05
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  ++ R  +++ QL+ L+  +  +         +I+  T LS+R   +WFQN R ++
Sbjct: 3   SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62

Query: 755 KK 756
           KK
Sbjct: 63  KK 64

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 10/64 (15%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQVWFQNSRA 113
             KR RT +T  QL  L+  F  +     + + R     +A +  L++R  ++WFQN R 
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLFN-----KYISRPRRVELAVMLNLTERHIKIWFQNRRM 56

Query: 114 RQKK 117
           + KK
Sbjct: 57  KWKK 60

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 10/64 (15%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLER-----IAQITGLSKRVTQVWFQNSRA 752
             KR RT +T  QL  L+  F  +     + + R     +A +  L++R  ++WFQN R 
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLFN-----KYISRPRRVELAVMLNLTERHIKIWFQNRRM 56

Query: 753 RQKK 756
           + KK
Sbjct: 57  KWKK 60

>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* Length = 83

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQV--WFQNSRARQ 115
                 FT+E +++L++ F  +      D + LE + + T LS+   Q+  W    RA++
Sbjct: 3   PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSR--IQIKNWVAARRAKE 60

Query: 116 KKH 118
           K  
Sbjct: 61  KTI 63

>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* Length = 83

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQV--WFQNSRARQ 754
                 FT+E +++L++ F  +      D + LE + + T LS+   Q+  W    RA++
Sbjct: 3   PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSR--IQIKNWVAARRAKE 60

Query: 755 KKH 757
           K  
Sbjct: 61  KTI 63

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens} Length = 65

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 3/58 (5%)

Query: 615 FGAKCSKCCRGIASSDWVRKARDHVYHL--ACFACEACKRQLSTGEEFALHEDRVLCK 670
               C  C   I          +  +H    CF C  C + L  G++F   E  V C 
Sbjct: 1   HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCS 57

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 4/65 (6%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD 678
           C KC   I         ++  YH   F C  C ++L    +    +  + C   + ++  
Sbjct: 18  CQKCHAIIDEQ--PLIFKNDPYHPDHFNCANCGKEL--TADARELKGELYCLPCHDKMGV 73

Query: 679 GGTTS 683
            G +S
Sbjct: 74  SGPSS 78

>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 = 39.5 bits (92), Expect = 2e-04
 Identities = 15/62 (24%), Positives = 29/62 (46%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
                ++ R  +T+ Q   L+  F  +          +A++  L++R  ++WFQN R + 
Sbjct: 9   HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68

Query: 116 KK 117
           KK
Sbjct: 69  KK 70

>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 = 39.5 bits (92), Expect = 2e-04
 Identities = 15/62 (24%), Positives = 29/62 (46%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
                ++ R  +T+ Q   L+  F  +          +A++  L++R  ++WFQN R + 
Sbjct: 9   HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68

Query: 755 KK 756
           KK
Sbjct: 69  KK 70

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 11/54 (20%), Positives = 24/54 (44%)

Query: 65  TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           T+F+  Q+  L+  F         +   +A+   ++    + WFQN R + ++ 
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 11/54 (20%), Positives = 24/54 (44%)

Query: 704 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           T+F+  Q+  L+  F         +   +A+   ++    + WFQN R + ++ 
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 28/57 (49%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           KR R T+T  Q   L+  F  +     +    IA    L++R  ++WFQN R + KK
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59

>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 28/57 (49%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           KR R T+T  Q   L+  F  +     +    IA    L++R  ++WFQN R + KK
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 58  SKAKRVRTTFTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQV--WFQNSR 112
           S          ++  ++L   F    +   P  +  E +A+  G++   +QV  WF N R
Sbjct: 1   SSGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITV--SQVSNWFGNKR 58

Query: 113 ARQKK 117
            R KK
Sbjct: 59  IRYKK 63

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQV--WFQNSR 751
           S          ++  ++L   F    +   P  +  E +A+  G++   +QV  WF N R
Sbjct: 1   SSGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITV--SQVSNWFGNKR 58

Query: 752 ARQKK 756
            R KK
Sbjct: 59  IRYKK 63

>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 Length = 60

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 7/56 (12%)

Query: 67  FTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQV--WFQNSRARQKK 117
           FT+E +++L++ F  +      D + LE + + T LS+   Q+  W  N R ++K 
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSR--IQIKNWVSNRRRKEKT 58

>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 Length = 60

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 7/56 (12%)

Query: 706 FTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQV--WFQNSRARQKK 756
           FT+E +++L++ F  +      D + LE + + T LS+   Q+  W  N R ++K 
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSR--IQIKNWVSNRRRKEKT 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	768
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.88
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.79
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.78
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.78
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.76
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.67
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.66
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.66
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.64
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.64
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.63
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.63
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.62
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.62
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.62
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.62
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.62
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.62
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.61
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.61
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.61
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.61
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.61
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.6
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.6
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.6
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.6
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.6
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.6
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.6
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.6
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.6
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.6
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.6
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.6
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.59
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.59
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.59
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.59
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.59
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.59
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.58
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.58
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.57
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.57
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.56
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.56
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.56
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.56
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.56
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.56
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.56
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.55
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.55
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.55
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.55
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.55
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.55
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.55
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.55
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.55
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.55
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.54
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.54
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.54
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.54
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.54
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.54
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.54
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.54
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.54
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.54
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.54
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.53
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.53
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.53
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.53
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.53
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.53
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.53
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.53
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.52
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.52
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.52
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.51
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.51
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.51
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.51
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.51
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.51
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.51
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.51
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.5
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.5
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.5
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.5
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.5
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.5
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.5
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.5
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.49
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.49
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.49
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.49
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.49
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.48
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.48
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.48
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.47
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.47
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.47
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.47
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.47
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.47
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.46
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.46
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.46
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.46
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.45
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.45
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.45
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.45
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.45
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.45
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.45
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.44
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.44
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.43
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.43
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.42
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.42
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.42
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.42
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.41
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.41
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.4
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.4
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.4
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.39
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.39
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.38
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.38
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.38
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.38
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.38
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.38
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.37
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.37
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.37
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.37
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.35
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.34
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.33
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.33
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.32
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.31
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.31
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.3
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.3
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.3
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.29
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.29
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.29
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.26
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.25
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.23
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.23
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.22
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.21
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.2
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.19
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.18
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.18
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.18
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.17
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.17
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.15
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.11
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.1
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.09
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.09
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.06
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.06
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.05
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.04
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.03
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.02
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.01
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.0
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.0
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.99
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	98.98
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	98.96
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.91
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.89
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.87
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.87
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.84
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	98.75
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	98.73
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	98.69
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	98.66
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	98.63
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	98.62
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	98.57
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	98.54
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	98.52
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	98.5
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.49
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	98.47
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	98.43
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	98.4
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	98.4
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	98.39
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	98.39
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	98.38
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	98.36
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	98.36
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.35
2cuq_A	80	Four and A half LIM domains 3; structural genomics	98.35
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	98.34
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	98.31
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	98.28
2cor_A	79	Pinch protein; LIM domain, particularly interestin	98.23
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	98.23
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	98.23
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	98.2
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	98.19
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	98.12
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	98.07
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	98.05
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	98.05
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	97.95
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	97.87
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	97.84
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	97.78
2co8_A	82	NEDD9 interacting protein with calponin homology a	97.77
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	97.67
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	97.38
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	97.25
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	96.4
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	80.99

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=99.88  E-value=1.2e-24  Score=213.98  Aligned_cols=157  Identities=27%  Similarity=0.429  Sum_probs=125.8

Q ss_pred             ccchhhhhhhhhhHH-HHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIALVL-SEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~-~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .+.|..|.+.|.+.. +.+.|+      .||+.||.|+.|+..+.                  +..|.+++.+    ||.
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~------~wH~~CF~C~~C~~~L~------------------~~~f~~~g~~----yC~   57 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDR------HWHSKCLKCSDCHVPLA------------------ERCFSRGESV----YCK   57 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSC------EECTTTSBCTTTCCBCC------------------SCCEESSSCE----ECH
T ss_pred             CCccccCCCccCCcEEEEECCc------EEccccCccCCCCCcCC------------------CCCcccCCee----eec
Confidence            356999999999874 456677      99999999999995433                  1226778888    456


Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEe-ecCcccccccccccccCCcccCCCC
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFAL-HEDRVLCKSHYLELVDGGTTSSDDG  687 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~-~~g~~~C~~~y~e~~~~~~~s~~~g  687 (768)
                      .||.++|+++|.+|+++|.+.+.++.|+++.||.+||+|..|+++|..|+.|+. .++++||+.||.++...+.    + 
T Consensus        58 ~~y~~~f~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~~----~-  132 (169)
T 2rgt_A           58 DDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGGS----G-  132 (169)
T ss_dssp             HHHHHHHSCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC-------
T ss_pred             ccccccccccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhccC----C-
Confidence            999999999999999999988888999999999999999999999977888865 5789999999988776421    0 


Q ss_pred             CCcccccCCCccccccccccHHHHHHHhhccccCCCCCHH
Q psy17256        688 ADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQ  727 (768)
Q Consensus       688 ~~~~~~~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~  727 (768)
                              ..+.+|+||.|+..|++.|+..|+.++||...
T Consensus       133 --------~~~~~rprt~~~~~q~~~l~~~f~~~~~~~~~  164 (169)
T 2rgt_A          133 --------GSGGSGGGTPMVAASPERHDGGLQANPVEVQS  164 (169)
T ss_dssp             ----------------EEEECCCCEECCSSCCCCCCCCCC
T ss_pred             --------CCCCcCCCCcccHHHHHHHHHHHhCCCCcccc
Confidence                    13467899999999999999999999998754

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=99.79  E-value=1.3e-20  Score=177.34  Aligned_cols=123  Identities=20%  Similarity=0.435  Sum_probs=105.7

Q ss_pred             cchhhhhhhhhhH-HHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        531 LEFHSFLKRIALV-LSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       531 ~~C~~c~k~Ia~~-~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      +.|..|.++|.++ ++.+.++      .||+.||+|+.|+..+.               +....+|.+++.+|    |..
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~------~wH~~CF~C~~C~~~L~---------------~~~~~~~~~~g~~y----C~~   57 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQ------YWHEDCLSCDLCGCRLG---------------EVGRRLYYKLGRKL----CRR   57 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTE------EEETTTCBCTTTCCBCS---------------STTCCEEEETTEEE----CHH
T ss_pred             ccCcCCCCEeCCcEEEEECCC------cccHHHcccCcCCCccc---------------cCCCeEEEECCEEe----ecC
Confidence            4599999999987 4667787      99999999999995432               11124678888994    569


Q ss_pred             hhhhhccc--ccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        610 ICFRSFGA--KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       610 ~y~~~f~~--~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ||.++|++  +|.+|+++|.+.|.+|.|+++.||++||+|..|+++|..|+.|++.++++||..||.+++.
T Consensus        58 ~y~~~~~~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~  128 (131)
T 2xjy_A           58 DYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTK  128 (131)
T ss_dssp             HHHHHHCCCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHH
T ss_pred             chhhhCCCccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhh
Confidence            99999999  9999999999878899999999999999999999999778899999999999999987654

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=99.78  E-value=2.8e-20  Score=173.79  Aligned_cols=120  Identities=14%  Similarity=0.236  Sum_probs=102.9

Q ss_pred             ccchhhhhhhhhh-HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIAL-VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~-~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      ++.|..|.+.|.+ .++.+.|+      .||+.||.|+.|+..+.   |              ..++.+++.+|    |.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---~--------------~~f~~~~g~~y----C~   55 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQ------NWHLKHFCCFDCDSILA---G--------------EIYVMVNDKPV----CK   55 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTE------EECGGGSBCTTTCCBCT---T--------------SEEEEETTEEE----EH
T ss_pred             CCCCccCCCEeCCceEEeeCCC------CccCCCCCcCCCCCCCC---c--------------CEEEeECCEEe----ch
Confidence            4669999999985 45667787      99999999999995432   1              23577888884    56


Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceec--ccCccccccccccCCCCceEeecCcccccccccccc
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYH--LACFACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H--~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      .||.++|+++|.+|+++|.+++.+|.|+++.||  ++||+|..|+++| .|+.|++.++++||+.||.+++
T Consensus        56 ~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l-~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           56 PCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             HHHHHHSCCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBC-TTSEEEEETTEEESSHHHHHSC
T ss_pred             HHhCcCcCccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCcc-CCCeeEeECCEEcchHHhhhhc
Confidence            999999999999999999987789999999999  9999999999999 5889999999999998887543

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=99.78  E-value=2.2e-20  Score=186.74  Aligned_cols=123  Identities=24%  Similarity=0.420  Sum_probs=105.6

Q ss_pred             cchhhhhhhhhhHH-HHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        531 LEFHSFLKRIALVL-SEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       531 ~~C~~c~k~Ia~~~-~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      +.|..|.+.|.+.. +.+.++      .||+.||.|+.|+..+..          +    | ..+|.+++.+|    |..
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~------~wH~~CF~C~~C~~~L~~----------~----g-~~~~~~~g~~y----C~~   60 (188)
T 1rut_X            6 KRCAGCGGKIADRFLLYAMDS------YWHSRCLKCSSCQAQLGD----------I----G-TSSYTKSGMIL----CRN   60 (188)
T ss_dssp             CBBTTTCCBCCCSEEEEETTE------EECGGGCBCTTTCCBHHH----------H----C-SEEEEETTEEE----CHH
T ss_pred             CcCccCCCEeCCceeEEecCc------EecccCcccCCCCccccc----------C----C-ceEEEeCCccc----ccc
Confidence            45999999999874 567777      999999999999964331          0    1 24678888884    569


Q ss_pred             hhhhhccc--ccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        610 ICFRSFGA--KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       610 ~y~~~f~~--~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ||.++|++  +|.+|+++|.+.|.+|.|+++.||.+||+|..|+++|..|+.|++.++++||+.||.+++.
T Consensus        61 cy~~~~~~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~  131 (188)
T 1rut_X           61 DYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALI  131 (188)
T ss_dssp             HHHHHHSCCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC
T ss_pred             ccccccccCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhc
Confidence            99999999  7999999999888899999999999999999999999778899999999999999987664

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus}

Probab=99.76  E-value=8.5e-20  Score=181.54  Aligned_cols=120  Identities=32%  Similarity=0.526  Sum_probs=101.7

Q ss_pred             ccchhhhhhhhhhHH-HHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIALVL-SEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~-~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .+.|..|.++|.+.. +.+.++      .||+.||.|+.|+..+.                  +..|.+++.+|    |.
T Consensus        60 ~~~C~~C~~~I~~~~~~~a~~~------~wH~~CF~C~~C~~~L~------------------~~~f~~~g~~y----C~  111 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFILKALDR------HWHSKCLKCSDCHVPLA------------------ERCFSRGESVY----CK  111 (182)
T ss_dssp             CCBCBTSSSBCCCSEEEEETTE------EECSSTTSCTTTCCCCS------------------SCCEEETTEEE----CH
T ss_pred             CCcCccCCCCccCceeEEecCC------eEccccCccCCCCCccC------------------CCceeECCEee----ec
Confidence            356999999999873 456777      99999999999995433                  12267888884    56


Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEe-ecCcccccccccccc
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFAL-HEDRVLCKSHYLELV  677 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~-~~g~~~C~~~y~e~~  677 (768)
                      .||.++|+++|.+|+++|.+.+.++.|.++.||.+||+|..|+++|..|+.|+. .++++||+.||.++.
T Consensus       112 ~~y~~~f~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~~  181 (182)
T 2jtn_A          112 DDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  181 (182)
T ss_dssp             HHHHHTTSCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHHT
T ss_pred             CccccccccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHhh
Confidence            899999999999999999988888999999999999999999999977888865 578999999997643

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A

Probab=99.67  E-value=6.1e-18  Score=169.57  Aligned_cols=121  Identities=14%  Similarity=0.233  Sum_probs=99.4

Q ss_pred             ccchhhhhhhhh-hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIA-LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia-~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      ++.|..|.+.|. ...+.+.++      .||+.||.|+.|+..+.               +  ..++.+++.+|    |.
T Consensus         7 ~~~C~~C~~~I~~~~~v~a~g~------~wH~~CF~C~~C~~~L~---------------~--~~~~~~~g~~y----C~   59 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEEVQCEGS------SFHKSCFLCMVCKKNLD---------------S--TTVAVHGDEIY----CK   59 (192)
T ss_dssp             CEECTTTCCEECSSCCEEETTE------EECTTTCBCTTTCCBCC---------------S--SSEEEETTEEE----EH
T ss_pred             CCcCccCCCeecceeEEEeCCc------eecCCCCcCcccCCcCC---------------C--CeeEecCCEee----Ch
Confidence            356999999995 445567777      99999999999996533               1  23677888884    56


Q ss_pred             hhhhhhcccc------------------------------------------------cccCCCCCCCCcceeeecCcee
Q psy17256        609 LICFRSFGAK------------------------------------------------CSKCCRGIASSDWVRKARDHVY  640 (768)
Q Consensus       609 ~~y~~~f~~~------------------------------------------------C~~C~~~I~~~e~~~~a~~~~~  640 (768)
                      .||.++|+++                                                |.+|+++|.+.+. +.|+++.|
T Consensus        60 ~cy~~~f~~~c~~c~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~a~~~~~  138 (192)
T 1b8t_A           60 SCYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEK-VIGAGKSW  138 (192)
T ss_dssp             HHHHHHHSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSSC-EEETTEEE
T ss_pred             hhhHhhcCccccccccccccEecCCCcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcEE-EecCCCcc
Confidence            8999999887                                                7789999987655 45999999


Q ss_pred             cccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        641 HLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       641 H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      |.+||+|..|+++|. +..|+..++++||+.||.++...
T Consensus       139 H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~~  176 (192)
T 1b8t_A          139 HKSCFRCAKCGKSLE-STTLADKDGEIYCKGCYAKNFGP  176 (192)
T ss_dssp             CTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHTCC
T ss_pred             chhcCCccccCCCCC-CCcccccCCEEeCHHHHHHhcCC
Confidence            999999999999995 45699999999999999887653

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.66  E-value=5.8e-17  Score=140.38  Aligned_cols=67  Identities=30%  Similarity=0.481  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ...++.+|.||.||..|+..||..|..++||+..+|.+||..+||++.+|+|||||||+|+|+..+.
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~   83 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN   83 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            4456788899999999999999999999999999999999999999999999999999999997654

>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=99.66  E-value=6.1e-17  Score=138.90  Aligned_cols=66  Identities=33%  Similarity=0.425  Sum_probs=61.6

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ...++.+|.||.||..|+..||..|..++||+..+|++||..+||++.+|+|||||||+|+|+...
T Consensus        12 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            345677889999999999999999999999999999999999999999999999999999998654

>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=99.64  E-value=1.1e-16  Score=137.37  Aligned_cols=66  Identities=50%  Similarity=0.755  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..+.+.+|.||.||..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            345677889999999999999999999999999999999999999999999999999999998654

>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=99.64  E-value=8.4e-17  Score=137.76  Aligned_cols=62  Identities=29%  Similarity=0.415  Sum_probs=58.6

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhh----CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQL----DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~----~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ..+++||.||.||..|+..||..|+.    ++||+..+|++||..+||++++|+|||||||+|+|+
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            34577889999999999999999999    999999999999999999999999999999999886

>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=99.63  E-value=1.2e-16  Score=133.47  Aligned_cols=64  Identities=27%  Similarity=0.459  Sum_probs=60.0

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .++.||.|+.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            3567888999999999999999999999999999999999999999999999999999998654

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=2.5e-16  Score=135.05  Aligned_cols=67  Identities=37%  Similarity=0.500  Sum_probs=62.1

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      .++.||.|+.||..|+..||..|..++||+..+|++||..+||++.+|+|||||||+|+|++.+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~   70 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQ   70 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccC
Confidence            3567889999999999999999999999999999999999999999999999999999999766443

>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=99.62  E-value=1.5e-16  Score=135.98  Aligned_cols=61  Identities=28%  Similarity=0.464  Sum_probs=57.3

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhh-----CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQL-----DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~-----~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ...++||.||.||..|+..|| .|..     ++||+..+|++||..+||++++|+|||||||+|+|+
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            345678899999999999999 8999     999999999999999999999999999999999886

>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=99.62  E-value=2.1e-16  Score=132.03  Aligned_cols=64  Identities=36%  Similarity=0.618  Sum_probs=60.3

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .++.+|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            4567889999999999999999999999999999999999999999999999999999998654

>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=99.62  E-value=1.8e-16  Score=132.40  Aligned_cols=64  Identities=30%  Similarity=0.611  Sum_probs=60.4

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .++.+|.||.||..|+..||..|+.++||+..++.+||..+||++.+|+|||||||+|+|+..+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            4567889999999999999999999999999999999999999999999999999999999755

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=2.3e-16  Score=131.82  Aligned_cols=63  Identities=37%  Similarity=0.546  Sum_probs=59.5

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ++.+|.|+.||..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            456888999999999999999999999999999999999999999999999999999998654

>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=99.62  E-value=3e-16  Score=133.55  Aligned_cols=67  Identities=24%  Similarity=0.408  Sum_probs=61.9

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      .+++++|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+.....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            4556788899999999999999999999999999999999999999999999999999999876543

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.62  E-value=1.8e-16  Score=129.66  Aligned_cols=61  Identities=31%  Similarity=0.482  Sum_probs=56.3

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      ..+|.|+.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+..
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            4678899999999999999999999999999999999999999999999999999999864

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.61  E-value=1.3e-16  Score=129.92  Aligned_cols=60  Identities=30%  Similarity=0.521  Sum_probs=53.1

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      +++|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            567889999999999999999999999999999999999999999999999999999985

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.1e-16  Score=131.97  Aligned_cols=64  Identities=30%  Similarity=0.425  Sum_probs=59.9

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .++.||.|+.||..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            4567889999999999999999999999999999999999999999999999999999998643

>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=99.61  E-value=4.8e-16  Score=133.34  Aligned_cols=66  Identities=47%  Similarity=0.825  Sum_probs=61.4

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ++.||.||.||..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|++.....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~   70 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQE   70 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999999999999999999999999999765443

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.61  E-value=3.2e-16  Score=134.45  Aligned_cols=66  Identities=35%  Similarity=0.536  Sum_probs=61.4

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ++.+|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+..+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            467888999999999999999999999999999999999999999999999999999999765443

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3

Probab=99.61  E-value=8.6e-17  Score=144.07  Aligned_cols=95  Identities=15%  Similarity=0.140  Sum_probs=80.8

Q ss_pred             ccchhhhhhhhh--hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccc
Q psy17256        530 HLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLS  607 (768)
Q Consensus       530 g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC  607 (768)
                      ++.|..|.++|.  +..+.+.++      .||..||.|+.|+..+.   |              ..++.+++.+|    |
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---~--------------~~~~~~~g~~y----C   57 (101)
T 2cup_A            5 SSGCVECRKPIGADSKEVHYKNR------FWHDTCFRCAKCLHPLA---N--------------ETFVAKDNKIL----C   57 (101)
T ss_dssp             CCBCSSSCCBCCSSSCEEEETTE------EEETTTCCCSSSCCCTT---S--------------SCCEEETTEEE----C
T ss_pred             CCcCcccCCcccCCceEEEECcc------ChhhcCCcccccCCCCC---c--------------CeeECcCCEEE----C
Confidence            456999999996  566777787      99999999999995432   1              23577888885    5


Q ss_pred             hhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccc
Q psy17256        608 VLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACK  651 (768)
Q Consensus       608 ~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~  651 (768)
                      ..||.++|+++|.+|+++|.++|.+|.|+++.||++||+|..|+
T Consensus        58 ~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           58 NKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             HHHHTTCCCCBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             hhHhhhhcCCccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence            69999999999999999999888899999999999999999985

>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=99.60  E-value=5.2e-16  Score=130.20  Aligned_cols=64  Identities=25%  Similarity=0.296  Sum_probs=59.2

Q ss_pred             CCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCCCC
Q psy17256         63 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  126 (768)
Q Consensus        63 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~~~  126 (768)
                      .|+.||.+|+.+||+.|..++||+..+|++||..+||++++|+|||||||+|+|+....|....
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w~~~~   69 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDN   69 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSSTTCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHHHHHH
Confidence            3567999999999999999999999999999999999999999999999999999877776544

>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=99.60  E-value=4.1e-16  Score=132.71  Aligned_cols=65  Identities=23%  Similarity=0.407  Sum_probs=60.8

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..++.+|.||.||..|+..||..|..++||+..+|.+||..+||++.+|+|||||||+|+|+..+
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k   73 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhh
Confidence            34567889999999999999999999999999999999999999999999999999999998754

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.60  E-value=3.7e-16  Score=129.70  Aligned_cols=65  Identities=28%  Similarity=0.435  Sum_probs=60.8

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      +||.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+.......
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   66 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD   66 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccccc
Confidence            57889999999999999999999999999999999999999999999999999999998765543

>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=99.60  E-value=2.3e-16  Score=135.28  Aligned_cols=66  Identities=33%  Similarity=0.434  Sum_probs=61.7

Q ss_pred             CCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ..++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||..+.
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~s   78 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPS   78 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccCC
Confidence            356778899999999999999999999999999999999999999999999999999999997653

>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=99.60  E-value=2.6e-16  Score=127.80  Aligned_cols=58  Identities=33%  Similarity=0.556  Sum_probs=53.4

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      .||.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            5788999999999999999999999999999999999999999999999999999997

>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=99.60  E-value=3.3e-16  Score=130.04  Aligned_cols=64  Identities=31%  Similarity=0.422  Sum_probs=60.0

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      +||.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+..+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   65 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG   65 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccccC
Confidence            4788999999999999999999999999999999999999999999999999999999766443

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.60  E-value=5.6e-16  Score=131.17  Aligned_cols=68  Identities=43%  Similarity=0.560  Sum_probs=62.8

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ..++++|.||.|+..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+..+.+.
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q   72 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQ   72 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhh
Confidence            34567889999999999999999999999999999999999999999999999999999999876543

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.60  E-value=5.8e-16  Score=130.39  Aligned_cols=66  Identities=27%  Similarity=0.461  Sum_probs=61.0

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      ..+.+|.|+.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+.....
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            345788899999999999999999999999999999999999999999999999999999975543

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.60  E-value=2.5e-16  Score=136.39  Aligned_cols=67  Identities=30%  Similarity=0.481  Sum_probs=62.6

Q ss_pred             cCCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        694 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       694 ~~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ...++.++.||.|+..|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+.
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~   83 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN   83 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            3456788899999999999999999999999999999999999999999999999999999998754

>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=99.60  E-value=3.2e-16  Score=134.73  Aligned_cols=65  Identities=43%  Similarity=0.580  Sum_probs=59.6

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..++++|.||.||..|+..||..|..++||+..+|.+||..+||++.+|++||||||+|+|++..
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            35677889999999999999999999999999999999999999999999999999999998754

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.60  E-value=4.2e-16  Score=136.13  Aligned_cols=64  Identities=30%  Similarity=0.465  Sum_probs=55.7

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      ..++.+|.||.||..|+..||..|..++||+..+|.+||..+||++.+|+|||||||+|+|++.
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            3456788999999999999999999999999999999999999999999999999999999864

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.60  E-value=7.3e-16  Score=135.95  Aligned_cols=69  Identities=22%  Similarity=0.382  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         55 HSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        55 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ..++++||.||.||..|+..||..|..++||+..+|.+||..+||++.+|+|||||||+|+|+......
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             SCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            345677889999999999999999999999999999999999999999999999999999999766543

>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=99.59  E-value=2.6e-16  Score=130.67  Aligned_cols=64  Identities=41%  Similarity=0.549  Sum_probs=60.4

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      +++|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+..+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            5688999999999999999999999999999999999999999999999999999999976643

>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=99.59  E-value=6.1e-16  Score=129.18  Aligned_cols=63  Identities=27%  Similarity=0.434  Sum_probs=59.0

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .+.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+...
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            356778999999999999999999999999999999999999999999999999999998654

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.59  E-value=4.8e-16  Score=124.86  Aligned_cols=57  Identities=28%  Similarity=0.493  Sum_probs=55.4

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ||.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            578999999999999999999999999999999999999999999999999999987

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.59  E-value=6.9e-16  Score=128.08  Aligned_cols=64  Identities=22%  Similarity=0.432  Sum_probs=60.1

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      +||.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+..+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~~   65 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHhh
Confidence            5788999999999999999999999999999999999999999999999999999999776543

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.59  E-value=3.2e-16  Score=132.69  Aligned_cols=70  Identities=43%  Similarity=0.568  Sum_probs=65.6

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccCC
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  765 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~~  765 (768)
                      .+++++.|+.|+.+|+..|+..|..++||+..++..||..+||++.+|+|||||||+|+||+++.+++++
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q~qq   75 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQMQQ   75 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCSSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhhccC
Confidence            4567888999999999999999999999999999999999999999999999999999999999887753

>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=99.59  E-value=4.5e-16  Score=128.47  Aligned_cols=61  Identities=43%  Similarity=0.723  Sum_probs=58.2

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      +++|.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            4678899999999999999999999999999999999999999999999999999999864

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.58  E-value=7e-16  Score=124.79  Aligned_cols=58  Identities=31%  Similarity=0.509  Sum_probs=55.6

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      ||.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|++
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            5789999999999999999999999999999999999999999999999999999985

>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=99.58  E-value=4.9e-16  Score=133.23  Aligned_cols=65  Identities=51%  Similarity=0.771  Sum_probs=61.1

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ..+.++.||.|+.+|+..|+..|..++||+..++..||.++||++.+|+|||||||+|+||+...
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   78 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPS   78 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhccC
Confidence            46678899999999999999999999999999999999999999999999999999999997643

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=6.7e-16  Score=132.41  Aligned_cols=63  Identities=19%  Similarity=0.300  Sum_probs=59.5

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhC----CCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLD----SNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~----~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      .++.+|.||.||..|+.+||..|+.+    +||+..+|++||..+||++.+|+|||||||+|+|+..
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            45678899999999999999999999    9999999999999999999999999999999999853

>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=99.57  E-value=7.3e-16  Score=132.46  Aligned_cols=63  Identities=27%  Similarity=0.430  Sum_probs=54.9

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ++.||.||.||..|+..||..|..++||+..+|++||..+||++++|+|||||||+|+|++.+
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            456889999999999999999999999999999999999999999999999999999998653

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.56  E-value=7.7e-16  Score=127.80  Aligned_cols=67  Identities=21%  Similarity=0.418  Sum_probs=62.8

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccCC
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  765 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~~  765 (768)
                      +++.|+.||.+|+..||..|..++||+...+..||..+||++.+|+|||||||+|+|+..+.+.+++
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~qq   68 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAAQQ   68 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCSSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHhhhcC
Confidence            4678999999999999999999999999999999999999999999999999999999988776653

>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=99.56  E-value=1.2e-15  Score=129.92  Aligned_cols=69  Identities=23%  Similarity=0.406  Sum_probs=63.6

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccC
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK  764 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~  764 (768)
                      .++.++.|+.|+..|+..||..|..++||+...+..||..+||++.+|+|||||||+|+|+........
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~~   74 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYE   74 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccccCC
Confidence            456788899999999999999999999999999999999999999999999999999999987766543

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-15  Score=125.91  Aligned_cols=62  Identities=37%  Similarity=0.584  Sum_probs=58.6

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .||.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..+.
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            36789999999999999999999999999999999999999999999999999999987654

>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=99.56  E-value=6.2e-16  Score=129.14  Aligned_cols=64  Identities=27%  Similarity=0.472  Sum_probs=60.2

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPS   68 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCTT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCCC
Confidence            4568889999999999999999999999999999999999999999999999999999997653

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.56  E-value=9.8e-16  Score=135.99  Aligned_cols=67  Identities=24%  Similarity=0.326  Sum_probs=58.1

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      .....+|.|+.||..|+..||..|..++||+..+|++||..+||++++|+|||||||+|+|+....|
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk~   87 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKW   87 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcccH
Confidence            3445677899999999999999999999999999999999999999999999999999999976544

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.1e-15  Score=127.68  Aligned_cols=64  Identities=36%  Similarity=0.546  Sum_probs=60.2

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||..+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPS   68 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTSTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCCC
Confidence            4567889999999999999999999999999999999999999999999999999999997654

>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=99.56  E-value=7.1e-16  Score=131.98  Aligned_cols=61  Identities=30%  Similarity=0.420  Sum_probs=58.1

Q ss_pred             CCccccccccccHHHHHHHhhcccc----CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQL----DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~----~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      .++++|.||.|+.+|+..||..|+.    ++||+..++++||..+||++++|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4667889999999999999999999    999999999999999999999999999999999876

>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=99.55  E-value=7.9e-16  Score=128.51  Aligned_cols=64  Identities=30%  Similarity=0.625  Sum_probs=60.6

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            5578889999999999999999999999999999999999999999999999999999998654

>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=99.55  E-value=9.8e-16  Score=124.36  Aligned_cols=60  Identities=23%  Similarity=0.459  Sum_probs=48.6

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      .++.+|.|+.|+..|+..||..|..++||+..++.+||..+||++.+|++||||||+++|
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            356788999999999999999999999999999999999999999999999999999975

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.55  E-value=1.2e-15  Score=123.51  Aligned_cols=58  Identities=38%  Similarity=0.504  Sum_probs=50.7

Q ss_pred             CCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         63 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        63 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      +|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            5899999999999999999999999999999999999999999999999999998653

>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=99.55  E-value=1.4e-15  Score=135.29  Aligned_cols=65  Identities=29%  Similarity=0.444  Sum_probs=57.1

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .++.++.||.||..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+|+..+.
T Consensus        31 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           31 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            35678889999999999999999999999999999999999999999999999999999997654

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.55  E-value=9.8e-16  Score=131.36  Aligned_cols=66  Identities=35%  Similarity=0.536  Sum_probs=61.9

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            456888999999999999999999999999999999999999999999999999999999876654

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=1.5e-15  Score=130.25  Aligned_cols=68  Identities=37%  Similarity=0.482  Sum_probs=62.9

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                      .++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~   71 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQN   71 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCC
Confidence            35678889999999999999999999999999999999999999999999999999999998766543

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.55  E-value=1.8e-15  Score=121.39  Aligned_cols=57  Identities=23%  Similarity=0.486  Sum_probs=54.8

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      ++|.|+.|+..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|
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            467899999999999999999999999999999999999999999999999999986

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.55  E-value=6.3e-16  Score=125.91  Aligned_cols=61  Identities=30%  Similarity=0.504  Sum_probs=53.6

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      +.++.||.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||++
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~q   62 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ   62 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGGC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhcC
Confidence            4578899999999999999999999999999999999999999999999999999999863

>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=99.55  E-value=1e-15  Score=127.81  Aligned_cols=65  Identities=35%  Similarity=0.616  Sum_probs=60.7

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            35578889999999999999999999999999999999999999999999999999999997654

>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=3.2e-15  Score=132.41  Aligned_cols=66  Identities=26%  Similarity=0.404  Sum_probs=62.2

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcC---------------CCcccccccccccHHHHhhhccc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------LSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~---------------l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .+++||.|+.|+..|+.+||..|+.++||+..+|++||..++               |++.+|++||||||+|+|++.+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            456788999999999999999999999999999999999999               99999999999999999998775


Q ss_pred             C
Q psy17256        122 G  122 (768)
Q Consensus       122 ~  122 (768)
                      .
T Consensus        84 ~   84 (95)
T 2cuf_A           84 A   84 (95)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.54  E-value=1e-15  Score=125.12  Aligned_cols=61  Identities=31%  Similarity=0.482  Sum_probs=56.3

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      +.++.|+.|+..|+..||..|..++||+...+..||..+||++.+|+|||||||+|+||.+
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            3578899999999999999999999999999999999999999999999999999999964

>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=99.54  E-value=2.2e-15  Score=121.33  Aligned_cols=60  Identities=28%  Similarity=0.353  Sum_probs=55.9

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhh-CCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      .+++||.||.|+.+||..|+..|+. ++||+...|+.||.++||++++|||||||||--.+
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            3467899999999999999999999 99999999999999999999999999999997543

>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=99.54  E-value=3.3e-15  Score=125.46  Aligned_cols=60  Identities=32%  Similarity=0.485  Sum_probs=56.8

Q ss_pred             CCCCccCCHHHHHHHHHhhhh-CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         61 KRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .+.|+.||..|+..||..|.. ++||+..+|.+||..+||++.+|+|||||||+|+|+...
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            457899999999999999996 999999999999999999999999999999999999764

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.54  E-value=3.6e-15  Score=125.53  Aligned_cols=61  Identities=30%  Similarity=0.440  Sum_probs=57.3

Q ss_pred             CCCCccCCHHHHHHHHHhhhh-CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         61 KRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ++.||.||..|+..||..|.. ++||+..+|.+||..+||++.+|+|||||||+|+|+....
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~   64 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   64 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccC
Confidence            467899999999999999995 9999999999999999999999999999999999997643

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.54  E-value=6.9e-15  Score=127.78  Aligned_cols=59  Identities=29%  Similarity=0.418  Sum_probs=55.1

Q ss_pred             cCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         66 TFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        66 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      .||..|+.+||..|..++||+..+|.+||..+||++++|+|||||||+||++..+....
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~   75 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEI   75 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhc
Confidence            69999999999999999999999999999999999999999999999999987665543

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=3.1e-15  Score=126.96  Aligned_cols=61  Identities=25%  Similarity=0.455  Sum_probs=57.1

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .+.|+.||..|+..||..|..++||+..+|++||..+||++.+|++||||||+|+|+..+.
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~   69 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS   69 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSS
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhccc
Confidence            4458999999999999999999999999999999999999999999999999999996654

>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=99.54  E-value=1.3e-15  Score=130.27  Aligned_cols=61  Identities=28%  Similarity=0.464  Sum_probs=57.2

Q ss_pred             CCCccccccccccHHHHHHHhhcccc-----CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQL-----DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~-----~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      ..++++|.||.||.+|+..|| .|..     ++||+..++++||..+||++++|+|||||||+|+|+
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            346678899999999999999 7999     999999999999999999999999999999999876

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.54  E-value=2.3e-15  Score=132.79  Aligned_cols=68  Identities=22%  Similarity=0.385  Sum_probs=62.6

Q ss_pred             CCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ..++.++.||.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+|++.....
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            34667888999999999999999999999999999999999999999999999999999999876554

>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=99.54  E-value=9.1e-16  Score=127.38  Aligned_cols=65  Identities=40%  Similarity=0.532  Sum_probs=61.2

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+|++++.+.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~~   66 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIV   66 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhccC
Confidence            46788999999999999999999999999999999999999999999999999999999877653

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.54  E-value=2.3e-15  Score=124.93  Aligned_cols=65  Identities=28%  Similarity=0.435  Sum_probs=60.7

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                      .++.||.|+.+|+..||..|..++||+...+..||..+||++.+|+|||||||+|+|++......
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   66 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD   66 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccccc
Confidence            47789999999999999999999999999999999999999999999999999999998765543

>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=99.54  E-value=3.9e-15  Score=125.97  Aligned_cols=60  Identities=22%  Similarity=0.405  Sum_probs=56.0

Q ss_pred             CCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         62 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        62 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ++|+.||..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+|++.+.
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            346679999999999999999999999999999999999999999999999999997654

>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=99.53  E-value=2.2e-15  Score=128.21  Aligned_cols=65  Identities=23%  Similarity=0.408  Sum_probs=61.2

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .++.++.|+.|+..|+..||..|..++||+..++..||..+||++.+|+|||||||+|+|+..+.
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            45678889999999999999999999999999999999999999999999999999999998764

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.53  E-value=2.4e-15  Score=119.91  Aligned_cols=54  Identities=20%  Similarity=0.415  Sum_probs=51.1

Q ss_pred             ccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         65 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        65 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      |.||..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+|++
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            679999999999999999999999999999999999999999999999999985

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.53  E-value=4.3e-15  Score=125.39  Aligned_cols=64  Identities=27%  Similarity=0.471  Sum_probs=59.2

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      ..++.|+.||..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+.....
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            3467899999999999999999999999999999999999999999999999999999876543

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=1.4e-15  Score=127.04  Aligned_cols=63  Identities=30%  Similarity=0.438  Sum_probs=59.6

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ++.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            456888999999999999999999999999999999999999999999999999999998754

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=4.4e-15  Score=127.77  Aligned_cols=72  Identities=25%  Similarity=0.509  Sum_probs=66.0

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ||+.||.++|+++|++|+++|.+.+.++.|+++.||.+||+|..|+++| .+..|+..++++||+.||.++..
T Consensus         5 yC~~~y~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~~~~C~~c~~~~~~   76 (82)
T 2ehe_A            5 SSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL-ADEPFTCQDSELLCNDCYCSAFS   76 (82)
T ss_dssp             CCCCCCCCCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBC-SSCCEEEETTEEEETTTSSCCGG
T ss_pred             echhHhCcccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCcc-CCCccEeeCCEEECHHHHhhhcC
Confidence            5668999999999999999999767799999999999999999999999 57789999999999999987664

>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=99.53  E-value=1.5e-15  Score=126.04  Aligned_cols=64  Identities=31%  Similarity=0.422  Sum_probs=60.1

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +++.|+.||.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||..+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   65 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG   65 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccccC
Confidence            4778999999999999999999999999999999999999999999999999999999876543

>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=99.53  E-value=1.6e-15  Score=123.08  Aligned_cols=58  Identities=33%  Similarity=0.556  Sum_probs=53.4

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      .++.|+.||.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            5788999999999999999999999999999999999999999999999999999997

>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=99.53  E-value=3.3e-15  Score=128.09  Aligned_cols=66  Identities=47%  Similarity=0.825  Sum_probs=61.5

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++.++.||.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~   70 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQE   70 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHh
Confidence            456888999999999999999999999999999999999999999999999999999999876544

>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=99.52  E-value=2.3e-15  Score=129.40  Aligned_cols=64  Identities=44%  Similarity=0.600  Sum_probs=59.8

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      .++.++.|+.|+..|+..|+..|..++||+...+..||..+||++.+|+|||||||+|+||+.+
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            5677889999999999999999999999999999999999999999999999999999999865

>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=99.52  E-value=2.9e-15  Score=125.05  Aligned_cols=64  Identities=27%  Similarity=0.435  Sum_probs=59.5

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .+.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+|+....
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS   68 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCCC
Confidence            3457789999999999999999999999999999999999999999999999999999997653

>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=99.52  E-value=3.6e-15  Score=144.75  Aligned_cols=62  Identities=27%  Similarity=0.514  Sum_probs=55.1

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      ..++||.||.||..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+||.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            35778899999999999999999999999999999999999999999999999999999985

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.51  E-value=3.9e-15  Score=125.27  Aligned_cols=64  Identities=28%  Similarity=0.505  Sum_probs=60.0

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .+.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK   68 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcc
Confidence            4568889999999999999999999999999999999999999999999999999999997544

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.51  E-value=4.5e-15  Score=127.68  Aligned_cols=73  Identities=22%  Similarity=0.412  Sum_probs=66.5

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      ||+.||.++|+++|.+|+++|.+.+.++.|+++.||.+||+|..|+++|. +..|+.+++++||+.||.++...
T Consensus         5 yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   77 (82)
T 1x63_A            5 SSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFPKGEDFYCVTCHETKFAS   77 (82)
T ss_dssp             CCCCCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCT-TSCEEEETTEEEEHHHHHHHTSC
T ss_pred             CchhHHccccCCcCccCCcccccCceEEEECccccccccCchhhCCCccC-CCccEeeCCEEECHHHHHHHhCC
Confidence            56799999999999999999998888999999999999999999999995 45799999999999999887653

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=2.5e-15  Score=128.83  Aligned_cols=65  Identities=18%  Similarity=0.279  Sum_probs=60.7

Q ss_pred             CCccccccccccHHHHHHHhhccccC----CCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLD----SNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~----~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .++.++.||.|+.+|+..||..|..+    +||+..++..||.++||++.+|+|||||||+|+|+....
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~~~   73 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIE   73 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhccCC
Confidence            45678889999999999999999999    999999999999999999999999999999999996543

>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=99.51  E-value=9.5e-15  Score=122.95  Aligned_cols=64  Identities=22%  Similarity=0.281  Sum_probs=59.3

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .++.++.|+.|+..|+..||..|..   ++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            3567788999999999999999987   999999999999999999999999999999999998654

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.51  E-value=3.2e-15  Score=120.06  Aligned_cols=57  Identities=28%  Similarity=0.493  Sum_probs=55.2

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      ++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|+||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            467999999999999999999999999999999999999999999999999999997

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=4.1e-15  Score=126.35  Aligned_cols=69  Identities=23%  Similarity=0.445  Sum_probs=63.2

Q ss_pred             cchhhhhhhcccccccCCCCCCC---CcceeeecCceecccCccccccccccCCCCceEeecCcccccccccc
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIAS---SDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLE  675 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~---~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e  675 (768)
                      ||+.||.++|+++|++|+++|.+   .+.++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.+
T Consensus         5 yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A            5 SSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNL-ANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBC-TTSCCCEETTEECCHHHHHH
T ss_pred             EchhHhchhhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCC-CCCccEeECCEEEChHHhcc
Confidence            56799999999999999999997   45689999999999999999999999 57789999999999999964

>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=99.51  E-value=2.1e-15  Score=124.41  Aligned_cols=61  Identities=43%  Similarity=0.723  Sum_probs=58.1

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      +.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|+|++.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            3578899999999999999999999999999999999999999999999999999999875

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.51  E-value=4.5e-15  Score=144.41  Aligned_cols=66  Identities=23%  Similarity=0.441  Sum_probs=52.7

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ..+++||.||.|+..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+||..+.
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            456778899999999999999999999999999999999999999999999999999999997654

>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=8.6e-15  Score=129.40  Aligned_cols=68  Identities=16%  Similarity=0.247  Sum_probs=62.1

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHc---------------------CCCcccccccccccHHHH
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQIT---------------------GLSKRVTQVWFQNSRARQ  115 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l---------------------~l~~~~vqvWFqNrRak~  115 (768)
                      .++.||.||.|++.|+.+||+.|+.++||+..+|++||..+                     .|++.+|+|||||||+++
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            35678899999999999999999999999999999999999                     799999999999999999


Q ss_pred             hhhcccCCC
Q psy17256        116 KKHLHTGKM  124 (768)
Q Consensus       116 k~~~~~~~~  124 (768)
                      |++.+....
T Consensus        83 kr~~~~~~~   91 (102)
T 2da6_A           83 AFRQKLAMD   91 (102)
T ss_dssp             HHHHHHHHS
T ss_pred             HHhhHhhhc
Confidence            987665443

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.50  E-value=4.2e-15  Score=122.97  Aligned_cols=63  Identities=37%  Similarity=0.582  Sum_probs=59.4

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|++||||||+|+|++....+
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~~q   64 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ   64 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCTTC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchhcc
Confidence            678999999999999999999999999999999999999999999999999999999876544

>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=99.50  E-value=4.3e-15  Score=132.16  Aligned_cols=66  Identities=30%  Similarity=0.475  Sum_probs=57.8

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++.++.||.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+.|+
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~gG   97 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREGG   97 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC--
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhccCc
Confidence            557888999999999999999999999999999999999999999999999999999999987653

>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=99.50  E-value=7.4e-15  Score=140.32  Aligned_cols=85  Identities=26%  Similarity=0.425  Sum_probs=63.5

Q ss_pred             HHhhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCccccc
Q psy17256         26 QVLQANFQLDSNPDGFGADSTDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQ  105 (768)
Q Consensus        26 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vq  105 (768)
                      ..|+.|.+.........        .......+++||.||.||..|+..||..|..++||+..+|.+||..+||++++|+
T Consensus        61 PlL~~wl~e~e~~~~~~--------~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~  132 (146)
T 1au7_A           61 AILSKWLEEAEQVGALY--------NEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVR  132 (146)
T ss_dssp             HHHHHHHHHCCC------------------------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             hHHHHHHHHhhcccCcc--------CcccCCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhch
Confidence            34777877664332111        1122234567888999999999999999999999999999999999999999999


Q ss_pred             ccccccHHHHhhh
Q psy17256        106 VWFQNSRARQKKH  118 (768)
Q Consensus       106 vWFqNrRak~k~~  118 (768)
                      |||||||+|+||+
T Consensus       133 vWFqNRR~k~kr~  145 (146)
T 1au7_A          133 VWFCNRRQREKRV  145 (146)
T ss_dssp             HHHHHHHHHTTSC
T ss_pred             hhhHhhhhhhhcc
Confidence            9999999999985

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=3.9e-15  Score=126.32  Aligned_cols=67  Identities=25%  Similarity=0.412  Sum_probs=61.3

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccCC
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  765 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~~  765 (768)
                      ..+.|+.||.+|+..||..|..++||+..++..||.++||++.+|++||||||+|+||+.+...+..
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~~~~s   74 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRSGPS   74 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSSCCCC
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccCCCCC
Confidence            3456899999999999999999999999999999999999999999999999999999877766543

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.50  E-value=3.9e-15  Score=130.01  Aligned_cols=64  Identities=30%  Similarity=0.462  Sum_probs=56.2

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      .++.++.||.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   88 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK   88 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhcC
Confidence            3557888999999999999999999999999999999999999999999999999999999753

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.50  E-value=1.1e-14  Score=125.13  Aligned_cols=73  Identities=26%  Similarity=0.539  Sum_probs=63.1

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccCC
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGG  680 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~~  680 (768)
                      ||..||.++|+++|++|+++|.+  .+|.|+++.||.+||+|..|+++|..|..|...++.+||..||.......
T Consensus         5 yC~~dy~~~~~~~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~~~   77 (81)
T 1v6g_A            5 SSGLDYQRLYGTRCFSCDQFIEG--EVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVSG   77 (81)
T ss_dssp             CCCSCGGGSCCCBCTTTCCBCCS--CCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSSCC
T ss_pred             cchHHHHhHhCCcCccccCEecc--ceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCCCC
Confidence            67799999999999999999995  48999999999999999999999976766655555579999998777643

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.50  E-value=4.2e-15  Score=120.19  Aligned_cols=58  Identities=31%  Similarity=0.509  Sum_probs=55.5

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      ++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|+||+
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            5779999999999999999999999999999999999999999999999999999985

>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=99.49  E-value=4e-15  Score=127.85  Aligned_cols=63  Identities=27%  Similarity=0.430  Sum_probs=54.9

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ++.++.||.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+.+
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            456888999999999999999999999999999999999999999999999999999999753

>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=99.49  E-value=3.2e-14  Score=124.35  Aligned_cols=60  Identities=25%  Similarity=0.362  Sum_probs=55.3

Q ss_pred             ccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         65 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        65 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      ..||..|+.+||..|..++||+..+|++||..+||++++|+|||||||+|+|+..+....
T Consensus        18 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~~   77 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD   77 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCCC
T ss_pred             ccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhhc
Confidence            349999999999999999999999999999999999999999999999999987665543

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.49  E-value=3.7e-15  Score=120.55  Aligned_cols=58  Identities=38%  Similarity=0.504  Sum_probs=50.7

Q ss_pred             ccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        702 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       702 ~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      .|+.||.+|+..||..|..++||+...+..||..+||++.+|++||||||+|+||+++
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            5899999999999999999999999999999999999999999999999999999764

>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=99.49  E-value=8.1e-15  Score=123.04  Aligned_cols=65  Identities=29%  Similarity=0.409  Sum_probs=59.5

Q ss_pred             ccccccccHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccC
Q psy17256        700 KRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK  764 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~  764 (768)
                      .+.|+.|+.+|+..||..|.. ++||+...+..||..+||++.+|+|||||||+|+||+.+.....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~   67 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSEC   67 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCCCcC
Confidence            356899999999999999996 99999999999999999999999999999999999988665543

>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=99.49  E-value=1.4e-14  Score=121.88  Aligned_cols=63  Identities=27%  Similarity=0.476  Sum_probs=58.7

Q ss_pred             CCCCCccCCHHHHHHHHHhh---hhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         60 AKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      +||.|+.|+..|+..||..|   ..++||+..++.+||..+||++.+|++||||||+|+|+.....
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            36789999999999999999   9999999999999999999999999999999999999876543

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.48  E-value=1.1e-14  Score=124.70  Aligned_cols=71  Identities=23%  Similarity=0.573  Sum_probs=64.6

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      ||+.||.++|+++|.+|+++|.+.  +|.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++...
T Consensus         5 yC~~cy~~~~~~~C~~C~~~I~~~--~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~~   75 (80)
T 2cuq_A            5 SSGPCYENKFAPRCARCSKTLTQG--GVTYRDQPWHRECLVCTGCQTPL-AGQQFTSRDEDPYCVACFGELFAS   75 (80)
T ss_dssp             SCCCCCCCCSSCCCTTTCCCCCSC--CEESSSSEECTTTCBCSSSCCBC-TTCCEEECSSSEEEHHHHHHHTTC
T ss_pred             EcHHHHccccCCcCCCCCCEecCc--EEEECCchhhhhhCCcccCCCcC-CCCeeEeECCEEECHHHHHHHcCC
Confidence            566899999999999999999865  78899999999999999999999 577899999999999999887653

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.48  E-value=1.1e-14  Score=122.59  Aligned_cols=64  Identities=28%  Similarity=0.401  Sum_probs=59.1

Q ss_pred             ccccccccHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                      ++.|+.|+.+|+..||..|.. ++||+..++..||..+||++.+|+|||||||+|+||+.+....
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~~~   67 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSE   67 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCCCc
Confidence            456899999999999999994 9999999999999999999999999999999999998865543

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.48  E-value=8.2e-15  Score=125.77  Aligned_cols=71  Identities=28%  Similarity=0.515  Sum_probs=64.6

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEe-ecCccccccccccccc
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFAL-HEDRVLCKSHYLELVD  678 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~-~~g~~~C~~~y~e~~~  678 (768)
                      ||+.||.++|+++|.+|+++|.  +.+|.|+++.||.+||+|..|+++|..|..|.+ .++++||+.||.++..
T Consensus         5 yC~~~y~~~~~~~C~~C~~~I~--~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~   76 (81)
T 1x6a_A            5 SSGKDYWGKFGEFCHGCSLLMT--GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS   76 (81)
T ss_dssp             CCCCCSSCCSSCBCTTTCCBCC--SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHC
T ss_pred             cchhHHhhhcCCcCccCCCCcC--ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhc
Confidence            6779999999999999999999  448999999999999999999999977888884 8899999999987765

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.47  E-value=7.2e-15  Score=117.10  Aligned_cols=54  Identities=20%  Similarity=0.415  Sum_probs=51.2

Q ss_pred             ccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        704 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       704 t~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      |.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||+
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            689999999999999999999999999999999999999999999999999986

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.47  E-value=8.6e-15  Score=119.94  Aligned_cols=59  Identities=22%  Similarity=0.392  Sum_probs=56.2

Q ss_pred             CCCCCCccCCHHHHHHHHHhh---hhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         59 KAKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ..++.|+.|+..|+..||..|   ..++||+..++.+||..+||++.+|++||||||+|+|+
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            357789999999999999999   99999999999999999999999999999999999987

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.47  E-value=1e-14  Score=122.16  Aligned_cols=59  Identities=22%  Similarity=0.326  Sum_probs=54.5

Q ss_pred             CCCCccCCHHHHHHHHHhh-hhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         61 KRVRTTFTEEQLQVLQANF-QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F-~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      .+.|+.++..|+.+||..| ..++||+..+|++||..+||++++|+|||||||+|+|+..
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            4456678899999999999 9999999999999999999999999999999999999754

>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=99.47  E-value=1.7e-14  Score=122.09  Aligned_cols=61  Identities=21%  Similarity=0.392  Sum_probs=56.8

Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      ++|+.||.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+|++.+..
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~   69 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK   69 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcc
Confidence            4567799999999999999999999999999999999999999999999999999987644

>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=99.47  E-value=1e-14  Score=122.38  Aligned_cols=58  Identities=28%  Similarity=0.369  Sum_probs=54.5

Q ss_pred             ccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        702 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       702 ~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      .|+.||.+|+..|+..|..++||+..+++.||..+||++++|+|||||||+|+|+...
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l   63 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHH
Confidence            4567999999999999999999999999999999999999999999999999998643

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.47  E-value=1.1e-14  Score=116.74  Aligned_cols=57  Identities=23%  Similarity=0.486  Sum_probs=54.6

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      +++.|+.|+.+|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|
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            467799999999999999999999999999999999999999999999999999986

>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=99.46  E-value=8.6e-15  Score=127.55  Aligned_cols=62  Identities=26%  Similarity=0.470  Sum_probs=57.9

Q ss_pred             CCCCccCCHHHHHHHHHhh---hhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         61 KRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      ||.|+.|+..|+..||..|   ..++||+..++.+||..+||++.+|++||||||+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            6789999999999999999   9999999999999999999999999999999999999976554

>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=99.46  E-value=7.1e-15  Score=119.25  Aligned_cols=59  Identities=22%  Similarity=0.448  Sum_probs=48.6

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      ++.++.|+.|+.+|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|
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            45788899999999999999999999999999999999999999999999999999976

>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=99.46  E-value=5.1e-14  Score=121.45  Aligned_cols=65  Identities=20%  Similarity=0.326  Sum_probs=59.2

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccC
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  122 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~  122 (768)
                      .++++.|+.|+..|+..|+..|..   ++||+..+|++||..+||++.+|++||||||+|+++.....
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            456778999999999999999987   69999999999999999999999999999999999875543

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.46  E-value=1.4e-14  Score=128.71  Aligned_cols=67  Identities=19%  Similarity=0.355  Sum_probs=54.1

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHH------------------cC---CCcccccccccccHHH
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQI------------------TG---LSKRVTQVWFQNSRAR  114 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~------------------l~---l~~~~vqvWFqNrRak  114 (768)
                      ..++.||.|+.|+..|+.+||..|+.++||+...|++||..                  +|   |++.+|+|||||||++
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            34677889999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             HhhhcccC
Q psy17256        115 QKKHLHTG  122 (768)
Q Consensus       115 ~k~~~~~~  122 (768)
                      ++++.+..
T Consensus        85 ~k~k~~~~   92 (99)
T 1lfb_A           85 EAFRHKLA   92 (99)
T ss_dssp             TSCCC---
T ss_pred             HHHhchhh
Confidence            88765443

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.45  E-value=1.2e-14  Score=129.02  Aligned_cols=63  Identities=25%  Similarity=0.375  Sum_probs=56.3

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      ....++.|+.|+.+|+..||..|..++||+..++..||.++||++++|+|||||||+|+||..
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            345667899999999999999999999999999999999999999999999999999999964

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.45  E-value=2.3e-14  Score=124.51  Aligned_cols=61  Identities=28%  Similarity=0.408  Sum_probs=56.9

Q ss_pred             cccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccCC
Q psy17256        705 TFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKS  765 (768)
Q Consensus       705 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~~  765 (768)
                      .+|.+|+..||..|..++||+..++..||..+||++++|+|||||||+||||+++...+..
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~~~   77 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDE   77 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhccc
Confidence            7999999999999999999999999999999999999999999999999999877666543

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-14  Score=121.98  Aligned_cols=65  Identities=26%  Similarity=0.461  Sum_probs=60.5

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcccc
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  763 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~  763 (768)
                      .++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||.+.....
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~   70 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCL   70 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSCCT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCCCC
Confidence            46789999999999999999999999999999999999999999999999999999998765543

>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=99.45  E-value=3e-14  Score=115.13  Aligned_cols=55  Identities=27%  Similarity=0.455  Sum_probs=53.2

Q ss_pred             CccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         64 RTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        64 Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      |+.|+..|+..||..|..   ++||+..++.+||..+||++.+|++||||||+|+|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            678999999999999999   9999999999999999999999999999999999974

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.45  E-value=2.4e-14  Score=126.77  Aligned_cols=69  Identities=25%  Similarity=0.386  Sum_probs=63.8

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhC---------------CCCCccccccccchhHHHhhhhc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------LSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lg---------------ls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .++.+|.|+.|+..|+..||..|..++||+...++.||..++               |++.+|++||||||+|+|++.+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            456788999999999999999999999999999999999999               99999999999999999999876


Q ss_pred             cccC
Q psy17256        761 GKMK  764 (768)
Q Consensus       761 ~~~~  764 (768)
                      ....
T Consensus        84 ~~~~   87 (95)
T 2cuf_A           84 AAIL   87 (95)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            5533

>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=99.45  E-value=1.6e-14  Score=116.30  Aligned_cols=59  Identities=27%  Similarity=0.340  Sum_probs=55.5

Q ss_pred             CCccccccccccHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHH
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ  754 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~  754 (768)
                      .++.+|.||.|+.+|+..|+..|+. ++||+...++.||.++||++++|+|||||+|--.
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            3567999999999999999999999 9999999999999999999999999999999753

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.45  E-value=2.9e-14  Score=118.05  Aligned_cols=57  Identities=19%  Similarity=0.376  Sum_probs=53.6

Q ss_pred             ccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         65 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        65 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ...|..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+|++...
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            468999999999999999999999999999999999999999999999999986543

>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=99.44  E-value=3e-14  Score=119.92  Aligned_cols=64  Identities=22%  Similarity=0.294  Sum_probs=59.4

Q ss_pred             CccccccccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ++.++.|+.|+.+|+..|+..|..   ++||+..++..||.++||++.+|+|||||||+|+|+....
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            456788999999999999999976   9999999999999999999999999999999999997654

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.44  E-value=2.6e-14  Score=115.72  Aligned_cols=52  Identities=31%  Similarity=0.565  Sum_probs=49.9

Q ss_pred             CCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         67 FTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        67 ~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      -|..|+.+||..|..++||+..+|.+||..+||++++|++||||||+|+|+.
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            3689999999999999999999999999999999999999999999999974

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.43  E-value=3e-14  Score=121.85  Aligned_cols=70  Identities=29%  Similarity=0.510  Sum_probs=63.2

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ||+.||.++|+++|++|+++|.+.  +|.|+++.||.+||+|..|+++|. +..|+.+++++||+.||.++..
T Consensus         5 yC~~~y~~~~~~~C~~C~~~I~~~--~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~~y~~~f~   74 (80)
T 1x3h_A            5 SSGKDFLAMFSPKCGGCNRPVLEN--YLSAMDTVWHPECFVCGDCFTSFS-TGSFFELDGRPFCELHYHHRRG   74 (80)
T ss_dssp             CCCCCCCCCCSCBCTTTCCBCCSS--CEEETTEEECTTTCBCSSSCCBSC-SSCCEESSSCEECHHHHHHHHS
T ss_pred             cchhHHhhhcCCccccCCCeecce--eEEECCCeEecCcCChhhCCCCCC-CCcEEeECCEEECHHHHHHHcC
Confidence            566899999999999999999964  789999999999999999999995 4469999999999999987765

>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=99.43  E-value=2.3e-14  Score=138.26  Aligned_cols=61  Identities=33%  Similarity=0.500  Sum_probs=57.7

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      +++||.||.|+..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            4667889999999999999999999999999999999999999999999999999999974

>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=99.42  E-value=4.5e-14  Score=118.82  Aligned_cols=63  Identities=25%  Similarity=0.471  Sum_probs=58.9

Q ss_pred             ccccccccHHHHHHHhhcc---ccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        700 KRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F---~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ++.|+.|+.+|+..|+..|   ..++||+..++..||..+||++.+|++||||||+|+|+......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~~   67 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccccc
Confidence            6789999999999999999   99999999999999999999999999999999999999766543

>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=99.42  E-value=6.3e-14  Score=122.04  Aligned_cols=60  Identities=27%  Similarity=0.416  Sum_probs=56.2

Q ss_pred             CCCCCCCccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         58 SKAKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        58 ~~~rr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      .++++.|+.|+..|+..||..|..   ++||+..+|.+||..+||++.+|++||||||+|+|.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            445667999999999999999999   999999999999999999999999999999999873

>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=99.42  E-value=8.1e-14  Score=121.74  Aligned_cols=59  Identities=25%  Similarity=0.385  Sum_probs=55.0

Q ss_pred             ccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        704 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       704 t~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ..+|.+|+..||..|..++||+..++..||..+||++++|+|||||||+|+|++.+...
T Consensus        18 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~   76 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL   76 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCC
T ss_pred             ccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhh
Confidence            34899999999999999999999999999999999999999999999999999876554

>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=99.42  E-value=7.5e-14  Score=134.25  Aligned_cols=61  Identities=33%  Similarity=0.616  Sum_probs=58.5

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ++++||.||.|+..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+||
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            4577889999999999999999999999999999999999999999999999999999997

>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=99.41  E-value=8.7e-14  Score=120.01  Aligned_cols=59  Identities=25%  Similarity=0.384  Sum_probs=54.1

Q ss_pred             CCCCccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         61 KRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      ++.|+.|+..|+..||..|..   ++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            344667999999999999999   99999999999999999999999999999999999864

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.41  E-value=3e-14  Score=116.68  Aligned_cols=59  Identities=22%  Similarity=0.398  Sum_probs=56.0

Q ss_pred             cccccccccHHHHHHHhhcc---ccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        699 AKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F---~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      .++.|+.|+.+|+..|+..|   ..++||+..++..||..+||++.+|++||||||+|+||.
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   64 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   64 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSCC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhccC
Confidence            46788999999999999999   999999999999999999999999999999999999873

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.40  E-value=2.6e-14  Score=119.70  Aligned_cols=61  Identities=21%  Similarity=0.317  Sum_probs=55.3

Q ss_pred             ccccccccHHHHHHHhhcc-ccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        700 KRVRTTFTEEQLQVLQANF-QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F-~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      .+.|++++.+|+..||..| ..++||+..++..||.++||++++|+|||||||+|+|+....
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~~s   70 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGPS   70 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCCCC
Confidence            3446667889999999999 999999999999999999999999999999999999986544

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.40  E-value=3.6e-14  Score=138.09  Aligned_cols=67  Identities=22%  Similarity=0.437  Sum_probs=53.0

Q ss_pred             CCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      ..++++|.||.|+..|+..||..|..++||+..++..||..+||++++|+|||||||+|+||+.+.+
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~  161 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAA  161 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC--
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCCC
Confidence            3567788999999999999999999999999999999999999999999999999999999987654

>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=99.40  E-value=8.4e-14  Score=123.09  Aligned_cols=67  Identities=16%  Similarity=0.265  Sum_probs=62.0

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHh---------------------CCCCCccccccccchhHH
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQIT---------------------GLSKRVTQVWFQNSRARQ  754 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~l---------------------gls~~~V~vWFQNrRak~  754 (768)
                      .++.+|.|+.|+..|+..||..|..++||+..+|++||..+                     .+++.+|+|||||||+|+
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            35678899999999999999999999999999999999999                     789999999999999999


Q ss_pred             Hhhhhccc
Q psy17256        755 KKHLHTGK  762 (768)
Q Consensus       755 kk~~~~~~  762 (768)
                      |++.+.+-
T Consensus        83 kr~~~~~~   90 (102)
T 2da6_A           83 AFRQKLAM   90 (102)
T ss_dssp             HHHHHHHH
T ss_pred             HHhhHhhh
Confidence            99876554

>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=99.39  E-value=5.4e-14  Score=136.50  Aligned_cols=62  Identities=27%  Similarity=0.514  Sum_probs=55.1

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      ..+++|.||.|+..|+..||..|..++||+..++..||..+||++++|+|||||||+|+||+
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            45678889999999999999999999999999999999999999999999999999999985

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1e-13  Score=113.30  Aligned_cols=53  Identities=26%  Similarity=0.490  Sum_probs=49.8

Q ss_pred             ccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         65 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        65 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ..++..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|.++
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            34578999999999999999999999999999999999999999999998776

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.38  E-value=5.1e-14  Score=116.63  Aligned_cols=59  Identities=19%  Similarity=0.372  Sum_probs=54.7

Q ss_pred             ccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        704 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       704 t~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ..+|..|+..||..|..++||+...+..||.++||++++|+|||||||+|+||++...+
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~~~   67 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE   67 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSSCC
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhhhh
Confidence            46789999999999999999999999999999999999999999999999999865543

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.38  E-value=4.8e-14  Score=125.20  Aligned_cols=71  Identities=18%  Similarity=0.304  Sum_probs=54.9

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHH------------------hC---CCCCccccccccchhHH
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQI------------------TG---LSKRVTQVWFQNSRARQ  754 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~------------------lg---ls~~~V~vWFQNrRak~  754 (768)
                      .++.+|.|+.|+..|+..||..|..++||+...|++||..                  +|   |++.+|+|||||||+++
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            4677889999999999999999999999999999999999                  88   99999999999999999


Q ss_pred             HhhhhccccCCC
Q psy17256        755 KKHLHTGKMKSS  766 (768)
Q Consensus       755 kk~~~~~~~~~s  766 (768)
                      |++.+.+....|
T Consensus        86 k~k~~~~~~~~s   97 (99)
T 1lfb_A           86 AFRHKLAMDTYK   97 (99)
T ss_dssp             SCCC--------
T ss_pred             HHhchhhhccCC
Confidence            988776655433

>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=99.38  E-value=1e-13  Score=120.77  Aligned_cols=62  Identities=26%  Similarity=0.470  Sum_probs=57.8

Q ss_pred             ccccccccHHHHHHHhhcc---ccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        700 KRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F---~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      +|.|+.|+.+|+..|+..|   ..++||+..++..||..+||++.+|++||||||+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            6779999999999999999   8999999999999999999999999999999999999986544

>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=99.38  E-value=1.7e-13  Score=118.10  Aligned_cols=68  Identities=19%  Similarity=0.320  Sum_probs=60.8

Q ss_pred             CccccccccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccC
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMK  764 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~  764 (768)
                      .++++.|+.|+.+|+..|+..|..   ++||+..++..||.++||++.||+|||||||+|+|+........
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~~~   75 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRN   75 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCCCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhccC
Confidence            456778999999999999999877   69999999999999999999999999999999999986655443

>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=99.38  E-value=7.8e-14  Score=112.69  Aligned_cols=55  Identities=27%  Similarity=0.455  Sum_probs=53.3

Q ss_pred             cccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        703 RTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       703 Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      |+.|+.+|+..|+..|..   ++||+..++..||.++||++.+|++||||||+|+||.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            688999999999999999   9999999999999999999999999999999999985

>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=99.37  E-value=6.7e-14  Score=133.67  Aligned_cols=62  Identities=32%  Similarity=0.557  Sum_probs=55.8

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      .++++|.||.|+.+|+..||..|..++||+..++..||..+||++++|+|||||||+|+||+
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            45678889999999999999999999999999999999999999999999999999999985

>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=99.37  E-value=1e-13  Score=112.50  Aligned_cols=50  Identities=24%  Similarity=0.482  Sum_probs=46.6

Q ss_pred             HHHHHHHHHhh-hhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         69 EEQLQVLQANF-QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        69 ~~Ql~~Le~~F-~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      ..|+.+||+.| ..++||+...|.+||.++||+++||+|||||||+|+|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            35799999999 679999999999999999999999999999999999863

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.37  E-value=9.5e-14  Score=112.43  Aligned_cols=51  Identities=31%  Similarity=0.597  Sum_probs=49.2

Q ss_pred             cHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        707 TEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       707 s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      +.+|+..||..|..++||+..++.+||..+||++++|++||||||+|||+-
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            578999999999999999999999999999999999999999999999974

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.37  E-value=1.5e-13  Score=117.79  Aligned_cols=69  Identities=23%  Similarity=0.520  Sum_probs=61.1

Q ss_pred             cchhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEee-cCccccccccccccc
Q psy17256        606 LSVLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALH-EDRVLCKSHYLELVD  678 (768)
Q Consensus       606 yC~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~-~g~~~C~~~y~e~~~  678 (768)
                      ||+.||. +++++|.+|+++|.+  .+|.|+++.||++||+|..|+++| .+..|... ++++||+.||.++..
T Consensus         6 yC~~~y~-~~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~g~~yC~~cy~~~f~   75 (81)
T 2dlo_A            6 SGEGCYV-ATLEKCATCSQPILD--RILRAMGKAYHPGCFTCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKFA   75 (81)
T ss_dssp             CCCCCCC-SSCCBCTTTCCBCCS--CCEEETTEEECTTTCBCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             ECHHHhh-cCCCccccCCCeecc--eeEEECCccccHHhcCcccCCCcc-CCCeeEECCCCEEECHHHHHHHhc
Confidence            5568998 799999999999994  489999999999999999999999 57778876 689999999987664

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=99.35  E-value=8.4e-14  Score=129.12  Aligned_cols=108  Identities=15%  Similarity=0.067  Sum_probs=84.9

Q ss_pred             ccchhhhhhhhhhHH-HHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIALVL-SEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~-~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .+.|..|.++|.+.. +.+.++      .||+.||+|+.|+..+.               |....++.+++.+|    |.
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~------~wH~~CF~C~~C~~~L~---------------~~~~~~~~~~g~~y----C~   59 (122)
T 1m3v_A            5 WKRCAGCGGKIADRFLLYAMDS------YWHSRCLKCSSCQAQLG---------------DIGTSSYTKSGMIL----CR   59 (122)
T ss_dssp             CCCBSSSSSCCCSSCCEEETTE------EECHHHHCCSSSCCCTT---------------TSEECCEEETTEEE----CH
T ss_pred             CCCCcccCCEeCCcEEEEECCc------eeHhhCCCcCCCCCccc---------------ccCCeEEEECCeee----cH
Confidence            355999999999874 667777      99999999999995432               11124678888994    56


Q ss_pred             hhhhhhccc--ccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        609 LICFRSFGA--KCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       609 ~~y~~~f~~--~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .||.++|++  +|++|+++|.+++  +.+.++              ++..|+.|+++++++||..||.+...
T Consensus        60 ~cy~~~f~~~~~C~~C~~~I~~~~--~~~~g~--------------~~l~g~~f~~~~~~~yC~~~~~~~~~  115 (122)
T 1m3v_A           60 NDYIRLFGNSGAGGSGGHMGSGGD--VMVVGE--------------PTLMGGEFGDEDERLITRLENTQFDA  115 (122)
T ss_dssp             HHHHHHHCCCCSSSCSSCCSCCEE--SSSSSS--------------SSCCSCTTCCTTCCCCEECTTTTTTC
T ss_pred             HHHHHHcCCCCccccCCCCcCchh--eEEcCC--------------cCCCCCccEecCCEeEccCcchhchh
Confidence            999999999  9999999999763  344442              23479999999999999999987654

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.34  E-value=2.3e-13  Score=132.75  Aligned_cols=66  Identities=26%  Similarity=0.325  Sum_probs=55.0

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      ...+.||.||.||..|+..||..|+.++||+..+|++||..+||++.+|+|||||||+|+|+....
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            345678899999999999999999999999999999999999999999999999999999986543

>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=99.33  E-value=2.3e-13  Score=118.45  Aligned_cols=60  Identities=27%  Similarity=0.416  Sum_probs=55.8

Q ss_pred             CccccccccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      .++++.|+.|+.+|+..|+..|..   ++||+..++..||..+||++.+|++||||||+|+|.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            345566899999999999999999   999999999999999999999999999999999873

>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=99.33  E-value=2.4e-13  Score=117.28  Aligned_cols=61  Identities=25%  Similarity=0.363  Sum_probs=55.2

Q ss_pred             ccccccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ++.|+.|+.+|+..|+..|..   ++||+..++..||..+||++.+|++||||||+|+|+....
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~~   66 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIA   66 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccccC
Confidence            344667999999999999999   9999999999999999999999999999999999997543

>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=99.32  E-value=3.6e-13  Score=129.46  Aligned_cols=61  Identities=33%  Similarity=0.616  Sum_probs=58.2

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      .++++|.|+.|+..|+..||..|..++||+..++..||.++||++++|+|||||||+|+||
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            4567888999999999999999999999999999999999999999999999999999987

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.31  E-value=9.3e-13  Score=110.71  Aligned_cols=64  Identities=23%  Similarity=0.426  Sum_probs=58.0

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .+|+++|++|+++|.+.  ++.|+++.||++||+|..|+++|..|..|++.++++||..||..+..
T Consensus         2 s~~~~~C~~C~~~I~~~--~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~   65 (73)
T 1wig_A            2 SSGSSGCDSCEKYITGR--VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAART   65 (73)
T ss_dssp             CCSCCSCSSSCCCCSSC--CBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSS
T ss_pred             CcCcCCcccCCCEecCe--eEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhc
Confidence            36889999999999964  88999999999999999999999668899999999999999987654

>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=99.31  E-value=1.9e-13  Score=110.91  Aligned_cols=50  Identities=24%  Similarity=0.452  Sum_probs=46.7

Q ss_pred             HHHHHHhhcc-ccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        709 EQLQVLQANF-QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       709 ~Ql~~Le~~F-~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      .|+..||..| ..++||+...+..||.++||+++||+|||||||+|+|+..
T Consensus        10 ~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~   60 (64)
T 1x2m_A           10 QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG   60 (64)
T ss_dssp             CHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSS
T ss_pred             hHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence            4799999999 6799999999999999999999999999999999999754

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.30  E-value=2e-12  Score=109.49  Aligned_cols=66  Identities=21%  Similarity=0.476  Sum_probs=59.3

Q ss_pred             hhcccccccCCCCCCC--CcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        613 RSFGAKCSKCCRGIAS--SDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~--~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      ++|+++|.+|+++|.+  .+.++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++...
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~f~~   69 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNKEIFCQKCGSGMDTD   69 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBC-SSSCEEEETTEEEETTTTCCCCCC
T ss_pred             CccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcC-CCCceEeECCEEECHHHhhhhhCC
Confidence            4689999999999996  45689999999999999999999999 578899999999999999887653

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=3.6e-13  Score=110.08  Aligned_cols=54  Identities=26%  Similarity=0.469  Sum_probs=49.9

Q ss_pred             ccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        704 TTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       704 t~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      ...+.+|+..||..|..++||+..++..||.++||++++|+|||||||+|.++.
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            345689999999999999999999999999999999999999999999997763

>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=99.30  E-value=6.4e-13  Score=128.20  Aligned_cols=61  Identities=33%  Similarity=0.500  Sum_probs=57.5

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      ++++|.|+.|+..|+..||..|..++||+..++..||..+||++++|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            4567789999999999999999999999999999999999999999999999999999984

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B

Probab=99.29  E-value=4.8e-13  Score=111.62  Aligned_cols=66  Identities=29%  Similarity=0.622  Sum_probs=59.1

Q ss_pred             hhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccc
Q psy17256        611 CFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       611 y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      |...++++|.+|+++|.+.|.++.|.++.||.+||+|..|+++|..+ .|+..+|++||+.||.++.
T Consensus         6 y~~~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~lf   71 (72)
T 3f6q_B            6 FQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLF   71 (72)
T ss_dssp             CCCCTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGG-CCEEETTEEECHHHHHHHT
T ss_pred             ccCcCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCC-CeEeECCeEeCHHHHHHhh
Confidence            34588999999999999888889999999999999999999999655 7889999999999997654

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.29  E-value=1e-12  Score=109.94  Aligned_cols=65  Identities=29%  Similarity=0.659  Sum_probs=59.4

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      .++++|.+|+++|.+.+.++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++.+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~~~~   67 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQL-RGQHFYAVERRAYCEGCYVATLES   67 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBC-TTSCEEESSSCEEEHHHHHHHHHT
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcC-CcCcCEeeCCeEECHHHHHHHHcc
Confidence            47889999999999877789999999999999999999999 688899999999999999887753

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.29  E-value=1.4e-12  Score=109.06  Aligned_cols=65  Identities=18%  Similarity=0.497  Sum_probs=58.9

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ++|+++|.+|+++|.+.+.+|.|+++.||.+||+|..|+++|. +..|+.+++++||+.||.++..
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   66 (72)
T 1x4k_A            2 SSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG-TKSFIPKDNQNFCVPCYEKQHA   66 (72)
T ss_dssp             CSCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCC-SSSEEEETTEEEEHHHHHHHTS
T ss_pred             CccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccC-CCccCccCCeEECHHHHhHHhC
Confidence            4688999999999998778999999999999999999999995 4579999999999999987765

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.26  E-value=2e-12  Score=108.12  Aligned_cols=65  Identities=20%  Similarity=0.448  Sum_probs=58.7

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ++|+++|.+|+++|.+.+.++.|+++.||.+||+|..|+++| .+..|+..++.+||+.||.++..
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   66 (72)
T 1wyh_A            2 SSGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPL-GSRSFVPDKGAHYCVPCYENKFA   66 (72)
T ss_dssp             CCCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBT-TTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcC-CCCccCCcCCeEECHHHHHHHcc
Confidence            468899999999999766799999999999999999999999 45679999999999999987765

>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=99.25  E-value=1.3e-12  Score=129.66  Aligned_cols=62  Identities=19%  Similarity=0.362  Sum_probs=53.9

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcC---------------------CCcccccccccccHHH
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------------LSKRVTQVWFQNSRAR  114 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~---------------------l~~~~vqvWFqNrRak  114 (768)
                      ..++.||.|+.|+..|+.+||+.|+.++||+...|++||..++                     |++.+|++||||||++
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4567889999999999999999999999999999999999999                     9999999999999998


Q ss_pred             Hhh
Q psy17256        115 QKK  117 (768)
Q Consensus       115 ~k~  117 (768)
                      ++.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            764

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.23  E-value=3.3e-12  Score=106.86  Aligned_cols=64  Identities=23%  Similarity=0.522  Sum_probs=57.8

Q ss_pred             hcccccccCCCCCCC--CcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIAS--SDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~--~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++++|.+|+++|.+  .+.++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~c~~~~~~   68 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPDCGKDISG   68 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBC-TTSCCEECSSSEECHHHHHTCCC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcC-CCCccEeECCEEEChhHcCcccC
Confidence            577899999999997  55789999999999999999999999 57889999999999999987664

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.23  E-value=1.1e-12  Score=127.83  Aligned_cols=67  Identities=25%  Similarity=0.317  Sum_probs=55.3

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      ..+.+|.|+.|+..|+..|+..|..++||+...+..||..+||++.+|+|||||||+|+|+....+.
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~~~  160 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEHH  160 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-----
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCCCC
Confidence            3556888999999999999999999999999999999999999999999999999999999766554

>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=99.22  E-value=3.5e-12  Score=105.29  Aligned_cols=56  Identities=23%  Similarity=0.364  Sum_probs=50.6

Q ss_pred             cCCHHHHHHHHHhhh---hCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         66 TFTEEQLQVLQANFQ---LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        66 ~~t~~Ql~~Le~~F~---~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      .|+.+|+..|+..|.   .++||+..+|++||..+||++.+|++||||||+|+|+....
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            599999999999999   99999999999999999999999999999999999986543

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B

Probab=99.21  E-value=2.7e-12  Score=105.52  Aligned_cols=63  Identities=24%  Similarity=0.501  Sum_probs=56.1

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ++|+++|.+|+++|.+  .++.|+++.||.+||+|..|+++| .+..|+..++.+||+.||.++..
T Consensus         2 ~~~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~y~~~f~   64 (66)
T 1nyp_A            2 SMGVPICGACRRPIEG--RVVNAMGKQWHVEHFVCAKCEKPF-LGHRHYERKGLAYCETHYNQLFG   64 (66)
T ss_dssp             CCCCCEETTTTEECCS--CEECCTTSBEETTTCBCTTTCCBC-SSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcCCCCCcccCCEecc--eEEEECccccccCcCEECCCCCCC-CCCceEeECCcEECHHHHHHHhC
Confidence            3678999999999994  378999999999999999999999 56789999999999999987654

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens}

Probab=99.20  E-value=4.2e-12  Score=104.11  Aligned_cols=61  Identities=23%  Similarity=0.518  Sum_probs=54.2

Q ss_pred             cccccccCCCCCCCCcceeeecCceec--ccCccccccccccCCCCceEeecCcccc-ccccccc
Q psy17256        615 FGAKCSKCCRGIASSDWVRKARDHVYH--LACFACEACKRQLSTGEEFALHEDRVLC-KSHYLEL  676 (768)
Q Consensus       615 f~~~C~~C~~~I~~~e~~~~a~~~~~H--~~CF~C~~C~~~L~~G~~f~~~~g~~~C-~~~y~e~  676 (768)
                      |+++|.+|+++|.+++.+|.|+++.||  .+||+|..|+++| .|..|+.++|++|| ..||..+
T Consensus         1 fa~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            1 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             -CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBC-TTSCCEEETTEEESSHHHHHTT
T ss_pred             CcCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcC-CCCceEEECCEEecCHHHhhhh
Confidence            688999999999976678999999999  9999999999999 67889999999999 7777543

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=99.19  E-value=2.4e-12  Score=117.87  Aligned_cols=104  Identities=13%  Similarity=0.060  Sum_probs=80.5

Q ss_pred             ccchhhhhhhhhhH-HHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIALV-LSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~~-~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .+.|..|.++|.+. .+.+.++      .||+.||+|+.|+..+.. .             | ..+|.+++.+    ||.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~------~wH~~CF~C~~C~~~L~~-~-------------g-~~~~~~~g~~----yC~   57 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQ------YWHEDCLSCDLCGCRLGE-V-------------G-RRLYYKLGRK----LCR   57 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSS------EECTTTCCCSSSCSCCCC-S-------------S-SCCCCBTTBC----CCH
T ss_pred             CCCCcCCCCeeCCcEEEEECch------hHHHhcCcccccCCchhc-C-------------C-CeeEEECCee----ech
Confidence            35699999999988 5677787      999999999999954320 0             1 1457788888    556


Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .||.++|+++|..|..   +  .+|.               |..++..|+.|.++++++||..||.+...
T Consensus        58 ~~y~~~f~~~c~~c~~---~--~~~~---------------~~~~~~~g~~f~~~~~~~~C~~~~~~~~~  107 (114)
T 1j2o_A           58 RDYLRLGGSGGHMGSG---G--DVMV---------------VGEPTLMGGEFGDEDERLITRLENTQFDA  107 (114)
T ss_dssp             HHHHHHHTSCCSSCBS---C--SCCC---------------SSCSSTTSSBCCCSSSCCCEEEECTTCCC
T ss_pred             HHHHHHhCcccCcCCC---C--ceeE---------------cCCccCCCCeeEEcCCEeecchhhhcccc
Confidence            9999999999998862   1  2332               45666689999999999999999987654

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.18  E-value=7.9e-12  Score=103.86  Aligned_cols=62  Identities=29%  Similarity=0.691  Sum_probs=56.2

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .|+++|.+|+++|.+.  .+.|+++.||++||+|..|+++| .+..|+.+++++||+.||.++..
T Consensus         3 ~~~~~C~~C~~~I~~~--~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   64 (70)
T 2d8z_A            3 SGSSGCVQCKKPITTG--GVTYREQPWHKECFVCTACRKQL-SGQRFTARDDFAYCLNCFCDLYA   64 (70)
T ss_dssp             CCCCBCSSSCCBCCSS--EEESSSSEEETTTSBCSSSCCBC-TTSCCEESSSSEECHHHHHHHTC
T ss_pred             CCCCCCcccCCeeccc--eEEECccccCCCCCccCCCCCcC-CcCceEeeCCeEECHHHHHHHhc
Confidence            5788999999999865  68999999999999999999999 57789999999999999987765

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.18  E-value=7.9e-12  Score=109.35  Aligned_cols=68  Identities=19%  Similarity=0.306  Sum_probs=60.3

Q ss_pred             hhhhhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        608 VLICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       608 ~~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      +..+...++++|.+|+++|.+  .++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++..
T Consensus        17 ~~~~~~~~~~~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~f~   84 (90)
T 2dar_A           17 EHIPAGKRTPMCAHCNQVIRG--PFLVALGKSWHPEEFNCAHCKNTM-AYIGFVEEKGALYCELCYEKFFA   84 (90)
T ss_dssp             EEECTTTCCCBBSSSCCBCCS--CEEEETTEEECTTTCBCSSSCCBC-SSSCBEESSSCEECHHHHHHHTS
T ss_pred             ccCCCCCCCCCCccCCCEecc--eEEEECCccccccCCccCCCCCCC-CCCEeEeECCEEECHHHHHHHcC
Confidence            355778899999999999974  478899999999999999999999 46679999999999999988765

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.18  E-value=5.2e-12  Score=107.00  Aligned_cols=65  Identities=28%  Similarity=0.628  Sum_probs=58.0

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ..++++|.+|+++|.+.+.++.|+++.||.+||+|..|+++|..+ .|+..+|++||+.||.++.+
T Consensus         8 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~   72 (77)
T 1g47_A            8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFA   72 (77)
T ss_dssp             CCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGG-CSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCC-CeEeECCeEeCHHHHHHHhh
Confidence            456789999999999778899999999999999999999999544 68999999999999987654

>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=99.17  E-value=4.9e-12  Score=104.40  Aligned_cols=57  Identities=23%  Similarity=0.352  Sum_probs=50.6

Q ss_pred             ccccHHHHHHHhhccc---cCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        704 TTFTEEQLQVLQANFQ---LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       704 t~~s~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ..|+.+|+..|+..|.   .++||+..++..||..+||++.||++||||||+|+||....
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            3689999999999999   99999999999999999999999999999999999987544

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.17  E-value=8.6e-12  Score=103.39  Aligned_cols=62  Identities=32%  Similarity=0.700  Sum_probs=56.0

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++++|.+|+++|.+.  ++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++..
T Consensus         3 ~~~~~C~~C~~~I~~~--~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   64 (69)
T 2cur_A            3 SGSSGCVKCNKAITSG--GITYQDQPWHADCFVCVTCSKKL-AGQRFTAVEDQYYCVDCYKNFVS   64 (69)
T ss_dssp             CCCCCCSSSCCCCCTT--CEEETTEEECTTTTBCTTTCCBC-TTSCEEECSSCEEEHHHHHHHHT
T ss_pred             CCcCCCcccCCEeCcc--eEEECccccccCcCEECCCCCCC-CCCccEeECCEEECHHHhHHHhc
Confidence            5788999999999864  78899999999999999999999 57789999999999999987654

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.15  E-value=1.3e-11  Score=102.58  Aligned_cols=62  Identities=26%  Similarity=0.492  Sum_probs=54.7

Q ss_pred             cccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        615 FGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       615 f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      ++++|.+|+++|.+  .++.|+++.||++||+|..|+++|.. ..|+.+++++||+.||.+....
T Consensus         4 ~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~~-~~f~~~~g~~yC~~c~~~~~~~   65 (70)
T 2d8x_A            4 GSSGCHQCGEFIIG--RVIKAMNNSWHPECFRCDLCQEVLAD-IGFVKNAGRHLCRPCHNREKAS   65 (70)
T ss_dssp             CSSBCSSSCCBCCS--CCEEETTEEECTTTSBCSSSCCBCSS-SCCEEETTEEECHHHHHHHHCC
T ss_pred             CCCcCccCCCEecc--eEEEECcccccccCCEeCCCCCcCCC-CccEeECCeEECHHHhhhhcCC
Confidence            56799999999995  47999999999999999999999954 4688899999999999877653

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.11  E-value=2.9e-11  Score=102.22  Aligned_cols=66  Identities=24%  Similarity=0.526  Sum_probs=57.5

Q ss_pred             hhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccc-cccccccc
Q psy17256        611 CFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK-SHYLELVD  678 (768)
Q Consensus       611 y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~-~~y~e~~~  678 (768)
                      .+..++++|.+|+++|.+++. +.|+++.||.+||+|..|+++| .+..|+.+++++||+ .||.++..
T Consensus         4 ~~~~~~~~C~~C~~~I~~~~~-v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~cy~~~f~   70 (76)
T 2cu8_A            4 GSSGMASKCPKCDKTVYFAEK-VSSLGKDWHKFCLKCERCSKTL-TPGGHAEHDGKPFCHKPCYATLFG   70 (76)
T ss_dssp             SCCCCCCBCTTTCCBCCTTTE-EEETTEEEETTTCBCSSSCCBC-CTTSCEEETTEEECTTTHHHHHSC
T ss_pred             ccCCCCCCCcCCCCEeECCeE-EEECCeEeeCCCCCCCCCCCcc-CCCceEeECCEEecchHHHHHhcc
Confidence            456788999999999996654 6799999999999999999999 466799999999999 79987664

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.10  E-value=2e-11  Score=122.30  Aligned_cols=62  Identities=19%  Similarity=0.379  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcC---------------------CCcccccccccccH
Q psy17256         54 SHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------------LSKRVTQVWFQNSR  112 (768)
Q Consensus        54 ~~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~---------------------l~~~~vqvWFqNrR  112 (768)
                      .+..++.||.|+.|++.|+.+||+.|+.++||+..+|++||..+|                     |++.+|++||||||
T Consensus       136 ~~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR  215 (221)
T 2h8r_A          136 EPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRR  215 (221)
T ss_dssp             ------CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhh
Confidence            345677899999999999999999999999999999999999987                     89999999999999


Q ss_pred             HHH
Q psy17256        113 ARQ  115 (768)
Q Consensus       113 ak~  115 (768)
                      +..
T Consensus       216 ~~~  218 (221)
T 2h8r_A          216 KEE  218 (221)
T ss_dssp             TTC
T ss_pred             hhh
Confidence            853

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3

Probab=99.09  E-value=2e-11  Score=108.92  Aligned_cols=64  Identities=22%  Similarity=0.527  Sum_probs=57.5

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++++|.+|+++|.+.+.++.|+++.||.+||+|..|+++| .+..|+..++++||+.||.++..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~~~   66 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTREDS   66 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCT-TSSCCEEETTEEECHHHHTTCCC
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCC-CcCeeECcCCEEEChhHhhhhcC
Confidence            56789999999998655689999999999999999999999 67789999999999999987654

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.09  E-value=3.6e-11  Score=102.57  Aligned_cols=62  Identities=18%  Similarity=0.268  Sum_probs=53.8

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ..++++|.+|+++|.+  .+|.|+++.||++||+|..|+++|. +..| .+++++||+.||.++..
T Consensus        12 ~~~~~~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~cy~~~f~   73 (79)
T 2cor_A           12 GLGKYICQKCHAIIDE--QPLIFKNDPYHPDHFNCANCGKELT-ADAR-ELKGELYCLPCHDKMGV   73 (79)
T ss_dssp             CCCCCBCTTTCCBCCS--CCCCCSSSCCCTTTSBCSSSCCBCC-TTCE-EETTEEECHHHHHTTSC
T ss_pred             ccCCCCCccCCCEecc--eEEEECcceeCCCCCEeCCCCCccC-CCCE-eECCEEeCHHHHHHhCC
Confidence            4567899999999994  4789999999999999999999995 4444 88999999999987765

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.06  E-value=7.4e-11  Score=101.35  Aligned_cols=62  Identities=21%  Similarity=0.548  Sum_probs=52.0

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceE--eecCcccccccccccccC
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFA--LHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~--~~~g~~~C~~~y~e~~~~  679 (768)
                      +.+|.+|+++|...+.+ .|+++.||.+||+|..|+++|.. ..|.  .+++++||+.||.++..+
T Consensus        15 ~~~C~~C~~~I~~~e~v-~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A           15 GDLCALCGEHLYVLERL-CVNGHFFHRSCFRCHTCEATLWP-GGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             SCBCSSSCCBCCTTTBC-CBTTBCCBTTTCBCSSSCCBCCT-TSEECCTTTCCCEETTTCCCCCCC
T ss_pred             CCCCcccCCCcccceEE-EECCCeeCCCcCEEcCCCCCcCC-CceeEeCcCCEEEChHHHHhhhcC
Confidence            46899999999876665 59999999999999999999954 4465  468999999999887653

>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=99.06  E-value=4.2e-11  Score=97.32  Aligned_cols=47  Identities=23%  Similarity=0.619  Sum_probs=44.5

Q ss_pred             HHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHH
Q psy17256         69 EEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ  115 (768)
Q Consensus        69 ~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~  115 (768)
                      .+|+..|+.+|..|++|+..++..||..+||+.++|||||||||++.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~   60 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ   60 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccccc
Confidence            46899999999999999999999999999999999999999999853

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens}

Probab=99.05  E-value=4.4e-11  Score=110.90  Aligned_cols=64  Identities=27%  Similarity=0.587  Sum_probs=56.4

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccC-CCCceEeecCcccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~-~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      ..++++|.+|+++|.+. .++.|+++.||.+||+|..|+++|. .|..|+.+++++||+.||.+++
T Consensus        58 ~~~~~~C~~C~~~I~~~-~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~F  122 (123)
T 2l4z_A           58 GLSWKRCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF  122 (123)
T ss_dssp             CSSCSBBSSSSSBCCSS-SEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHC
T ss_pred             CccCCcCcCCCCCcCCc-EEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhc
Confidence            46678999999999964 4588999999999999999999996 3678999999999999998754

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.04  E-value=2.8e-11  Score=103.20  Aligned_cols=60  Identities=32%  Similarity=0.620  Sum_probs=54.1

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++|.+|+++|.+.  ++.|+++.||.+||+|..|+++| .+..|+.+++++||+.||.++..
T Consensus        15 ~~~C~~C~~~I~~~--~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~~~   74 (79)
T 1x62_A           15 LPMCDKCGTGIVGV--FVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARERVS   74 (79)
T ss_dssp             CCCCSSSCCCCCSS--CEECSSCEECTTTTSCSSSCCCH-HHHCCEESSSCEECHHHHHHHHS
T ss_pred             CCccccCCCCccCc--EEEECcceeCcCcCeeCCCCCCC-CCCCeEeECCEEECHHHHHHHhC
Confidence            57999999999964  89999999999999999999999 56678999999999999987765

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=99.03  E-value=7.2e-11  Score=103.00  Aligned_cols=61  Identities=31%  Similarity=0.592  Sum_probs=54.0

Q ss_pred             cccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        615 FGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       615 f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ...+|.+|+++|.+  .+|.|+++.||.+||+|..|+++|. +..|+.+++++||+.||.++..
T Consensus        24 ~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~y~~~f~   84 (89)
T 1x64_A           24 RMPLCDKCGSGIVG--AVVKARDKYRHPECFVCADCNLNLK-QKGYFFVEGELYCETHARARTS   84 (89)
T ss_dssp             SCCBCTTTCCBCCS--CCEESSSCEECTTTCCCSSSCCCTT-TSCCEEETTEEECHHHHHHHSS
T ss_pred             cCCCcccCCCEecc--cEEEECCceECccCCEecCCCCCCC-CCCeEeECCEEECHHHHHHHhC
Confidence            45799999999996  4799999999999999999999994 5568889999999999987765

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.02  E-value=1.4e-10  Score=99.17  Aligned_cols=61  Identities=26%  Similarity=0.621  Sum_probs=53.4

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      .++|.+|+++|..++ ++.|+++.||.+||+|..|+++|. + .|+.+++++||+.||.++...
T Consensus        15 ~~~C~~C~~~I~~~~-~v~a~~~~wH~~CF~C~~C~~~L~-~-~~~~~~g~~yC~~~y~~~fg~   75 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQ-SLLALDKQWHVSCFKCQTCSVILT-G-EYISKDGVPYCESDYHAQFGS   75 (80)
T ss_dssp             CSCCTTTCCCCSSSC-CEEETTEEECTTTCBCSSSCCBCS-S-CCEEETTEEECTTHHHHHTTC
T ss_pred             CCCCcCcCCeeCCCe-EEEECCcccccccCCcCcCCCCcC-C-CeEEECCEEECHHHHHHHcCC
Confidence            468999999998654 577999999999999999999994 5 599999999999999887653

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=99.01  E-value=5.8e-11  Score=110.38  Aligned_cols=95  Identities=19%  Similarity=0.357  Sum_probs=71.4

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccCCcccCCCCCCcccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDGGTTSSDDGADSESS  693 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~~~~s~~~g~~~~~~  693 (768)
                      .|+++|.+|+++|..++ ++.|+|+.||++||+|..|+++| .+..|+.++|++||+.||.++...              
T Consensus         1 ~~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~~~~--------------   64 (126)
T 2xqn_T            1 SEKPRCAGCDELIFSNE-YTQAENQNWHLKHFCCFDCDSIL-AGEIYVMVNDKPVCKPCYVKNHAV--------------   64 (126)
T ss_dssp             -CCCBBTTTSSBCCSSC-EEEETTEEECGGGSBCTTTCCBC-TTSEEEEETTEEEEHHHHHHHSCC--------------
T ss_pred             CcCCCCccCCCEeCCce-EEeeCCCCccCCCCCcCCCCCCC-CcCEEEeECCEEechHHhCcCcCc--------------
Confidence            37899999999999653 68899999999999999999999 577899999999999999876542              


Q ss_pred             cCCCccccccccccH--HHHHHHhhccc--cCCCCCHHH
Q psy17256        694 HSKSKAKRVRTTFTE--EQLQVLQANFQ--LDSNPDGQD  728 (768)
Q Consensus       694 ~~~~k~rr~Rt~~s~--~Ql~~Le~~F~--~~~~p~~~~  728 (768)
                          +..+....|.+  ..+..+...|+  ...|-....
T Consensus        65 ----~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C   99 (126)
T 2xqn_T           65 ----VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCC   99 (126)
T ss_dssp             ----BCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTT
T ss_pred             ----cCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCC
Confidence                23333334442  22445566677  666655443

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A

Probab=99.00  E-value=9.6e-11  Score=100.26  Aligned_cols=63  Identities=29%  Similarity=0.659  Sum_probs=53.5

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++++|.+|+++|.+++ ++.|.++.||.+||+|..|+++|. +..|+.+++++||+.||.++..
T Consensus         5 ~~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   67 (81)
T 1a7i_A            5 GGGNKCGACGRTVYHAE-EVQCDGRSFHRCCFLCMVCRKNLD-STTVAIHDAEVYCKSCYGKKYG   67 (81)
T ss_dssp             ---CBCSSSCCBCSSTT-EEEETTEEEESSSEECSSSCCEEC-SSCCEEETTEEECSHHHHHHCC
T ss_pred             CCCCcCcCcCccccCce-eEEeCCcccccccCccCCCCCCCC-CCCeEeeCCEEECHHHHHHHhC
Confidence            34679999999998655 578999999999999999999994 5579999999999999987765

>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=99.00  E-value=7e-11  Score=96.06  Aligned_cols=46  Identities=22%  Similarity=0.613  Sum_probs=44.1

Q ss_pred             HHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhH
Q psy17256        708 EEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR  753 (768)
Q Consensus       708 ~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak  753 (768)
                      .+|+..|+.+|..+++|+..++..||..+||+.++|+|||||||++
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            4689999999999999999999999999999999999999999985

>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=98.99  E-value=2.9e-11  Score=120.04  Aligned_cols=61  Identities=20%  Similarity=0.366  Sum_probs=53.8

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhC---------------------CCCCccccccccchhHH
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------------LSKRVTQVWFQNSRARQ  754 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lg---------------------ls~~~V~vWFQNrRak~  754 (768)
                      .++.+|.|+.|+..|+..|++.|..++||+...|+.||..++                     |++.+|++||||||+++
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            467789999999999999999999999999999999999999                     99999999999999997


Q ss_pred             Hh
Q psy17256        755 KK  756 (768)
Q Consensus       755 kk  756 (768)
                      |.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            64

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.98  E-value=1.1e-10  Score=102.18  Aligned_cols=67  Identities=27%  Similarity=0.648  Sum_probs=57.2

Q ss_pred             hhhhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCcccccccccccccC
Q psy17256        611 CFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       611 y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      |...++.+|.+|+++|.+.+. +.|+++.||.+||+|..|+++|..+ .|+..++++||+.||.++...
T Consensus        10 ~~~~~~~~C~~C~~~I~~~~~-v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~~   76 (91)
T 2d8y_A           10 FQAPARETCVECQKTVYPMER-LLANQQVFHISCFRCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFKS   76 (91)
T ss_dssp             SCSSSSCBCTTTCCBCCTTSE-EECSSSEEETTTCBCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSCC
T ss_pred             cCCCCCCcCccCCCccCCcee-EEECCCEECCCCCeeCCCCCCCCCC-CcEeECCEEECHHHHHHHhCC
Confidence            444567899999999997654 6899999999999999999999544 588999999999999887764

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3

Probab=98.96  E-value=2.3e-10  Score=96.57  Aligned_cols=60  Identities=25%  Similarity=0.595  Sum_probs=52.5

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccc-cccccccc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCK-SHYLELVD  678 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~-~~y~e~~~  678 (768)
                      ++|.+|+++|..++ .+.|+++.||.+||+|..|+++|. +..|+.+++++||+ .||.++..
T Consensus         1 p~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~cy~~~f~   61 (76)
T 1iml_A            1 PKCPKCDKEVYFAE-RVTSLGKDWHRPCLKCEKCGKTLT-SGGHAEHEGKPYCNHPCYSAMFG   61 (76)
T ss_dssp             CBCTTTSSBCCGGG-EEEETTEEEETTTCBCTTTCCBCC-TTTEEEETTEEEETTTHHHHHSS
T ss_pred             CcCCCCCCEEECce-EEEECCccccCCCCCccccCccCC-CCceECcCCeEeeCHHHHHHHhC
Confidence            58999999999654 478999999999999999999995 44799999999999 69987765

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=98.91  E-value=4e-10  Score=97.09  Aligned_cols=56  Identities=25%  Similarity=0.341  Sum_probs=51.8

Q ss_pred             ccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         65 TTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        65 t~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..|+..++..|+..|..   ++||+..+|++||..+||++.||++||||+|+|+++...
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~   68 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDML   68 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHH
Confidence            46899999999999987   999999999999999999999999999999999987643

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.89  E-value=4.3e-10  Score=102.73  Aligned_cols=63  Identities=29%  Similarity=0.633  Sum_probs=55.5

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCC-CCceEeecCcccccccccccccC
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLST-GEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~-G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      .++|.+|+++|.+. .++.|+++.||.+||+|..|+++|.. |..|+.+++++||+.||.++...
T Consensus         3 ~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~   66 (114)
T 1j2o_A            3 LLTCGGCQQNIGDR-YFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGS   66 (114)
T ss_dssp             CBCBSSSCSCBCSS-EEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTS
T ss_pred             CCCCcCCCCeeCCc-EEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCc
Confidence            36899999999954 47889999999999999999999963 67899999999999999887654

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=98.87  E-value=3.6e-10  Score=97.44  Aligned_cols=57  Identities=25%  Similarity=0.334  Sum_probs=52.4

Q ss_pred             ccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        704 TTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       704 t~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ..|+.+++..|+..|..   ++||+..++..||.++||++.||++||||+|+|+++....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~   69 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLR   69 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHH
Confidence            46788999999999977   9999999999999999999999999999999999987543

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.87  E-value=2.6e-10  Score=105.47  Aligned_cols=64  Identities=27%  Similarity=0.593  Sum_probs=56.4

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccC-CCCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLS-TGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~-~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++++|++|+++|.+. .++.|+++.||++||+|..|+.+|. .|..|+.+++++||+.||.++..
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~   67 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   67 (122)
T ss_dssp             SCCCCBSSSSSCCCSS-CCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHC
T ss_pred             CCCCCCcccCCEeCCc-EEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcC
Confidence            4678999999999975 3578999999999999999999995 25779999999999999988765

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=98.84  E-value=4.5e-10  Score=112.55  Aligned_cols=60  Identities=20%  Similarity=0.396  Sum_probs=53.3

Q ss_pred             CCCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhC---------------------CCCCccccccccchhH
Q psy17256        695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------------LSKRVTQVWFQNSRAR  753 (768)
Q Consensus       695 ~~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lg---------------------ls~~~V~vWFQNrRak  753 (768)
                      ..++.+|.|+.|+..|+..|+..|..++||+..+|+.||..++                     |++.+|++||||||++
T Consensus       138 ~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             ccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            4577899999999999999999999999999999999999987                     7899999999999986


Q ss_pred             H
Q psy17256        754 Q  754 (768)
Q Consensus       754 ~  754 (768)
                      .
T Consensus       218 ~  218 (221)
T 2h8r_A          218 E  218 (221)
T ss_dssp             C
T ss_pred             h
Confidence            3

>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=98.75  E-value=9.6e-10  Score=122.15  Aligned_cols=57  Identities=21%  Similarity=0.411  Sum_probs=53.8

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      .++.|+.|+..|+..||+.|+.++||+..+|++||.++||+++||+|||||||+|+|
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            456688999999999999999999999999999999999999999999999999876

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=98.73  E-value=3.9e-09  Score=98.62  Aligned_cols=61  Identities=30%  Similarity=0.694  Sum_probs=54.2

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCccccccccccCC-CCceEeecCccccccccccccc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLST-GEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~-G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ++|++|+++|.+. .++.|+++.||++||+|..|+.+|.. |..|+.++|++||+.||.++..
T Consensus         3 ~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~   64 (131)
T 2xjy_A            3 LTCGGCQQNIGDR-YFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG   64 (131)
T ss_dssp             CBBTTTCCBCCSS-EEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHC
T ss_pred             ccCcCCCCEeCCc-EEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCC
Confidence            6899999999964 36889999999999999999999963 6789999999999999988764

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=98.69  E-value=3.5e-09  Score=105.38  Aligned_cols=64  Identities=27%  Similarity=0.596  Sum_probs=56.1

Q ss_pred             hcccccccCCCCCCCCcceeeecCceecccCccccccccccCC-CCceEeecCccccccccccccc
Q psy17256        614 SFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLST-GEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       614 ~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~-G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ++.++|++|+++|.+. .++.|+++.||.+||+|..|+.+|.. |..|+.+++++||+.||.++..
T Consensus         3 l~~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~   67 (188)
T 1rut_X            3 LSWKRCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   67 (188)
T ss_dssp             -CCCBBTTTCCBCCCS-EEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CCCCcCccCCCEeCCc-eeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccc
Confidence            4678999999999964 46889999999999999999999965 6789999999999999987654

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus}

Probab=98.66  E-value=5.1e-09  Score=103.60  Aligned_cols=63  Identities=24%  Similarity=0.536  Sum_probs=53.5

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      ....++|.+|+++|... .++.|+++.||.+||+|..|+++|. +..| .++|++||+.||.++..
T Consensus        57 ~~~~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~~y~~~f~  119 (182)
T 2jtn_A           57 TPEIPMCAGCDQHILDR-FILKALDRHWHSKCLKCSDCHVPLA-ERCF-SRGESVYCKDDFFKRFG  119 (182)
T ss_dssp             CCSCCBCBTSSSBCCCS-EEEEETTEEECSSTTSCTTTCCCCS-SCCE-EETTEEECHHHHHHTTS
T ss_pred             CCCCCcCccCCCCccCc-eeEEecCCeEccccCccCCCCCccC-CCce-eECCEeeecCccccccc
Confidence            45567999999999964 4678999999999999999999994 4445 68999999999987764

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3

Probab=98.63  E-value=4e-09  Score=88.97  Aligned_cols=70  Identities=11%  Similarity=-0.092  Sum_probs=55.7

Q ss_pred             cchhhhhhhhh-hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch-
Q psy17256        531 LEFHSFLKRIA-LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV-  608 (768)
Q Consensus       531 ~~C~~c~k~Ia-~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~-  608 (768)
                      |.|..|.++|. +..+.+.++      .||+.||.|+.|+..+.               +  ..++.+++.+    ||. 
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~~~~~~g~~----yC~~   53 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGK------DWHRPCLKCEKCGKTLT---------------S--GGHAEHEGKP----YCNH   53 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTE------EEETTTCBCTTTCCBCC---------------T--TTEEEETTEE----EETT
T ss_pred             CcCCCCCCEEECceEEEECCc------cccCCCCCccccCccCC---------------C--CceECcCCeE----eeCH
Confidence            45899999997 666677777      99999999999995433               1  2357788888    456 


Q ss_pred             hhhhhhcccccccCCCCCC
Q psy17256        609 LICFRSFGAKCSKCCRGIA  627 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~  627 (768)
                      .||.++|+++|.+|++++.
T Consensus        54 ~cy~~~f~~~C~~C~~~~~   72 (76)
T 1iml_A           54 PCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             THHHHHSSCCCSSCCCSSS
T ss_pred             HHHHHHhCccCCCcCCcee
Confidence            5999999999999997664

>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=98.62  E-value=3.5e-09  Score=117.64  Aligned_cols=58  Identities=21%  Similarity=0.401  Sum_probs=54.5

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      ..++.++.++..|+..|++.|+.++||+..+|.+||.++||+++||+|||||||+|+|
T Consensus       364 ~~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          364 AQTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            3466788999999999999999999999999999999999999999999999999976

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A

Probab=98.57  E-value=5.8e-09  Score=89.06  Aligned_cols=70  Identities=9%  Similarity=-0.099  Sum_probs=46.2

Q ss_pred             ccchhhhhhhhh-hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIA-LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia-~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      ++.|..|.+.|. ...+.+.++      .||+.||+|+.|+..+..                 ..++.+++.+||    .
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~------~~H~~CF~C~~C~~~L~~-----------------~~~~~~~~~~yC----~   59 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGR------SFHRCCFLCMVCRKNLDS-----------------TTVAIHDAEVYC----K   59 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTE------EEESSSEECSSSCCEECS-----------------SCCEEETTEEEC----S
T ss_pred             CCcCcCcCccccCceeEEeCCc------ccccccCccCCCCCCCCC-----------------CCeEeeCCEEEC----H
Confidence            456999999995 555667777      999999999999954331                 235777888854    5


Q ss_pred             hhhhhhcccccccCCCCC
Q psy17256        609 LICFRSFGAKCSKCCRGI  626 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I  626 (768)
                      .||.++|+++|.+|++..
T Consensus        60 ~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A           60 SCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             HHHHHHCC----------
T ss_pred             HHHHHHhCCcccccCCcc
Confidence            899999999999999765

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A

Probab=98.54  E-value=1.9e-08  Score=100.36  Aligned_cols=61  Identities=30%  Similarity=0.675  Sum_probs=53.3

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      +++|.+|+++|..++. +.|+++.||.+||+|..|+++|. +..|+.+++++||+.||.++..
T Consensus         7 ~~~C~~C~~~I~~~~~-v~a~g~~wH~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~   67 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEE-VQCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKKYG   67 (192)
T ss_dssp             CEECTTTCCEECSSCC-EEETTEEECTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHHS
T ss_pred             CCcCccCCCeecceeE-EEeCCceecCCCCcCcccCCcCC-CCeeEecCCEeeChhhhHhhcC
Confidence            4699999999986654 57999999999999999999994 4569999999999999987754

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=98.52  E-value=2.8e-08  Score=97.12  Aligned_cols=60  Identities=25%  Similarity=0.583  Sum_probs=50.9

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCccccccccccCCCCceEeecCccccccccccccc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACFACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .++|.+|+++|.+. .++.|+|+.||.+||+|..|+.+|. +..| .++|++||+.||.++..
T Consensus         6 ~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~~y~~~f~   65 (169)
T 2rgt_A            6 IPMCAGCDQHILDR-FILKALDRHWHSKCLKCSDCHVPLA-ERCF-SRGESVYCKDDFFKRFG   65 (169)
T ss_dssp             -CBBSSSSSBCCSS-SCEECSSCEECTTTSBCTTTCCBCC-SCCE-ESSSCEECHHHHHHHHS
T ss_pred             CCccccCCCccCCc-EEEEECCcEEccccCccCCCCCcCC-CCCc-ccCCeeeeccccccccc
Confidence            47999999999864 4678999999999999999999994 4444 78999999999987654

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.50  E-value=1e-08  Score=86.45  Aligned_cols=69  Identities=6%  Similarity=-0.164  Sum_probs=55.0

Q ss_pred             cccchhhhhhhhhh----HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccc
Q psy17256        529 LHLEFHSFLKRIAL----VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKG  604 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~----~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~  604 (768)
                      .++.|..|.++|.+    ..+.+.++      .||..||.|+.|+..+.                + ..++.+++.+|| 
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~------~wH~~CF~C~~C~~~L~----------------~-~~f~~~~g~~yC-   59 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDS------QWHSECFNCGKCSVSLV----------------G-KGFLTQNKEIFC-   59 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTE------EEEGGGCBCTTTCCBCS----------------S-SCEEEETTEEEE-
T ss_pred             cCCCCccCCCcccCCCCceeEEECCc------ccCcccCChhhCCCcCC----------------C-CceEeECCEEEC-
Confidence            35669999999997    67777787      99999999999985432                1 235778888854 


Q ss_pred             ccchhhhhhhcccccccCCC
Q psy17256        605 RLSVLICFRSFGAKCSKCCR  624 (768)
Q Consensus       605 ~yC~~~y~~~f~~~C~~C~~  624 (768)
                         ..||.++|+++|+.|.+
T Consensus        60 ---~~cy~~~f~~~C~~~sg   76 (76)
T 1x68_A           60 ---QKCGSGMDTDISGPSSG   76 (76)
T ss_dssp             ---TTTTCCCCCCSSSSSCC
T ss_pred             ---HHHhhhhhCCcCCCCCC
Confidence               58999999999998863

>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=98.49  E-value=2.6e-08  Score=71.11  Aligned_cols=22  Identities=36%  Similarity=0.721  Sum_probs=19.3

Q ss_pred             CccccccccchhHHHhhhhccc
Q psy17256        741 RVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       741 ~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +||+||||||||||||++....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            5899999999999999987643

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.47  E-value=1.5e-08  Score=86.15  Aligned_cols=77  Identities=6%  Similarity=-0.147  Sum_probs=59.2

Q ss_pred             cccccccccccccccccccccCCccccchhhhhhhhhhHHHHHhhcccccccccccceEEEecccccccccccccccccc
Q psy17256        505 LKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKP  584 (768)
Q Consensus       505 ~ky~~~c~~~~~~F~Pl~~s~~G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~  584 (768)
                      ..|+..|+..             ..++.|..|.++|.+..+.+.++      .||..||+|+.|+..+.           
T Consensus         3 ~~yC~~~y~~-------------~~~~~C~~C~~~I~~~~v~a~~~------~~H~~CF~C~~C~~~L~-----------   52 (80)
T 1x3h_A            3 SGSSGKDFLA-------------MFSPKCGGCNRPVLENYLSAMDT------VWHPECFVCGDCFTSFS-----------   52 (80)
T ss_dssp             CCCCCCCCCC-------------CCSCBCTTTCCBCCSSCEEETTE------EECTTTCBCSSSCCBSC-----------
T ss_pred             CccchhHHhh-------------hcCCccccCCCeecceeEEECCC------eEecCcCChhhCCCCCC-----------
Confidence            3566676654             23567999999999887777787      99999999999995433           


Q ss_pred             ccccCCCCcceeecccccccccchhhhhhhccccccc
Q psy17256        585 YGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSK  621 (768)
Q Consensus       585 ~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~~C~~  621 (768)
                          +  ..++.+++.+|    |..||.++|+++|++
T Consensus        53 ----~--~~~~~~~~~~y----C~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           53 ----T--GSFFELDGRPF----CELHYHHRRGSGPSS   79 (80)
T ss_dssp             ----S--SCCEESSSCEE----CHHHHHHHHSSSCCC
T ss_pred             ----C--CcEEeECCEEE----CHHHHHHHcCCCCCC
Confidence                1  23567788884    569999999999964

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.43  E-value=2e-08  Score=87.60  Aligned_cols=68  Identities=15%  Similarity=-0.064  Sum_probs=54.0

Q ss_pred             CccccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccccc
Q psy17256        527 GALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRL  606 (768)
Q Consensus       527 G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~y  606 (768)
                      +..++.|..|.+.|.+..+.+.++      .||+.||.|+.|+..+.   +              ..++.+++.+|    
T Consensus        22 ~~~~~~C~~C~~~I~~~~v~a~~~------~~H~~CF~C~~C~~~L~---~--------------~~f~~~~g~~y----   74 (90)
T 2dar_A           22 GKRTPMCAHCNQVIRGPFLVALGK------SWHPEEFNCAHCKNTMA---Y--------------IGFVEEKGALY----   74 (90)
T ss_dssp             TTCCCBBSSSCCBCCSCEEEETTE------EECTTTCBCSSSCCBCS---S--------------SCBEESSSCEE----
T ss_pred             CCCCCCCccCCCEecceEEEECCc------cccccCCccCCCCCCCC---C--------------CEeEeECCEEE----
Confidence            345667999999999888888887      99999999999995433   1              13567788884    


Q ss_pred             chhhhhhhccccccc
Q psy17256        607 SVLICFRSFGAKCSK  621 (768)
Q Consensus       607 C~~~y~~~f~~~C~~  621 (768)
                      |..||.++|+++|+.
T Consensus        75 C~~cy~~~f~~~c~s   89 (90)
T 2dar_A           75 CELCYEKFFASGPSS   89 (90)
T ss_dssp             CHHHHHHHTSCCCCC
T ss_pred             CHHHHHHHcCCCCCC
Confidence            568999999999963

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.40  E-value=2e-08  Score=82.89  Aligned_cols=65  Identities=9%  Similarity=-0.168  Sum_probs=52.0

Q ss_pred             ccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        530 HLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      ++.|..|.+.|.+..+.+.++      .||+.||.|+.|+..+.   |              ..++.+++.+|    |..
T Consensus         5 ~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~---~--------------~~~~~~~~~~y----C~~   57 (69)
T 2cur_A            5 SSGCVKCNKAITSGGITYQDQ------PWHADCFVCVTCSKKLA---G--------------QRFTAVEDQYY----CVD   57 (69)
T ss_dssp             CCCCSSSCCCCCTTCEEETTE------EECTTTTBCTTTCCBCT---T--------------SCEEECSSCEE----EHH
T ss_pred             cCCCcccCCEeCcceEEECcc------ccccCcCEECCCCCCCC---C--------------CccEeECCEEE----CHH
Confidence            456999999998877777777      99999999999995432   1              23567778884    569


Q ss_pred             hhhhhccccccc
Q psy17256        610 ICFRSFGAKCSK  621 (768)
Q Consensus       610 ~y~~~f~~~C~~  621 (768)
                      ||.++|+++|++
T Consensus        58 cy~~~f~~~C~g   69 (69)
T 2cur_A           58 CYKNFVSGPSSG   69 (69)
T ss_dssp             HHHHHHTCSCCC
T ss_pred             HhHHHhcCCCCC
Confidence            999999999975

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.40  E-value=3.4e-08  Score=83.15  Aligned_cols=68  Identities=10%  Similarity=-0.038  Sum_probs=52.9

Q ss_pred             Cccccchhhhhhhhh-hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccc
Q psy17256        527 GALHLEFHSFLKRIA-LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGR  605 (768)
Q Consensus       527 G~~g~~C~~c~k~Ia-~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~  605 (768)
                      .+.++.|..|.++|. ...+.+.++      .||+.||.|+.|+..+..                 ..++.+++.+    
T Consensus         6 ~~~~~~C~~C~~~I~~~~~v~a~~~------~~H~~CF~C~~C~~~L~~-----------------~~~~~~~g~~----   58 (76)
T 2cu8_A            6 SGMASKCPKCDKTVYFAEKVSSLGK------DWHKFCLKCERCSKTLTP-----------------GGHAEHDGKP----   58 (76)
T ss_dssp             CCCCCBCTTTCCBCCTTTEEEETTE------EEETTTCBCSSSCCBCCT-----------------TSCEEETTEE----
T ss_pred             CCCCCCCcCCCCEeECCeEEEECCe------EeeCCCCCCCCCCCccCC-----------------CceEeECCEE----
Confidence            345677999999998 556667777      999999999999954331                 2356788888    


Q ss_pred             cch-hhhhhhccccccc
Q psy17256        606 LSV-LICFRSFGAKCSK  621 (768)
Q Consensus       606 yC~-~~y~~~f~~~C~~  621 (768)
                      ||. .||.++|+++|.+
T Consensus        59 yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A           59 FCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             ECTTTHHHHHSCSSCSC
T ss_pred             ecchHHHHHhcccccCC
Confidence            456 5999999999974

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.39  E-value=3e-08  Score=83.64  Aligned_cols=68  Identities=7%  Similarity=-0.166  Sum_probs=52.2

Q ss_pred             CCccccchhhhhhhhh--hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccc
Q psy17256        526 DGALHLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLK  603 (768)
Q Consensus       526 ~G~~g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c  603 (768)
                      +++.++.|..|.+.|.  +.++.+.++      .||..||.|+.|+..+..                 +.++.+++.+| 
T Consensus         7 ~~~~~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~~-----------------~~~~~~~g~~y-   62 (77)
T 1g47_A            7 NALASATCERCKGGFAPAEKIVNSNGE------LYHEQCFVCAQCFQQFPE-----------------GLFYEFEGRKY-   62 (77)
T ss_dssp             SCCCCCBCSSSCCBCCSTTTCEEETTE------EECTTTCCCTTTCCCCGG-----------------GCSEEETTEEE-
T ss_pred             cCCCCCCchhcCCccCCCceEEEeCcc------EeccccCeECCCCCCCCC-----------------CCeEeECCeEe-
Confidence            4455677999999995  666678887      999999999999955431                 23577888884 


Q ss_pred             cccchhhhhhhcccccc
Q psy17256        604 GRLSVLICFRSFGAKCS  620 (768)
Q Consensus       604 ~~yC~~~y~~~f~~~C~  620 (768)
                         |..||.++|+++|+
T Consensus        63 ---C~~~y~~~f~~~C~   76 (77)
T 1g47_A           63 ---CEHDFQMLFAPCWI   76 (77)
T ss_dssp             ---CHHHHHHHCCCC--
T ss_pred             ---CHHHHHHHhhcccC
Confidence               56999999999995

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.39  E-value=2.9e-08  Score=84.87  Aligned_cols=77  Identities=8%  Similarity=-0.174  Sum_probs=58.5

Q ss_pred             cccccccccccccccccccccCCccccchhhhhhhhh--hHHHHHhhcccccccccccceEEEecccccccccccccccc
Q psy17256        505 LKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIV  582 (768)
Q Consensus       505 ~ky~~~c~~~~~~F~Pl~~s~~G~~g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~  582 (768)
                      ..|+..|+..             ..++.|..|.++|.  +.++.+.++      .||+.||+|+.|+..+.         
T Consensus         3 ~~yC~~~y~~-------------~~~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------   54 (82)
T 2ehe_A            3 SGSSGPCYDN-------------TFANTCAECQQLIGHDSRELFYEDR------HFHEGCFRCCRCQRSLA---------   54 (82)
T ss_dssp             CCCCCCCCCC-------------CCSCBCTTTCCBCCSSCCBCCCSSC------CCBTTTSBCTTTCCBCS---------
T ss_pred             ceechhHhCc-------------ccCCcCccCCCccccCcEEEEeCCc------cccccCCeecCCCCccC---------
Confidence            3567777654             24567999999998  667777787      99999999999995432         


Q ss_pred             ccccccCCCCcceeecccccccccchhhhhhhccccccc
Q psy17256        583 KPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSK  621 (768)
Q Consensus       583 ~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~~C~~  621 (768)
                             + ..++.+++.+||    ..||.++|+++|++
T Consensus        55 -------~-~~f~~~~~~~~C----~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           55 -------D-EPFTCQDSELLC----NDCYCSAFSSGPSS   81 (82)
T ss_dssp             -------S-CCEEEETTEEEE----TTTSSCCGGGSSCC
T ss_pred             -------C-CccEeeCCEEEC----HHHHhhhcCCCCCC
Confidence                   1 235678888854    58999999999964

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.38  E-value=2.6e-08  Score=82.38  Aligned_cols=65  Identities=9%  Similarity=-0.040  Sum_probs=51.4

Q ss_pred             ccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        530 HLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      ++.|..|.++|.+..+.+.++      .||+.||.|+.|+..+.                + ..++.+++.+|    |..
T Consensus         5 ~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~----------------~-~~~~~~~~~~y----C~~   57 (70)
T 2d8z_A            5 SSGCVQCKKPITTGGVTYREQ------PWHKECFVCTACRKQLS----------------G-QRFTARDDFAY----CLN   57 (70)
T ss_dssp             CCBCSSSCCBCCSSEEESSSS------EEETTTSBCSSSCCBCT----------------T-SCCEESSSSEE----CHH
T ss_pred             CCCCcccCCeeccceEEECcc------ccCCCCCccCCCCCcCC----------------c-CceEeeCCeEE----CHH
Confidence            456999999998877777777      99999999999995432                1 23567778884    569


Q ss_pred             hhhhhccccccc
Q psy17256        610 ICFRSFGAKCSK  621 (768)
Q Consensus       610 ~y~~~f~~~C~~  621 (768)
                      ||.++|+++|++
T Consensus        58 cy~~~f~~~c~~   69 (70)
T 2d8z_A           58 CFCDLYASGPSS   69 (70)
T ss_dssp             HHHHHTCCCCTT
T ss_pred             HHHHHhccccCC
Confidence            999999999964

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.36  E-value=3.2e-08  Score=84.35  Aligned_cols=63  Identities=11%  Similarity=-0.011  Sum_probs=50.1

Q ss_pred             cchhhhhhhhh-hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        531 LEFHSFLKRIA-LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       531 ~~C~~c~k~Ia-~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      +.|..|.++|. ..++.+.++      .||+.||+|+.|+..+.                +  .++.+++.+|    |..
T Consensus        16 ~~C~~C~~~I~~~~~v~a~~~------~wH~~CF~C~~C~~~L~----------------~--~~~~~~g~~y----C~~   67 (80)
T 2dj7_A           16 SHCAGCKEEIKHGQSLLALDK------QWHVSCFKCQTCSVILT----------------G--EYISKDGVPY----CES   67 (80)
T ss_dssp             SCCTTTCCCCSSSCCEEETTE------EECTTTCBCSSSCCBCS----------------S--CCEEETTEEE----CTT
T ss_pred             CCCcCcCCeeCCCeEEEECCc------ccccccCCcCcCCCCcC----------------C--CeEEECCEEE----CHH
Confidence            45999999996 456667777      99999999999984321                1  3578888995    458


Q ss_pred             hhhhhccccccc
Q psy17256        610 ICFRSFGAKCSK  621 (768)
Q Consensus       610 ~y~~~f~~~C~~  621 (768)
                      ||.++|+++|++
T Consensus        68 ~y~~~fg~~C~~   79 (80)
T 2dj7_A           68 DYHAQFGSGPSS   79 (80)
T ss_dssp             HHHHHTTCCSTT
T ss_pred             HHHHHcCCCCCC
Confidence            999999999974

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.36  E-value=4e-08  Score=83.77  Aligned_cols=65  Identities=9%  Similarity=-0.049  Sum_probs=49.9

Q ss_pred             ccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceee-cccccccccch
Q psy17256        530 HLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIR-VRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~-~~~~~c~~yC~  608 (768)
                      ++.|..|.++|.+.++.+.++      .||+.||+|+.|+..+.   |.              .++.+ ++.+    ||.
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~---~~--------------~f~~~~~g~~----yC~   67 (81)
T 2dlo_A           15 LEKCATCSQPILDRILRAMGK------AYHPGCFTCVVCHRGLD---GI--------------PFTVDATSQI----HCI   67 (81)
T ss_dssp             CCBCTTTCCBCCSCCEEETTE------EECTTTCBCSSSCCBCT---TS--------------CEECCTTCCC----EEH
T ss_pred             CCccccCCCeecceeEEECCc------cccHHhcCcccCCCccC---CC--------------eeEECCCCEE----ECH
Confidence            456999999999887788887      99999999999985432   11              12333 5677    456


Q ss_pred             hhhhhhccccccc
Q psy17256        609 LICFRSFGAKCSK  621 (768)
Q Consensus       609 ~~y~~~f~~~C~~  621 (768)
                      .||.++|+++|++
T Consensus        68 ~cy~~~f~~~C~~   80 (81)
T 2dlo_A           68 EDFHRKFASGPSS   80 (81)
T ss_dssp             HHHHHHTTSSSCC
T ss_pred             HHHHHHhcCcCCC
Confidence            9999999999974

>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=98.35  E-value=1.3e-07  Score=67.55  Aligned_cols=22  Identities=36%  Similarity=0.721  Sum_probs=19.0

Q ss_pred             ccccccccccHHHHhhhcccCC
Q psy17256        102 RVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus       102 ~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      +||+|||||||+|||++.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            5899999999999999877643

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.35  E-value=4.2e-08  Score=83.37  Aligned_cols=77  Identities=10%  Similarity=-0.079  Sum_probs=58.5

Q ss_pred             cccccccccccccccccccccCCccccchhhhhhhhhhHHHHHhhcccccccccccceEEEecccccccccccccccccc
Q psy17256        505 LKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKP  584 (768)
Q Consensus       505 ~ky~~~c~~~~~~F~Pl~~s~~G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~  584 (768)
                      ..|+..|+.+             ..++.|..|.+.|.+..+.+.++      .||..||+|+.|+..+.           
T Consensus         3 ~~yC~~cy~~-------------~~~~~C~~C~~~I~~~~v~a~~~------~~H~~CF~C~~C~~~L~-----------   52 (80)
T 2cuq_A            3 SGSSGPCYEN-------------KFAPRCARCSKTLTQGGVTYRDQ------PWHRECLVCTGCQTPLA-----------   52 (80)
T ss_dssp             CCSCCCCCCC-------------CSSCCCTTTCCCCCSCCEESSSS------EECTTTCBCSSSCCBCT-----------
T ss_pred             cEEcHHHHcc-------------ccCCcCCCCCCEecCcEEEECCc------hhhhhhCCcccCCCcCC-----------
Confidence            3566676654             23567999999998887777777      99999999999995432           


Q ss_pred             ccccCCCCcceeecccccccccchhhhhhhccccccc
Q psy17256        585 YGFDDGAGLMYIRVRILLKGRLSVLICFRSFGAKCSK  621 (768)
Q Consensus       585 ~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~~C~~  621 (768)
                           + ..++.+++.+|    |..||.++|+++|+.
T Consensus        53 -----~-~~~~~~~~~~y----C~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           53 -----G-QQFTSRDEDPY----CVACFGELFASGPSS   79 (80)
T ss_dssp             -----T-CCEEECSSSEE----EHHHHHHHTTCSTTC
T ss_pred             -----C-CeeEeECCEEE----CHHHHHHHcCCCCCC
Confidence                 1 23567788884    569999999999963

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.34  E-value=4.4e-08  Score=81.41  Aligned_cols=66  Identities=9%  Similarity=-0.169  Sum_probs=52.2

Q ss_pred             cccchhhhhhhhh--hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccccc
Q psy17256        529 LHLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRL  606 (768)
Q Consensus       529 ~g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~y  606 (768)
                      .++.|..|.++|.  +.++.+.++      .||..||.|+.|+..+.               +  ..++.+++.+|    
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~~~~~~~~~y----   56 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQ------TWHEHCFLCSGCEQPLG---------------S--RSFVPDKGAHY----   56 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTC------CEETTTCBCTTTCCBTT---------------T--SCEEEETTEEE----
T ss_pred             cCCCCccCCCccccCccEEEECcc------ccCcccCeECCCCCcCC---------------C--CccCCcCCeEE----
Confidence            3566999999998  567777887      99999999999995432               1  23567788884    


Q ss_pred             chhhhhhhccccccc
Q psy17256        607 SVLICFRSFGAKCSK  621 (768)
Q Consensus       607 C~~~y~~~f~~~C~~  621 (768)
                      |..||.++|+++|+.
T Consensus        57 C~~cy~~~f~~~C~~   71 (72)
T 1wyh_A           57 CVPCYENKFASGPSS   71 (72)
T ss_dssp             EHHHHHHHTSCCCCC
T ss_pred             CHHHHHHHccCcCCC
Confidence            569999999999963

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.31  E-value=7.7e-08  Score=83.63  Aligned_cols=65  Identities=6%  Similarity=-0.240  Sum_probs=52.2

Q ss_pred             ccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        530 HLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      .+.|..|.+.|.+..+.+.++      .||..||.|+.|+..+.               +  ..+|.+++.+|    |..
T Consensus        25 ~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~~~~~~g~~y----C~~   77 (89)
T 1x64_A           25 MPLCDKCGSGIVGAVVKARDK------YRHPECFVCADCNLNLK---------------Q--KGYFFVEGELY----CET   77 (89)
T ss_dssp             CCBCTTTCCBCCSCCEESSSC------EECTTTCCCSSSCCCTT---------------T--SCCEEETTEEE----CHH
T ss_pred             CCCcccCCCEecccEEEECCc------eECccCCEecCCCCCCC---------------C--CCeEeECCEEE----CHH
Confidence            345999999999987777787      99999999999995432               1  23577788884    568


Q ss_pred             hhhhhccccccc
Q psy17256        610 ICFRSFGAKCSK  621 (768)
Q Consensus       610 ~y~~~f~~~C~~  621 (768)
                      ||.++|+++|.+
T Consensus        78 ~y~~~f~p~~~g   89 (89)
T 1x64_A           78 HARARTSGPSSG   89 (89)
T ss_dssp             HHHHHSSSCCCC
T ss_pred             HHHHHhCCCCCC
Confidence            999999999864

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.28  E-value=5.3e-08  Score=80.94  Aligned_cols=66  Identities=11%  Similarity=-0.131  Sum_probs=51.9

Q ss_pred             cccchhhhhhhhh--hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccccc
Q psy17256        529 LHLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRL  606 (768)
Q Consensus       529 ~g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~y  606 (768)
                      .++.|..|.+.|.  +.++.+.++      .||..||.|+.|+..+.               +  ..++.+++.+|    
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~~~~~~~~~y----   56 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGS------SWHETCFICHRCQQPIG---------------T--KSFIPKDNQNF----   56 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTE------EEETTTTCCSSSCCCCC---------------S--SSEEEETTEEE----
T ss_pred             cCCCCccCCCcccCCceEEEECcC------eecccCCcccccCCccC---------------C--CccCccCCeEE----
Confidence            3566999999998  456777787      99999999999995432               1  24567888884    


Q ss_pred             chhhhhhhccccccc
Q psy17256        607 SVLICFRSFGAKCSK  621 (768)
Q Consensus       607 C~~~y~~~f~~~C~~  621 (768)
                      |..||.++|+++|+.
T Consensus        57 C~~cy~~~f~~~C~~   71 (72)
T 1x4k_A           57 CVPCYEKQHASGPSS   71 (72)
T ss_dssp             EHHHHHHHTSSCCCC
T ss_pred             CHHHHhHHhCCCCCC
Confidence            569999999999963

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.23  E-value=1.2e-07  Score=80.52  Aligned_cols=66  Identities=6%  Similarity=-0.302  Sum_probs=52.4

Q ss_pred             CccccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccccc
Q psy17256        527 GALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRL  606 (768)
Q Consensus       527 G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~y  606 (768)
                      +...+.|..|.+.|.+..+.+.++      .||+.||.|+.|+..+.               +   .+|.+++.+|    
T Consensus        12 ~~~~~~C~~C~~~I~~~~v~a~~~------~~H~~CF~C~~C~~~L~---------------~---~~f~~~g~~y----   63 (79)
T 2cor_A           12 GLGKYICQKCHAIIDEQPLIFKND------PYHPDHFNCANCGKELT---------------A---DARELKGELY----   63 (79)
T ss_dssp             CCCCCBCTTTCCBCCSCCCCCSSS------CCCTTTSBCSSSCCBCC---------------T---TCEEETTEEE----
T ss_pred             ccCCCCCccCCCEecceEEEECcc------eeCCCCCEeCCCCCccC---------------C---CCEeECCEEe----
Confidence            334566999999999888888888      99999999999995433               1   1367888884    


Q ss_pred             chhhhhhhcccccc
Q psy17256        607 SVLICFRSFGAKCS  620 (768)
Q Consensus       607 C~~~y~~~f~~~C~  620 (768)
                      |..||.++|++++.
T Consensus        64 C~~cy~~~f~p~~s   77 (79)
T 2cor_A           64 CLPCHDKMGVSGPS   77 (79)
T ss_dssp             CHHHHHTTSCCSSC
T ss_pred             CHHHHHHhCCCCCC
Confidence            56899999999774

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.23  E-value=1.1e-07  Score=81.26  Aligned_cols=65  Identities=17%  Similarity=0.019  Sum_probs=51.7

Q ss_pred             cccchhhhhhhhh--hHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccccc
Q psy17256        529 LHLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRL  606 (768)
Q Consensus       529 ~g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~y  606 (768)
                      .++.|..|.+.|.  ++++.+.++      .||+.||+|+.|+..+.               +  ..++.+++.+|    
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~~~~~~~~~y----   66 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGT------VWHKDCFTCSNCKQVIG---------------T--GSFFPKGEDFY----   66 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSC------EEETTTCCCSSSCCCCT---------------T--SCEEEETTEEE----
T ss_pred             cCCcCccCCcccccCceEEEECcc------ccccccCchhhCCCccC---------------C--CccEeeCCEEE----
Confidence            3566999999998  677778887      99999999999995433               1  24577888884    


Q ss_pred             chhhhhhhcccccc
Q psy17256        607 SVLICFRSFGAKCS  620 (768)
Q Consensus       607 C~~~y~~~f~~~C~  620 (768)
                      |..||.++|+++|.
T Consensus        67 C~~cy~~~f~~~~~   80 (82)
T 1x63_A           67 CVTCHETKFASGPS   80 (82)
T ss_dssp             EHHHHHHHTSCCCS
T ss_pred             CHHHHHHHhCCCCC
Confidence            56999999999985

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B

Probab=98.23  E-value=1.1e-07  Score=77.67  Aligned_cols=63  Identities=14%  Similarity=0.007  Sum_probs=50.2

Q ss_pred             cccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        529 LHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .++.|..|.+.|.+..+.+.++      .||+.||.|+.|+..+.                + ..++.+++.+|    |.
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~----------------~-~~~~~~~g~~y----C~   56 (66)
T 1nyp_A            4 GVPICGACRRPIEGRVVNAMGK------QWHVEHFVCAKCEKPFL----------------G-HRHYERKGLAY----CE   56 (66)
T ss_dssp             CCCEETTTTEECCSCEECCTTS------BEETTTCBCTTTCCBCS----------------S-SCCEEETTEEE----CH
T ss_pred             CCCCCcccCCEecceEEEECcc------ccccCcCEECCCCCCCC----------------C-CceEeECCcEE----CH
Confidence            3456999999999887778887      99999999999995432                1 24577888885    56


Q ss_pred             hhhhhhcccc
Q psy17256        609 LICFRSFGAK  618 (768)
Q Consensus       609 ~~y~~~f~~~  618 (768)
                      .||.++|+++
T Consensus        57 ~~y~~~f~~k   66 (66)
T 1nyp_A           57 THYNQLFGDV   66 (66)
T ss_dssp             HHHHHHCSCC
T ss_pred             HHHHHHhCCC
Confidence            8999999975

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.20  E-value=1.6e-07  Score=79.92  Aligned_cols=67  Identities=9%  Similarity=-0.109  Sum_probs=52.3

Q ss_pred             cccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcce-eecccccccccc
Q psy17256        529 LHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMY-IRVRILLKGRLS  607 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~-~~~~~~~c~~yC  607 (768)
                      .++.|..|.++|.+..+.+.++      .||+.||.|+.|+..+.               +|.. ++ .+++.+|    |
T Consensus        14 ~~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------------~g~~-f~~~~~~~~~----C   67 (81)
T 1x6a_A           14 FGEFCHGCSLLMTGPFMVAGEF------KYHPECFACMSCKVIIE---------------DGDA-YALVQHATLY----C   67 (81)
T ss_dssp             SSCBCTTTCCBCCSCCBCCTTC------CBCTTSCBCTTTCCBCC---------------TTSC-EEECSSSCEE----E
T ss_pred             cCCcCccCCCCcCceEEEECCc------eeccccCCccCCCCccC---------------CCCc-EEEeeCCEEE----C
Confidence            4667999999999888888888      99999999999995432               2222 23 4677884    5


Q ss_pred             hhhhhhhccccccc
Q psy17256        608 VLICFRSFGAKCSK  621 (768)
Q Consensus       608 ~~~y~~~f~~~C~~  621 (768)
                      ..||.++|++.|.+
T Consensus        68 ~~c~~~~~~~~~sg   81 (81)
T 1x6a_A           68 GKCHNEVVSGPSSG   81 (81)
T ss_dssp             HHHHHHHHCTTSCC
T ss_pred             HHHHHHHhcCCCCC
Confidence            68999999999864

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.19  E-value=9e-08  Score=81.26  Aligned_cols=65  Identities=5%  Similarity=-0.221  Sum_probs=51.8

Q ss_pred             ccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        530 HLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      .+.|..|.+.|.+.++.+.++      .||..||.|+.|+..+.   +              ..++.+++.+|    |..
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~---~--------------~~~~~~~g~~y----C~~   67 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFVKLRDR------HRHPECYVCTDCGTNLK---Q--------------KGHFFVEDQIY----CEK   67 (79)
T ss_dssp             CCCCSSSCCCCCSSCEECSSC------EECTTTTSCSSSCCCHH---H--------------HCCEESSSCEE----CHH
T ss_pred             CCccccCCCCccCcEEEECcc------eeCcCcCeeCCCCCCCC---C--------------CCeEeECCEEE----CHH
Confidence            456999999999887777787      99999999999995543   1              13567778884    568


Q ss_pred             hhhhhccccccc
Q psy17256        610 ICFRSFGAKCSK  621 (768)
Q Consensus       610 ~y~~~f~~~C~~  621 (768)
                      ||.++|++++.+
T Consensus        68 cy~~~~~p~g~g   79 (79)
T 1x62_A           68 HARERVSGPSSG   79 (79)
T ss_dssp             HHHHHHSSCCCC
T ss_pred             HHHHHhCCCCCC
Confidence            999999999753

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.12  E-value=2.1e-07  Score=77.35  Aligned_cols=63  Identities=8%  Similarity=-0.101  Sum_probs=49.3

Q ss_pred             ccchhhhhhhhhh----HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccc
Q psy17256        530 HLEFHSFLKRIAL----VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGR  605 (768)
Q Consensus       530 g~~C~~c~k~Ia~----~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~  605 (768)
                      ++.|..|.++|.+    .++.+.++      .||..||.|+.|+..+.   |              ..++.+++.+|   
T Consensus         5 ~~~C~~C~~~I~~~~~~~~~~a~~~------~wH~~CF~C~~C~~~L~---~--------------~~f~~~~g~~y---   58 (72)
T 1x4l_A            5 SSGCAGCTNPISGLGGTKYISFEER------QWHNDCFNCKKCSLSLV---G--------------RGFLTERDDIL---   58 (72)
T ss_dssp             SCSBTTTTBCCCCSSSCSCEECSSC------EECTTTCBCSSSCCBCT---T--------------SCCEECSSSEE---
T ss_pred             CCCCcCCCccccCCCCcceEEECCc------ccCcccCEeccCCCcCC---C--------------CccEeECCEEE---
Confidence            4569999999986    66677787      99999999999995432   1              23466788885   


Q ss_pred             cchhhhhhhccccc
Q psy17256        606 LSVLICFRSFGAKC  619 (768)
Q Consensus       606 yC~~~y~~~f~~~C  619 (768)
                       |..||.++|++++
T Consensus        59 -C~~c~~~~~~p~~   71 (72)
T 1x4l_A           59 -CPDCGKDISGPSS   71 (72)
T ss_dssp             -CHHHHHTCCCSSC
T ss_pred             -ChhHcCcccCCCC
Confidence             5689999999987

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.07  E-value=3.3e-07  Score=75.73  Aligned_cols=64  Identities=14%  Similarity=-0.058  Sum_probs=50.7

Q ss_pred             ccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccchh
Q psy17256        530 HLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVL  609 (768)
Q Consensus       530 g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~  609 (768)
                      .+.|..|.+.|.+..+.+.++      .||+.||+|+.|+..+.               +  ..++.+++.+|    |..
T Consensus         5 ~~~C~~C~~~I~~~~~~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~f~~~~g~~y----C~~   57 (70)
T 2d8x_A            5 SSGCHQCGEFIIGRVIKAMNN------SWHPECFRCDLCQEVLA---------------D--IGFVKNAGRHL----CRP   57 (70)
T ss_dssp             SSBCSSSCCBCCSCCEEETTE------EECTTTSBCSSSCCBCS---------------S--SCCEEETTEEE----CHH
T ss_pred             CCcCccCCCEecceEEEECcc------cccccCCEeCCCCCcCC---------------C--CccEeECCeEE----CHH
Confidence            355999999999888888887      99999999999995433               1  23566788885    568


Q ss_pred             hhhhhcccccc
Q psy17256        610 ICFRSFGAKCS  620 (768)
Q Consensus       610 ~y~~~f~~~C~  620 (768)
                      ||.++|++++.
T Consensus        58 c~~~~~~~~~~   68 (70)
T 2d8x_A           58 CHNREKASGPS   68 (70)
T ss_dssp             HHHHHHCCCSC
T ss_pred             HhhhhcCCCCC
Confidence            99999998764

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.05  E-value=4.2e-07  Score=79.29  Aligned_cols=66  Identities=8%  Similarity=-0.214  Sum_probs=50.0

Q ss_pred             ccchhhhhhhhhh-HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        530 HLEFHSFLKRIAL-VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       530 g~~C~~c~k~Ia~-~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      ++.|..|.+.|.+ ..+.+.++      .||..||.|+.|...+.               +  ..++.+++.+    ||.
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~------~~H~~CF~C~~C~~~L~---------------~--~~~~~~~g~~----yC~   67 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQ------VFHISCFRCSYCNNKLS---------------L--GTYASLHGRI----YCK   67 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSS------EEETTTCBCTTTCCBCC---------------T--TTCCCSSSCC----CCH
T ss_pred             CCcCccCCCccCCceeEEECCC------EECCCCCeeCCCCCCCC---------------C--CCcEeECCEE----ECH
Confidence            3569999999964 34456676      99999999999985433               1  1256777888    456


Q ss_pred             hhhhhhcccccccC
Q psy17256        609 LICFRSFGAKCSKC  622 (768)
Q Consensus       609 ~~y~~~f~~~C~~C  622 (768)
                      .||.++|+++|.-+
T Consensus        68 ~~y~~~f~~kc~~~   81 (91)
T 2d8y_A           68 PHFNQLFKSKGNYD   81 (91)
T ss_dssp             HHHHHHSCCCSCCC
T ss_pred             HHHHHHhCCCcCcc
Confidence            99999999999733

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens}

Probab=97.95  E-value=9.2e-07  Score=81.69  Aligned_cols=63  Identities=17%  Similarity=0.048  Sum_probs=48.2

Q ss_pred             cccchhhhhhhhhhHH-HHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccc
Q psy17256        529 LHLEFHSFLKRIALVL-SEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLS  607 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~~~-~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC  607 (768)
                      ..+.|..|.++|.+.. +.+.++      .||+.||+|+.|+..+.               +....+|.+++.+    ||
T Consensus        60 ~~~~C~~C~~~I~~~~~v~a~~~------~wH~~CF~C~~C~~~L~---------------~~g~~f~~~dg~~----yC  114 (123)
T 2l4z_A           60 SWKRCAGCGGKIADRFLLYAMDS------YWHSRCLKCSSCQAQLG---------------DIGTSSYTKSGMI----LC  114 (123)
T ss_dssp             SCSBBSSSSSBCCSSSEEEETTE------EEETTTSBCTTTCCBGG---------------GTTCCCBCSSSCC----BC
T ss_pred             cCCcCcCCCCCcCCcEEEEeCCc------EEcccccCcCcCCCccc---------------ccCCceEEECCEE----eC
Confidence            3566999999999885 677787      99999999999995432               1001357788888    45


Q ss_pred             hhhhhhhcc
Q psy17256        608 VLICFRSFG  616 (768)
Q Consensus       608 ~~~y~~~f~  616 (768)
                      ..||.++||
T Consensus       115 ~~cy~~~Fg  123 (123)
T 2l4z_A          115 RNDYIRLFG  123 (123)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHhhhhcC
Confidence            689999986

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=97.87  E-value=1.1e-06  Score=72.97  Aligned_cols=65  Identities=8%  Similarity=-0.126  Sum_probs=48.9

Q ss_pred             ccchhhhhhhhhh--HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccc
Q psy17256        530 HLEFHSFLKRIAL--VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLS  607 (768)
Q Consensus       530 g~~C~~c~k~Ia~--~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC  607 (768)
                      ++.|..|.++|..  ..+.+.++      .||..||.|+.|+..+.                + ..++.+++.+|    |
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~------~~H~~CF~C~~C~~~L~----------------~-~~~~~~~~~~y----C   57 (72)
T 1x61_A            5 SSGCGGCGEDVVGDGAGVVALDR------VFHVGCFVCSTCRAQLR----------------G-QHFYAVERRAY----C   57 (72)
T ss_dssp             CCCCSSSCSCCCSSSCCEECSSS------EECTTTCBCSSSCCBCT----------------T-SCEEESSSCEE----E
T ss_pred             CCCCccCCCccCCCceEEEECCC------eEcccCCcccccCCcCC----------------c-CcCEeeCCeEE----C
Confidence            4569999999974  56677787      99999999999995432                1 23577788884    5


Q ss_pred             hhhhhhhcccccccC
Q psy17256        608 VLICFRSFGAKCSKC  622 (768)
Q Consensus       608 ~~~y~~~f~~~C~~C  622 (768)
                      ..||.++|+ +|..+
T Consensus        58 ~~cy~~~~~-~~~~~   71 (72)
T 1x61_A           58 EGCYVATLE-SGPSS   71 (72)
T ss_dssp             HHHHHHHHH-TCSSC
T ss_pred             HHHHHHHHc-cCCCC
Confidence            689999984 56554

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=97.84  E-value=1.8e-06  Score=72.10  Aligned_cols=64  Identities=13%  Similarity=-0.060  Sum_probs=49.8

Q ss_pred             cccchhhhhhhhhhHHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeecccccccccch
Q psy17256        529 LHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSV  608 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~  608 (768)
                      .++.|..|.++|.+..+.+.++      .||+.||.|+.|+..+.               +|. .++.+++.+||    .
T Consensus         4 ~~~~C~~C~~~I~~~~v~a~~~------~wH~~CF~C~~C~~~L~---------------~~~-~f~~~~~~~yC----~   57 (73)
T 1wig_A            4 GSSGCDSCEKYITGRVLEAGEK------HYHPSCALCVRCGQMFA---------------EGE-EMYLQGSSIWH----P   57 (73)
T ss_dssp             SCCSCSSSCCCCSSCCBCCSSC------CBCTTTSCCSSSCCCCC---------------SSC-CCEEETTEEEC----T
T ss_pred             CcCCcccCCCEecCeeEEeCCC------CCCCCcCEeCCCCCCCC---------------CCC-eeEeeCCEEEC----h
Confidence            4567999999999988888887      99999999999995432               122 46778888855    5


Q ss_pred             hhhhhhcccc
Q psy17256        609 LICFRSFGAK  618 (768)
Q Consensus       609 ~~y~~~f~~~  618 (768)
                      .||.++++..
T Consensus        58 ~C~~~~~~~~   67 (73)
T 1wig_A           58 ACRQAARTED   67 (73)
T ss_dssp             THHHHTSSSS
T ss_pred             HHChHhhccc
Confidence            7898888764

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B

Probab=97.78  E-value=1.7e-06  Score=71.51  Aligned_cols=61  Identities=8%  Similarity=-0.162  Sum_probs=46.9

Q ss_pred             cccchhhhhhhhhh--HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcceeeccccccccc
Q psy17256        529 LHLEFHSFLKRIAL--VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRL  606 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~--~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~y  606 (768)
                      .++.|..|.+.|..  .++.+.++      .||+.||.|+.|+..+..                 +.++.+++.+|    
T Consensus        10 ~~~~C~~C~~~i~~~e~~~~~~~~------~~H~~CF~C~~C~~~L~~-----------------~~~~~~~g~~y----   62 (72)
T 3f6q_B           10 ASATCERCKGGFAPAEKIVNSNGE------LYHEQCFVCAQCFQQFPE-----------------GLFYEFEGRKY----   62 (72)
T ss_dssp             TTCBCTTTCCBCCTTCEEEEETTE------EEETTTSSCTTTCCCCGG-----------------GCCEEETTEEE----
T ss_pred             CCccchhcCccccCCceEEEeCcC------eeCcCCCcccCCCCCCCC-----------------CCeEeECCeEe----
Confidence            45669999999984  35667787      899999999999965431                 23567888884    


Q ss_pred             chhhhhhhcc
Q psy17256        607 SVLICFRSFG  616 (768)
Q Consensus       607 C~~~y~~~f~  616 (768)
                      |..||.++||
T Consensus        63 C~~~y~~lf~   72 (72)
T 3f6q_B           63 CEHDFQMLFA   72 (72)
T ss_dssp             CHHHHHHHTC
T ss_pred             CHHHHHHhhC
Confidence            5689999886

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=97.77  E-value=3e-06  Score=72.35  Aligned_cols=65  Identities=8%  Similarity=-0.188  Sum_probs=46.3

Q ss_pred             ccchhhhhhhhhh-HHHHHhhcccccccccccceEEEeccccccccccccccccccccccCCCCcc-eeecccccccccc
Q psy17256        530 HLEFHSFLKRIAL-VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLM-YIRVRILLKGRLS  607 (768)
Q Consensus       530 g~~C~~c~k~Ia~-~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~-~~~~~~~~c~~yC  607 (768)
                      .+.|..|.+.|.. ..+.+.++      .||..||+|+.|+..+..               + .++ +.+++.+|    |
T Consensus        15 ~~~C~~C~~~I~~~e~v~a~~~------~wH~~CF~C~~C~~~L~~---------------~-~~~~~~~~g~~y----C   68 (82)
T 2co8_A           15 GDLCALCGEHLYVLERLCVNGH------FFHRSCFRCHTCEATLWP---------------G-GYEQHPGDGHFY----C   68 (82)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTB------CCBTTTCBCSSSCCBCCT---------------T-SEECCTTTCCCE----E
T ss_pred             CCCCcccCCCcccceEEEECCC------eeCCCcCEEcCCCCCcCC---------------C-ceeEeCcCCEEE----C
Confidence            4569999999953 34556777      999999999999954331               1 111 24677885    5


Q ss_pred             hhhhhhhcccccc
Q psy17256        608 VLICFRSFGAKCS  620 (768)
Q Consensus       608 ~~~y~~~f~~~C~  620 (768)
                      ..||.++|+.-+.
T Consensus        69 ~~~y~~~~~~~~~   81 (82)
T 2co8_A           69 LQHLPQTDSGPSS   81 (82)
T ss_dssp             TTTCCCCCCCCCC
T ss_pred             hHHHHhhhcCCCC
Confidence            5899999987654

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens}

Probab=97.67  E-value=4.1e-06  Score=70.37  Aligned_cols=69  Identities=4%  Similarity=-0.156  Sum_probs=50.2

Q ss_pred             cccccccccccccccccccccCCccccchhhhhhhhhh-----HHHHHhhcccccccccccceEEEeccccccccccccc
Q psy17256        505 LKYNTAAEDLRASFTPLVCSTDGALHLEFHSFLKRIAL-----VLSEKWKKMYGHVLSWLRVRTEFSILKAVSLRLRGTR  579 (768)
Q Consensus       505 ~ky~~~c~~~~~~F~Pl~~s~~G~~g~~C~~c~k~Ia~-----~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~~~~~g~r  579 (768)
                      ..|+..|+.+.             .++.|..|.++|.+     ..+.+.++      .||+.||+|+.|+..+.   |  
T Consensus         3 ~~yC~~cy~~~-------------~~~~C~~C~~~I~~~g~~~~~~~a~~~------~~H~~CF~C~~C~~~L~---~--   58 (77)
T 2egq_A            3 SGSSGDCYKNF-------------VAKKCAGCKNPITGFGKGSSVVAYEGQ------SWHDYCFHCKKCSVNLA---N--   58 (77)
T ss_dssp             SSCCTTCCCSC-------------CCCCCSSSCCCCCCCSSCCCEEEETTE------EEETTTCBCSSSCCBCT---T--
T ss_pred             CeEchhHhchh-------------hCccCcccCCcccCCCCCceeEEECcc------eeCcccCEehhcCCCCC---C--
Confidence            35677776552             45679999999986     66777787      99999999999995432   1  


Q ss_pred             cccccccccCCCCcceeecccccccccchhhhhh
Q psy17256        580 QIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFR  613 (768)
Q Consensus       580 ~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~  613 (768)
                                  ..++.+++.+|    |..||.+
T Consensus        59 ------------~~f~~~~~~~y----C~~cy~~   76 (77)
T 2egq_A           59 ------------KRFVFHQEQVY----CPDCAKK   76 (77)
T ss_dssp             ------------SCCCEETTEEC----CHHHHHH
T ss_pred             ------------CccEeECCEEE----ChHHhcc
Confidence                        23567888885    4578865

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=97.38  E-value=1.6e-05  Score=67.46  Aligned_cols=38  Identities=8%  Similarity=-0.132  Sum_probs=32.5

Q ss_pred             cccchhhhhhhhhhHHHHHhhcccccccccccceEEEecccccc
Q psy17256        529 LHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRTEFSILKAVS  572 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~~c~~c~~~~  572 (768)
                      .++.|..|.+.|.+..+.+.++      .||+.||.|+.|+..+
T Consensus        14 ~~~~C~~C~~~I~~~~v~a~~~------~wH~~CF~C~~C~~~L   51 (81)
T 1v6g_A           14 YGTRCFSCDQFIEGEVVSALGK------TYHPDCFVCAVCRLPF   51 (81)
T ss_dssp             CCCBCTTTCCBCCSCCEEETTE------EECTTTSSCSSSCCCC
T ss_pred             hCCcCccccCEeccceEEECCc------eeCccCCccccCCCCC
Confidence            4567999999999888888887      9999999999999543

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens}

Probab=97.25  E-value=2.1e-05  Score=63.81  Aligned_cols=58  Identities=12%  Similarity=-0.034  Sum_probs=43.7

Q ss_pred             ccchhhhhhhhh--hHHHHHhhcccccccccc--cceEEEeccccccccccccccccccccccCCCCcceeecccccccc
Q psy17256        530 HLEFHSFLKRIA--LVLSEKWKKMYGHVLSWL--RVRTEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGR  605 (768)
Q Consensus       530 g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh--~~~~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~  605 (768)
                      ++.|..|.++|.  +..+.+.++      .||  +.||+|+.|+..+.   |              ..++.+++.+||+ 
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~------~wH~~~~CF~C~~C~~~L~---~--------------~~f~~~~g~~yC~-   57 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNF------SWHASTECFLCSCCSKCLI---G--------------QKFMPVEGMVFCS-   57 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTE------EEETTTTTSBCTTTCCBCT---T--------------SCCEEETTEEESS-
T ss_pred             cCCCcCCCCeeccCceEEEECCC------ccCCCCCCEECCCCCCcCC---C--------------CceEEECCEEecC-
Confidence            456999999999  677888888      999  99999999995432   1              2357788888663 


Q ss_pred             cchhhhhh
Q psy17256        606 LSVLICFR  613 (768)
Q Consensus       606 yC~~~y~~  613 (768)
                        ..||.+
T Consensus        58 --~~C~~k   63 (65)
T 2iyb_E           58 --VECKKR   63 (65)
T ss_dssp             --HHHHHT
T ss_pred             --HHHhhh
Confidence              255544

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4

Probab=96.40  E-value=0.0011  Score=45.61  Aligned_cols=29  Identities=28%  Similarity=0.722  Sum_probs=25.1

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ..+|..|++.+.+.|.++ +.|+.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~-~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVN-CLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCC-SSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEE-ECCeEecccCC
Confidence            468999999999886655 88999999998

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.99  E-value=0.57  Score=37.94  Aligned_cols=39  Identities=21%  Similarity=0.404  Sum_probs=36.4

Q ss_pred             HHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccc
Q psy17256         72 LQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN  110 (768)
Q Consensus        72 l~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqN  110 (768)
                      .+.|+++|...+.+.......|+.+.+|+..+|+-||..
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            467999999999999999999999999999999999953

---

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	768
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	7e-17
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	7e-17
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-15
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-15
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-15
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-15
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-15
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-15
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-15
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	5e-15
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-15
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-15
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-15
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-15
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-15
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	6e-15
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	5e-15
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	5e-15
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-14
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-14
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-14
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-14
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-14
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-14
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-14
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-14
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-14
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-14
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	6e-14
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	6e-14
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-13
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-13
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-13
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-13
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-13
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-13
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	2e-13
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	2e-13
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-13
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-13
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-12
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-12
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-12
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-12
d1rutx3	31	g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus	3e-12
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	4e-12
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	4e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-12
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-11
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-11
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	4e-11
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	4e-11
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-10
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-10
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	7e-10
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	7e-10
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-08
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-08
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	7e-08
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-07

>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 = 73.3 bits (180), Expect = 7e-17
 Identities = 26/60 (43%), Positives = 36/60 (60%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           K  RVRT   E+QL  L+  +  +  PD    E++ ++TGLS RV +VWFQN R + KK 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 = 73.3 bits (180), Expect = 7e-17
 Identities = 26/60 (43%), Positives = 36/60 (60%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           K  RVRT   E+QL  L+  +  +  PD    E++ ++TGLS RV +VWFQN R + KK 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 = 69.9 bits (171), Expect = 1e-15
 Identities = 27/60 (45%), Positives = 35/60 (58%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           K +R RTTF+  QL  L+  F+    PD    E +AQ T L++   QVWFQN RAR +K 
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

>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 = 69.9 bits (171), Expect = 1e-15
 Identities = 27/60 (45%), Positives = 35/60 (58%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           K +R RTTF+  QL  L+  F+    PD    E +AQ T L++   QVWFQN RAR +K 
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

>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 = 69.9 bits (171), Expect = 1e-15
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           ++ R  +++ QL+ L+  +  +         +I+  T LS+R   +WFQN R ++KK
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 69.9 bits (171), Expect = 1e-15
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           ++ R  +++ QL+ L+  +  +         +I+  T LS+R   +WFQN R ++KK
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 = 69.8 bits (171), Expect = 1e-15
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           +R RT+FT+EQ++ L+  F+    PD    ER+A    L +   QVWF N RA+ ++ 
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 59

>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 = 69.8 bits (171), Expect = 1e-15
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           +R RT+FT+EQ++ L+  F+    PD    ER+A    L +   QVWF N RA+ ++ 
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 59

>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 = 70.0 bits (171), Expect = 2e-15
 Identities = 21/74 (28%), Positives = 30/74 (40%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVT 104
           +   T   S         +RT FT  QL  L+  F  +          IA    L++   
Sbjct: 12  NPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQV 71

Query: 105 QVWFQNSRARQKKH 118
           ++WFQN R +QKK 
Sbjct: 72  KIWFQNRRMKQKKR 85

>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 = 68.5 bits (167), Expect = 5e-15
 Identities = 20/66 (30%), Positives = 28/66 (42%)

Query: 692 SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 751
           S         +RT FT  QL  L+  F  +          IA    L++   ++WFQN R
Sbjct: 20  SEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRR 79

Query: 752 ARQKKH 757
            +QKK 
Sbjct: 80  MKQKKR 85

>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 = 69.5 bits (170), Expect = 2e-15
 Identities = 15/68 (22%), Positives = 31/68 (45%)

Query: 51  SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 110
           + +       ++ R  +T+ Q   L+  F  +          +A++  L++R  ++WFQN
Sbjct: 4   AANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQN 63

Query: 111 SRARQKKH 118
            R + KK 
Sbjct: 64  RRMKMKKI 71

>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 = 69.5 bits (170), Expect = 2e-15
 Identities = 15/68 (22%), Positives = 31/68 (45%)

Query: 690 SESSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQN 749
           + +       ++ R  +T+ Q   L+  F  +          +A++  L++R  ++WFQN
Sbjct: 4   AANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQN 63

Query: 750 SRARQKKH 757
            R + KK 
Sbjct: 64  RRMKMKKI 71

>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 = 68.3 bits (167), Expect = 3e-15
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           K  +  F+ +Q   L+  F+        + +R+A++  LS+R  + WFQN RA+ ++
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 68.3 bits (167), Expect = 3e-15
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           K  +  F+ +Q   L+  F+        + +R+A++  LS+R  + WFQN RA+ ++
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 68.9 bits (168), Expect = 4e-15
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 684 SDDGADSESSHSKSKAKRVRTTFTEEQLQVLQANFQLD----SNPDGQDLERIAQITGLS 739
           S   + S  S S    KR RT FT EQ + + A  +         D   +E+    TG+ 
Sbjct: 2   SSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVR 61

Query: 740 KRVTQVWFQNSRARQKKH 757
           ++V ++W  N++      
Sbjct: 62  RQVLKIWMHNNKNSGPSS 79

>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 = 68.5 bits (167), Expect = 6e-15
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 45  STDHTDSESSHSKSKAKRVRTTFTEEQLQVLQANFQLD----SNPDGQDLERIAQITGLS 100
           S+  + S  S S    KR RT FT EQ + + A  +         D   +E+    TG+ 
Sbjct: 2   SSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVR 61

Query: 101 KRVTQVWFQNSRARQKKH 118
           ++V ++W  N++      
Sbjct: 62  RQVLKIWMHNNKNSGPSS 79

>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 = 67.6 bits (165), Expect = 5e-15
 Identities = 18/56 (32%), Positives = 27/56 (48%)

Query: 62  RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           R RT FT +QL  L+  F  ++         +A    L +   +VWFQN R + K+
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 67.6 bits (165), Expect = 5e-15
 Identities = 18/56 (32%), Positives = 27/56 (48%)

Query: 701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           R RT FT +QL  L+  F  ++         +A    L +   +VWFQN R + K+
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           +R RT FT +QLQ L+A FQ +  PD    E IA  T L++   +VWF+N RA+ +K 
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           +R RT FT +QLQ L+A FQ +  PD    E IA  T L++   +VWF+N RA+ +K 
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 67.0 bits (163), Expect = 1e-14
 Identities = 17/75 (22%), Positives = 33/75 (44%)

Query: 53  SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 112
           S    +K ++ R  FT+ Q   L+  F+        + E +A +  L+    ++WFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 113 ARQKKHLHTGKMKSS 127
            + K+  +    +  
Sbjct: 62  YKTKRAQNEKGYEGH 76

>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 = 67.0 bits (163), Expect = 1e-14
 Identities = 17/75 (22%), Positives = 33/75 (44%)

Query: 692 SSHSKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 751
           S    +K ++ R  FT+ Q   L+  F+        + E +A +  L+    ++WFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 752 ARQKKHLHTGKMKSS 766
            + K+  +    +  
Sbjct: 62  YKTKRAQNEKGYEGH 76

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 19/66 (28%), Positives = 29/66 (43%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH 120
           +R RTTFT  Q+  L+ +F          L  ++    L     ++WF+N R R K    
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 121 TGKMKS 126
             K +S
Sbjct: 62  QHKDQS 67

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 19/66 (28%), Positives = 29/66 (43%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH 759
           +R RTTFT  Q+  L+ +F          L  ++    L     ++WF+N R R K    
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 760 TGKMKS 765
             K +S
Sbjct: 62  QHKDQS 67

>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 = 66.1 bits (161), Expect = 2e-14
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           ++ RT FT  QL  L+  F+        +    +    L++   ++WFQN RA+ K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 66.1 bits (161), Expect = 2e-14
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           ++ RT FT  QL  L+  F+        +    +    L++   ++WFQN RA+ K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 65.6 bits (160), Expect = 3e-14
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           R T+T  Q   L+  F  +     +    IA    L++R  ++WFQN R + KK 
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 65.6 bits (160), Expect = 3e-14
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           R T+T  Q   L+  F  +     +    IA    L++R  ++WFQN R + KK 
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 64.5 bits (157), Expect = 6e-14
 Identities = 17/53 (32%), Positives = 31/53 (58%)

Query: 62  RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 114
           R RT F+ EQL  L+  F  +     +  ++++   GL++   ++WFQN+RA+
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 64.5 bits (157), Expect = 6e-14
 Identities = 17/53 (32%), Positives = 31/53 (58%)

Query: 701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 753
           R RT F+ EQL  L+  F  +     +  ++++   GL++   ++WFQN+RA+
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 114
           S S   R RT  + E L +LQ+    +   PD + +  ++    L K     +FQN R  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62

Query: 115 QKKH 118
            K  
Sbjct: 63  VKHS 66

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR 753
           S S   R RT  + E L +LQ+    +   PD + +  ++    L K     +FQN R  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62

Query: 754 QKKH 757
            K  
Sbjct: 63  VKHS 66

>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 = 64.2 bits (156), Expect = 1e-13
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 60  AKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 116
           A+R R  F ++  ++L   F     +  P  +  E +A+  G++      WF N R R K
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60

Query: 117 KHLHTGKMKSSQN 129
           K  + GK +   N
Sbjct: 61  K--NIGKFQEEAN 71

>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 = 64.2 bits (156), Expect = 1e-13
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 699 AKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           A+R R  F ++  ++L   F     +  P  +  E +A+  G++      WF N R R K
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60

Query: 756 KHLHTGKMKSSQN 768
           K  + GK +   N
Sbjct: 61  K--NIGKFQEEAN 71

>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 = 63.8 bits (155), Expect = 1e-13
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 62  RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           + RTT +      L+ +F   S P  Q++ R+A+   L K V +VWF N R R+K+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>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 = 63.8 bits (155), Expect = 1e-13
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           + RTT +      L+ +F   S P  Q++ R+A+   L K V +VWF N R R+K+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 14/58 (24%), Positives = 29/58 (50%)

Query: 61  KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
           ++ R  F++ Q+  L+  F+        + E +A +  L+    ++WFQN R + K+ 
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 14/58 (24%), Positives = 29/58 (50%)

Query: 700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
           ++ R  F++ Q+  L+  F+        + E +A +  L+    ++WFQN R + K+ 
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

>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 = 62.2 bits (151), Expect = 4e-13
 Identities = 12/53 (22%), Positives = 28/53 (52%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 116
           +++ + +    L+  F+   + + ++ E +A+  G++    +VWF N R R K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 62.2 bits (151), Expect = 4e-13
 Identities = 12/53 (22%), Positives = 28/53 (52%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           +++ + +    L+  F+   + + ++ E +A+  G++    +VWF N R R K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 61.6 bits (149), Expect = 9e-13
 Identities = 20/60 (33%), Positives = 26/60 (43%)

Query: 59  KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
             KR RT+        L+  F     P  Q +  IA   GL K V +VWF N R + K+ 
Sbjct: 7   ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66

>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 = 61.6 bits (149), Expect = 9e-13
 Identities = 20/60 (33%), Positives = 26/60 (43%)

Query: 698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
             KR RT+        L+  F     P  Q +  IA   GL K V +VWF N R + K+ 
Sbjct: 7   ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 15/81 (18%)

Query: 62  RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIA---------------QITGLSKRVTQV 106
             R T+ +E L V+++ F  +  PD    E IA                +  ++      
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 107 WFQNSRARQKKHLHTGKMKSS 127
           WF N R   K+  +   +  S
Sbjct: 62  WFANRRKEIKRRANIAAILES 82

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 15/81 (18%)

Query: 701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIA---------------QITGLSKRVTQV 745
             R T+ +E L V+++ F  +  PD    E IA                +  ++      
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 746 WFQNSRARQKKHLHTGKMKSS 766
           WF N R   K+  +   +  S
Sbjct: 62  WFANRRKEIKRRANIAAILES 82

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 60  AKRVRTTFTEEQLQVLQANFQLDSN-PDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 118
                 T TE+Q+++L+ NF   +  PD   L  IA   GL++  TQ WF+   A  ++ 
Sbjct: 1   GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 699 AKRVRTTFTEEQLQVLQANFQLDSN-PDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH 757
                 T TE+Q+++L+ NF   +  PD   L  IA   GL++  TQ WF+   A  ++ 
Sbjct: 1   GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 60.9 bits (148), Expect = 1e-12
 Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 60  AKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 116
            K  R    +    V+++          P   + ++IA  T L+      WF N+R R  
Sbjct: 2   GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL 61

Query: 117 K 117
           +
Sbjct: 62  Q 62

>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 = 60.9 bits (148), Expect = 1e-12
 Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 699 AKRVRTTFTEEQLQVLQANF---QLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
            K  R    +    V+++          P   + ++IA  T L+      WF N+R R  
Sbjct: 2   GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL 61

Query: 756 K 756
           +
Sbjct: 62  Q 62

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 31

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.0 bits (143), Expect = 3e-12
 Identities = 13/27 (48%), Positives = 19/27 (70%)

Query: 619 CSKCCRGIASSDWVRKARDHVYHLACF 645
           CS C + I +S+ V +A+ +VYHL CF
Sbjct: 5   CSACGQSIPASELVMRAQGNVYHLKCF 31

>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 = 59.1 bits (143), Expect = 4e-12
 Identities = 15/49 (30%), Positives = 23/49 (46%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 112
           R  FT+ Q + L A F+ +  P  +    I+Q  GL       +F N+R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 59.1 bits (143), Expect = 4e-12
 Identities = 15/49 (30%), Positives = 23/49 (46%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR 751
           R  FT+ Q + L A F+ +  P  +    I+Q  GL       +F N+R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 58.8 bits (142), Expect = 7e-12
 Identities = 16/54 (29%), Positives = 28/54 (51%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           RT+        L+ +F  +  P  +D+  IA+   + K V +VWF N R ++K+
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 58.8 bits (142), Expect = 7e-12
 Identities = 16/54 (29%), Positives = 28/54 (51%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           RT+        L+ +F  +  P  +D+  IA+   + K V +VWF N R ++K+
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 57.5 bits (139), Expect = 2e-11
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 67  FTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           FT+E +++L++ F  +      D + LE + + T LS+   + W  N R ++K 
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 57.5 bits (139), Expect = 2e-11
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 706 FTEEQLQVLQANFQLDSN---PDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           FT+E +++L++ F  +      D + LE + + T LS+   + W  N R ++K 
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 56.7 bits (137), Expect = 4e-11
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 68  TEEQLQVLQANFQLDS-NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
           T +   +L+  F   + +PD + LE +++      R  Q WF+  R ++K 
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 56.7 bits (137), Expect = 4e-11
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 707 TEEQLQVLQANFQLDS-NPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
           T +   +L+  F   + +PD + LE +++      R  Q WF+  R ++K 
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 53.6 bits (129), Expect = 5e-10
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 62  RVRTTFTEEQLQVLQANFQLDS-NPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 116
           +       E    L+  F   +  PD + L+ +++    S R  Q WF++ R + K
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 53.6 bits (129), Expect = 5e-10
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 701 RVRTTFTEEQLQVLQANFQLDS-NPDGQDLERIAQITGLSKRVTQVWFQNSRARQK 755
           +       E    L+  F   +  PD + L+ +++    S R  Q WF++ R + K
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 53.6 bits (128), Expect = 7e-10
 Identities = 18/70 (25%), Positives = 30/70 (42%)

Query: 58  SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 117
               +     T EQL+VLQA+F   S    ++L R+   T L++R    WF   +  +  
Sbjct: 2   DFTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL 61

Query: 118 HLHTGKMKSS 127
                ++  S
Sbjct: 62  KEEKMEIDES 71

>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 = 53.6 bits (128), Expect = 7e-10
 Identities = 18/70 (25%), Positives = 30/70 (42%)

Query: 697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK 756
               +     T EQL+VLQA+F   S    ++L R+   T L++R    WF   +  +  
Sbjct: 2   DFTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL 61

Query: 757 HLHTGKMKSS 766
                ++  S
Sbjct: 62  KEEKMEIDES 71

>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 = 50.2 bits (119), Expect = 1e-08
 Identities = 10/76 (13%), Positives = 22/76 (28%), Gaps = 21/76 (27%)

Query: 64  RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQIT---------------------GLSKR 102
           R  +     Q+L   ++   NP  ++ E + +                        +++ 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 103 VTQVWFQNSRARQKKH 118
               WF N R  +   
Sbjct: 61  RVYNWFANRRKEEAFR 76

>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 = 50.2 bits (119), Expect = 1e-08
 Identities = 10/76 (13%), Positives = 22/76 (28%), Gaps = 21/76 (27%)

Query: 703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQIT---------------------GLSKR 741
           R  +     Q+L   ++   NP  ++ E + +                        +++ 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 742 VTQVWFQNSRARQKKH 757
               WF N R  +   
Sbjct: 61  RVYNWFANRRKEEAFR 76

>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 = 48.2 bits (114), Expect = 7e-08
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 56  SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 115
           S S  KR     T+EQL +L++ F        +D +++ QITGL +     WF ++R   
Sbjct: 3   SGSSGKR----KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYAL 58

Query: 116 KKHLHTGKMKSSQNRPKYG 134
           K        + + + P  G
Sbjct: 59  KHGQLK-WFRDNASGPSSG 76

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 695 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQ 754
           S S  KR     T+EQL +L++ F        +D +++ QITGL +     WF ++R   
Sbjct: 3   SGSSGKR----KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYAL 58

Query: 755 KK 756
           K 
Sbjct: 59  KH 60

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	768
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.7
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.68
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.68
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.67
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.67
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.67
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.66
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.65
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.65
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.64
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.64
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.64
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.64
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.63
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.63
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.62
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.62
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.62
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.61
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.61
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.61
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.61
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.59
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.59
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.59
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.59
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.59
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.58
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.58
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.57
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.56
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.56
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.55
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.55
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.54
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.53
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.52
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.52
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.52
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.51
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.51
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.49
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.48
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.47
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.45
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.45
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.45
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.44
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.43
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.39
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.39
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.38
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.37
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.34
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.29
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.28
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.28
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.24
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.23
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.2
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.18
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.15
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.1
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.03
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.67
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.59
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.42
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.31
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	98.06
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.98
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.97
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.78
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.72
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.59
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.56
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.45
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	97.44
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.42
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.3
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.13
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.94
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.91
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	96.9
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	96.88
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	96.8
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	96.73
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.62
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	96.59
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	96.47
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	96.45
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	96.36
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.24
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.2
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	96.18
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.18
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	96.12
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.96
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.94
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.87
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	95.83
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	95.45
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.4
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	95.4
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	95.37
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	95.22
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	95.21
d2co8a2	36	Nedd9 interacting protein with calponin homology,	95.01
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	94.74
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	94.72
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	94.49
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	93.62
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	93.42
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	93.22
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	92.76
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	92.74
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	92.52
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	92.26
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	92.18
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	92.17
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	91.79
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	91.65
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	91.25
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	90.94
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	90.58
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	90.39
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	90.38
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	90.25
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	90.18
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	89.93
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	89.88
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	89.67
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	89.32
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	88.92
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	88.9
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	88.67
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	88.22
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	88.22
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	86.7
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	84.79
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	83.8
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	82.9
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	82.5
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	81.99

>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=99.70  E-value=1.9e-18  Score=136.06  Aligned_cols=58  Identities=28%  Similarity=0.532  Sum_probs=55.6

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      +||.||.||..|+.+||..|..++||+..+|++||..+||++.+|+|||||||+|+||
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            3677999999999999999999999999999999999999999999999999999986

>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=99.68  E-value=5.6e-18  Score=132.00  Aligned_cols=55  Identities=31%  Similarity=0.479  Sum_probs=53.9

Q ss_pred             CccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         64 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        64 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      ||.||.+|+..||..|..++||+...|.+||..+||++++|+|||||||+|+||+
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

>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=99.68  E-value=7.5e-18  Score=133.11  Aligned_cols=57  Identities=28%  Similarity=0.493  Sum_probs=55.4

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ||+|+.||+.|+.+||..|+.++||+..+|++||..+||++.+|+|||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            568999999999999999999999999999999999999999999999999999987

>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=99.67  E-value=9.9e-18  Score=136.15  Aligned_cols=63  Identities=29%  Similarity=0.463  Sum_probs=58.8

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCC
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ||.||.||..|+.+||..|+.++||+..+|.+||..+||++++|+|||||||+|+|++.....
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~~   64 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHK   64 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhcc
Confidence            567999999999999999999999999999999999999999999999999999998765443

>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=99.67  E-value=7.9e-18  Score=132.32  Aligned_cols=57  Identities=32%  Similarity=0.503  Sum_probs=55.2

Q ss_pred             CCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         62 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        62 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      |.||.||+.|+..||..|..++||+...|++||..+||++.+|+|||||||+|+||+
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            579999999999999999999999999999999999999999999999999999974

>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=99.67  E-value=1.5e-17  Score=138.59  Aligned_cols=65  Identities=23%  Similarity=0.407  Sum_probs=60.1

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..+..||.||.||.+|+.+||..|+.++||+..+|++||..+||++++|+|||||||+|+|+..+
T Consensus         9 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~   73 (77)
T d1pufa_           9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHH
Confidence            34456778999999999999999999999999999999999999999999999999999998654

>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=99.66  E-value=1.7e-17  Score=130.45  Aligned_cols=57  Identities=28%  Similarity=0.497  Sum_probs=55.0

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      |+.|+.||+.|+..||..|+.++||+..++++||..+||++.+|+|||||||+++||
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            467999999999999999999999999999999999999999999999999999986

>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=99.65  E-value=1.7e-17  Score=138.45  Aligned_cols=65  Identities=25%  Similarity=0.426  Sum_probs=60.2

Q ss_pred             CCCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         56 SKSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        56 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      .+.+++|.||.||.+|+.+||..|+.++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   69 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhh
Confidence            34567788999999999999999999999999999999999999999999999999999987544

>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=99.65  E-value=1.7e-17  Score=128.55  Aligned_cols=53  Identities=32%  Similarity=0.574  Sum_probs=51.6

Q ss_pred             CCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHH
Q psy17256         62 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR  114 (768)
Q Consensus        62 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak  114 (768)
                      |+||.||..|+..||..|+.++||+..+|++||..+||++++|+|||||||+|
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            57999999999999999999999999999999999999999999999999986

>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=2.3e-17  Score=140.96  Aligned_cols=64  Identities=30%  Similarity=0.451  Sum_probs=56.2

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ..+++|.|+.||..|+.+||..|+.++||+..+|++||..+||++++|+|||||||+|+|++.+
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            3456788999999999999999999999999999999999999999999999999999998754

>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=99.64  E-value=2.5e-17  Score=132.96  Aligned_cols=62  Identities=44%  Similarity=0.603  Sum_probs=58.8

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ++||.||.||.+|+..||..|..++||+..++++||..+||++.+|++||||||+|+|++..
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            46788999999999999999999999999999999999999999999999999999998654

>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=99.64  E-value=4.2e-17  Score=132.72  Aligned_cols=62  Identities=23%  Similarity=0.454  Sum_probs=58.5

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhccc
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  121 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~  121 (768)
                      +||.||.||..|+.+||..|..++||+..+|.+||..+||++.+|+|||||||+|+|+....
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~   63 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccc
Confidence            46789999999999999999999999999999999999999999999999999999986543

>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=3.8e-17  Score=133.07  Aligned_cols=61  Identities=36%  Similarity=0.575  Sum_probs=57.5

Q ss_pred             CCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         60 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        60 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      +||.||+||.+|+.+||..|..++||+..+|++||..+||++.+|+|||||+|+++|+..+
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            3678999999999999999999999999999999999999999999999999999998643

>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=99.63  E-value=1.7e-17  Score=130.60  Aligned_cols=57  Identities=28%  Similarity=0.538  Sum_probs=55.1

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      +++||.||.+|+.+||..|..++||+...++.||..+||++.+|+|||||||+|+||
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            567899999999999999999999999999999999999999999999999999986

>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=99.63  E-value=2.5e-17  Score=128.30  Aligned_cols=55  Identities=31%  Similarity=0.479  Sum_probs=53.8

Q ss_pred             cccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       703 Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      ||.||.+|+..||..|..++||+...+..||..+||++++|+|||||||+|+||+
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            7899999999999999999999999999999999999999999999999999985

>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=99.62  E-value=9.6e-17  Score=131.64  Aligned_cols=60  Identities=32%  Similarity=0.485  Sum_probs=56.3

Q ss_pred             CCCCccCCHHHHHHHHHhhhh-CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         61 KRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      ++.|++||.+|+.+||..|.+ ++||+...|++||..+||++++|+|||||||+|+|+...
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            567999999999999999986 789999999999999999999999999999999998653

>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=99.62  E-value=6.8e-17  Score=131.16  Aligned_cols=61  Identities=28%  Similarity=0.468  Sum_probs=57.7

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      +|.||+||.+|+..||..|..++||+...+..||..+||++++|+|||||||+|+|++...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            5679999999999999999999999999999999999999999999999999999986544

>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=99.62  E-value=4.1e-17  Score=128.20  Aligned_cols=57  Identities=32%  Similarity=0.503  Sum_probs=55.2

Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      |.||.||.+|+..||..|..++||+...+..||..+||++.+|+|||||||+|+||+
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            579999999999999999999999999999999999999999999999999999984

>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=99.61  E-value=5.1e-17  Score=129.17  Aligned_cols=58  Identities=45%  Similarity=0.658  Sum_probs=56.3

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      ||.||.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            6789999999999999999999999999999999999999999999999999999985

>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=99.61  E-value=5.1e-17  Score=128.24  Aligned_cols=57  Identities=28%  Similarity=0.493  Sum_probs=55.3

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      +++|+.||++|+..|+..|..++||+..++..||..+||++.+|+|||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            467999999999999999999999999999999999999999999999999999997

>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=99.61  E-value=9.5e-17  Score=133.64  Aligned_cols=64  Identities=23%  Similarity=0.417  Sum_probs=59.9

Q ss_pred             CccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        697 SKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       697 ~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      +..++.||.||.+|+.+||..|..++||+..+++.||..+||++.+|+|||||||+|+|+..+.
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            4457789999999999999999999999999999999999999999999999999999997654

>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=99.61  E-value=6.4e-17  Score=127.09  Aligned_cols=57  Identities=28%  Similarity=0.497  Sum_probs=55.1

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      |+.|+.||.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|+||
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            467899999999999999999999999999999999999999999999999999986

>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=99.59  E-value=7.6e-17  Score=134.43  Aligned_cols=67  Identities=24%  Similarity=0.413  Sum_probs=61.2

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +.++++.||.||.+|+.+|+..|..++||+..+++.||..+||++.+|+|||||||+|+|+......
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   72 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKG   72 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhccC
Confidence            3566778999999999999999999999999999999999999999999999999999998755443

>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=99.59  E-value=1.2e-16  Score=136.38  Aligned_cols=64  Identities=30%  Similarity=0.451  Sum_probs=56.4

Q ss_pred             CCccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ..++++.|+.||.+|+.+|+..|..++||+..+++.||..+||++++|+|||||||+|+||+.+
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            3456788999999999999999999999999999999999999999999999999999999764

>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=99.59  E-value=1.6e-16  Score=129.28  Aligned_cols=64  Identities=22%  Similarity=0.432  Sum_probs=59.5

Q ss_pred             cccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccc
Q psy17256        699 AKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGK  762 (768)
Q Consensus       699 ~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~  762 (768)
                      +++.||.||.+|+.+|+..|..++||+...+..||..+||++.+|+|||||||+|+|+......
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~~   65 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccchh
Confidence            4678999999999999999999999999999999999999999999999999999998765443

>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=99.59  E-value=1.4e-16  Score=128.59  Aligned_cols=62  Identities=44%  Similarity=0.603  Sum_probs=58.8

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      ++++.||.|+.+|+..||..|..++||+..++..||..+||++.+|++||||+|+|+|++..
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            35778999999999999999999999999999999999999999999999999999999764

>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=99.59  E-value=2.1e-16  Score=127.83  Aligned_cols=62  Identities=42%  Similarity=0.699  Sum_probs=58.5

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcc
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  120 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~  120 (768)
                      +.+|.||.||.+|+..||..|..|+||+..++++||..+||++.+|++||||||++.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999988643

>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=99.58  E-value=1.1e-16  Score=123.86  Aligned_cols=53  Identities=32%  Similarity=0.574  Sum_probs=51.5

Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhH
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRAR  753 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak  753 (768)
                      |+||.||.+|+..||..|..++||+..++..||..+||++.+|+|||||||+|
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            57999999999999999999999999999999999999999999999999996

>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=99.58  E-value=2.7e-16  Score=128.96  Aligned_cols=61  Identities=31%  Similarity=0.470  Sum_probs=57.2

Q ss_pred             ccccccccHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHT  760 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~  760 (768)
                      ++.|+.||.+|+..||..|.. ++||+...++.||..+||++++|+|||||||+|+||.+..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~~   63 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   63 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccCC
Confidence            567999999999999999986 7899999999999999999999999999999999998654

>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=99.57  E-value=2.2e-16  Score=127.88  Aligned_cols=60  Identities=33%  Similarity=0.473  Sum_probs=56.9

Q ss_pred             CCCCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      .+||.||.|+.+|+..|+..|..++||+..++++||..+||++.+|+|||||+|+++|+.
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            346789999999999999999999999999999999999999999999999999999874

>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=99.56  E-value=3.6e-16  Score=127.21  Aligned_cols=62  Identities=35%  Similarity=0.551  Sum_probs=58.4

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhcc
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTG  761 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~  761 (768)
                      +|.||.||.+|+..|+..|..++||+..+++.||..+||++.+|+|||||+|+|+|+..+..
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            56799999999999999999999999999999999999999999999999999999876543

>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=99.56  E-value=2e-16  Score=125.72  Aligned_cols=59  Identities=44%  Similarity=0.632  Sum_probs=56.7

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      +|.||.||.+|+..|+..|..++||+..++..||..+||++.+|++||||+|+|+||++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~~   60 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   60 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhcC
Confidence            67899999999999999999999999999999999999999999999999999999863

>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=99.55  E-value=6.2e-16  Score=121.82  Aligned_cols=57  Identities=35%  Similarity=0.571  Sum_probs=54.9

Q ss_pred             CCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         62 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        62 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      |.||.|+.+|+..||..|..++||+..++.+||..+||++.+|+|||||||+++|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            569999999999999999999999999999999999999999999999999999874

>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=99.55  E-value=7.5e-16  Score=130.17  Aligned_cols=63  Identities=25%  Similarity=0.412  Sum_probs=58.1

Q ss_pred             CCCCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcC---------------CCcccccccccccHHHHhhhcccCC
Q psy17256         61 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------LSKRVTQVWFQNSRARQKKHLHTGK  123 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~---------------l~~~~vqvWFqNrRak~k~~~~~~~  123 (768)
                      ||.|+.||++|+.+||..|+.|+||+..+|++||..+|               |++.+|+|||||||+|+|++...+.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            57899999999999999999999999999999999875               9999999999999999999766543

>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=99.54  E-value=8e-16  Score=118.88  Aligned_cols=53  Identities=23%  Similarity=0.477  Sum_probs=51.5

Q ss_pred             CccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         64 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        64 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      ||.||++|+.+||..|..++||+..++.+||..+||++.+|++||||||+|.|
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            78999999999999999999999999999999999999999999999999875

>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=99.53  E-value=1.4e-15  Score=125.10  Aligned_cols=59  Identities=27%  Similarity=0.388  Sum_probs=55.4

Q ss_pred             CCCCCCccCCHHHHHHHHHhhh-hCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         59 KAKRVRTTFTEEQLQVLQANFQ-LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        59 ~~rr~Rt~~t~~Ql~~Le~~F~-~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ..+|.|+.||.+|+.+||..|+ .++||+..++++||..+||++++|++||||+|++.|+
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            4567899999999999999997 4999999999999999999999999999999999886

>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=99.52  E-value=6.7e-16  Score=124.82  Aligned_cols=62  Identities=42%  Similarity=0.699  Sum_probs=58.5

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      +.+|.||.||.+|+..|+..|..++||+..+++.||.++||++.+|++||||||+|.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999988643

>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=2.6e-15  Score=126.15  Aligned_cols=61  Identities=26%  Similarity=0.413  Sum_probs=55.6

Q ss_pred             CCCCCCCCccCCHHHHHHHHHhhhh----CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         57 KSKAKRVRTTFTEEQLQVLQANFQL----DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        57 ~~~~rr~Rt~~t~~Ql~~Le~~F~~----~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      ..++||.||.||..|++.|+..|++    ++||+..++++||..+||++.+|+|||||+|+++|+
T Consensus        14 ~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             ccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            3456789999999999999988886    899999999999999999999999999999987764

>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=99.52  E-value=2.2e-15  Score=118.16  Aligned_cols=56  Identities=29%  Similarity=0.524  Sum_probs=54.2

Q ss_pred             CCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhh
Q psy17256         63 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  118 (768)
Q Consensus        63 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~  118 (768)
                      +||.|+.+|+..||..|..++||+..++++||..+||++.+|++||||||+++|+.
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            48999999999999999999999999999999999999999999999999999974

>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=99.51  E-value=1.4e-15  Score=128.43  Aligned_cols=67  Identities=25%  Similarity=0.401  Sum_probs=62.0

Q ss_pred             ccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhC---------------CCCCccccccccchhHHHhhhhccccC
Q psy17256        700 KRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------LSKRVTQVWFQNSRARQKKHLHTGKMK  764 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lg---------------ls~~~V~vWFQNrRak~kk~~~~~~~~  764 (768)
                      +|.|+.|+.+|+.+||..|..++||+..+|+.||..+|               |++.+|+|||||||+|+||+...+...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~~~   80 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAAIL   80 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCCCS
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHHhh
Confidence            57899999999999999999999999999999999875               899999999999999999998887766


Q ss_pred             CC
Q psy17256        765 SS  766 (768)
Q Consensus       765 ~s  766 (768)
                      +|
T Consensus        81 e~   82 (82)
T d2cufa1          81 ES   82 (82)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.51  E-value=1.1e-15  Score=123.76  Aligned_cols=60  Identities=33%  Similarity=0.473  Sum_probs=56.9

Q ss_pred             ccccccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      .+++.||.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||+|+|+||.
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            356789999999999999999999999999999999999999999999999999999874

>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=99.49  E-value=1.9e-15  Score=118.93  Aligned_cols=57  Identities=35%  Similarity=0.571  Sum_probs=54.9

Q ss_pred             cccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        701 RVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       701 r~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      |.||.|+.+|+..|+..|..++||+..++..||..+||++.+|+|||||||+|+|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            468999999999999999999999999999999999999999999999999999875

>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=99.48  E-value=3.9e-15  Score=113.74  Aligned_cols=50  Identities=30%  Similarity=0.385  Sum_probs=49.0

Q ss_pred             CCccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccH
Q psy17256         63 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR  112 (768)
Q Consensus        63 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrR  112 (768)
                      +||.||..|+..||..|+.++||+..++.+||.++||++++|++||||||
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            58999999999999999999999999999999999999999999999997

>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=99.47  E-value=2.6e-15  Score=115.94  Aligned_cols=53  Identities=23%  Similarity=0.477  Sum_probs=51.5

Q ss_pred             cccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       703 Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      ||.||++|+..|+..|..++||+..++..||.++||++.+|++||||||+|.|
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            68999999999999999999999999999999999999999999999999975

>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=99.45  E-value=5.6e-15  Score=121.34  Aligned_cols=60  Identities=27%  Similarity=0.349  Sum_probs=55.9

Q ss_pred             ccccccccccHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        698 KAKRVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       698 k~rr~Rt~~s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      ..++.|+.|+.+|+.+|+..|.. ++||+..+++.||.++||++++|++||||+|+|+|+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            35678999999999999999975 8999999999999999999999999999999998874

>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=99.45  E-value=3.2e-14  Score=118.30  Aligned_cols=58  Identities=29%  Similarity=0.425  Sum_probs=53.4

Q ss_pred             CCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         67 FTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        67 ~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      +|.+|+.+||..|..++||+..++++||..+||++++|++||||||++.++.......
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~   68 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEI   68 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCC
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhc
Confidence            5899999999999999999999999999999999999999999999998876655443

>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=99.45  E-value=6.6e-15  Score=115.36  Aligned_cols=56  Identities=29%  Similarity=0.524  Sum_probs=54.2

Q ss_pred             ccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        702 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       702 ~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      +||.|+.+|+..|+..|..++||+..++..||.++||++.+|++||||||+|+||.
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            48999999999999999999999999999999999999999999999999999984

>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=99.44  E-value=4.6e-14  Score=117.41  Aligned_cols=61  Identities=26%  Similarity=0.308  Sum_probs=55.3

Q ss_pred             CccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhcccCCC
Q psy17256         64 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKM  124 (768)
Q Consensus        64 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~~~~~~  124 (768)
                      ++.+|.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++|+....+..
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~~~~~   67 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFR   67 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSSTT
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchHHhhh
Confidence            3458999999999999999999999999999999999999999999999999986555443

>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=99.43  E-value=1.4e-14  Score=121.63  Aligned_cols=61  Identities=26%  Similarity=0.413  Sum_probs=55.1

Q ss_pred             CCccccccccccHHHHHHHhhcccc----CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        696 KSKAKRVRTTFTEEQLQVLQANFQL----DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       696 ~~k~rr~Rt~~s~~Ql~~Le~~F~~----~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      ..+++|.||.||.+|+..|+..|+.    ++||+..+++.||.++||++.+|+|||||+|+++|+
T Consensus        14 ~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             ccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            3556788999999999999877775    899999999999999999999999999999988765

>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=99.39  E-value=2.6e-14  Score=109.10  Aligned_cols=50  Identities=30%  Similarity=0.385  Sum_probs=49.0

Q ss_pred             ccccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccch
Q psy17256        702 VRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSR  751 (768)
Q Consensus       702 ~Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrR  751 (768)
                      +||.||.+|+..|+..|..++||+..++..||.++||++.+|++||||||
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

>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=99.39  E-value=8.8e-14  Score=114.73  Aligned_cols=59  Identities=27%  Similarity=0.530  Sum_probs=55.2

Q ss_pred             CCCCccCCHHHHHHHHHhhh---hCCCCCHHHHHHHHHHcCCCcccccccccccHHHHhhhc
Q psy17256         61 KRVRTTFTEEQLQVLQANFQ---LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~~~  119 (768)
                      ||+|+.|+.+|+.+|+..|.   .++||+..++++||..+||++.+|++||||+|++.|+..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            56789999999999999997   488999999999999999999999999999999998754

>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=99.38  E-value=4.5e-14  Score=117.38  Aligned_cols=56  Identities=18%  Similarity=0.337  Sum_probs=52.8

Q ss_pred             CccCCHHHHHHHHHhhhhCCCCCHHHHHHHHHHcC---------------------CCcccccccccccHHHHhhhc
Q psy17256         64 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------------LSKRVTQVWFQNSRARQKKHL  119 (768)
Q Consensus        64 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~la~~l~---------------------l~~~~vqvWFqNrRak~k~~~  119 (768)
                      |+.||+.|+..||+.|+.++||+..+|++||.+++                     |++.+|++||||||++.|++.
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            68899999999999999999999999999999994                     899999999999999998864

>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=99.37  E-value=7.8e-14  Score=115.93  Aligned_cols=62  Identities=29%  Similarity=0.413  Sum_probs=56.1

Q ss_pred             cccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhhccccCCC
Q psy17256        705 TFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLHTGKMKSS  766 (768)
Q Consensus       705 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~~~~~~~s  766 (768)
                      ..|.+|+.+|+..|..++||+..+++.||..+||++++|++||||||+|.|+.+.......+
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~~~~   71 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDES   71 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhcccC
Confidence            35899999999999999999999999999999999999999999999998887776665543

>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=99.34  E-value=9e-14  Score=106.56  Aligned_cols=50  Identities=26%  Similarity=0.474  Sum_probs=46.9

Q ss_pred             CHHHHHHHHHhhhh-CCCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         68 TEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        68 t~~Ql~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      |.+|..+||..|.. ++||+..++++||..+||++++|+|||||||+++|+
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            46799999999986 799999999999999999999999999999999885

>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=99.31  E-value=2.2e-13  Score=112.33  Aligned_cols=60  Identities=27%  Similarity=0.514  Sum_probs=55.4

Q ss_pred             ccccccccHHHHHHHhhccc---cCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhhh
Q psy17256        700 KRVRTTFTEEQLQVLQANFQ---LDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHLH  759 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~~  759 (768)
                      +++|+.|+.+|+.+|+..|.   .++||+..+++.||.++||++.+|++||||+|+|+|+...
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            55789999999999999997   4889999999999999999999999999999999987653

>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=99.29  E-value=4.4e-13  Score=111.35  Aligned_cols=56  Identities=29%  Similarity=0.399  Sum_probs=52.6

Q ss_pred             cccccHHHHHHHhhccccCCCCCHHHHHHHHHHhCCCCCccccccccchhHHHhhh
Q psy17256        703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       703 Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~~  758 (768)
                      ++.+|.+|+.+|+..|..++||+..++..||..+||++.+|++||||+|+|+|+..
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            34579999999999999999999999999999999999999999999999999854

>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=99.28  E-value=1.4e-13  Score=105.54  Aligned_cols=50  Identities=26%  Similarity=0.474  Sum_probs=46.8

Q ss_pred             cHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHHHh
Q psy17256        707 TEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  756 (768)
Q Consensus       707 s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk  756 (768)
                      |++|..+||..|.. ++||+..++..||.++||++++|++||||||+|+|+
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            46789999999977 789999999999999999999999999999999875

>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=99.28  E-value=2.9e-13  Score=106.45  Aligned_cols=55  Identities=24%  Similarity=0.360  Sum_probs=50.8

Q ss_pred             CCCccCCHHHHHHHHHhhhh-CCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         62 RVRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        62 r~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      +.|+.++.+|..+||..|.. ++||+..++++||..+||++++|++||||||+++|
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            45677889999999999986 68999999999999999999999999999999986

>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=99.24  E-value=4.9e-13  Score=111.01  Aligned_cols=56  Identities=18%  Similarity=0.337  Sum_probs=52.6

Q ss_pred             cccccHHHHHHHhhccccCCCCCHHHHHHHHHHhC---------------------CCCCccccccccchhHHHhhh
Q psy17256        703 RTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITG---------------------LSKRVTQVWFQNSRARQKKHL  758 (768)
Q Consensus       703 Rt~~s~~Ql~~Le~~F~~~~~p~~~~r~~LA~~lg---------------------ls~~~V~vWFQNrRak~kk~~  758 (768)
                      |+.|+++|+.+|+..|..++||+...|+.||.+++                     |++.+|++||||||++.|++.
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            67899999999999999999999999999999994                     888999999999999998864

>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=99.23  E-value=1.7e-12  Score=102.55  Aligned_cols=51  Identities=29%  Similarity=0.515  Sum_probs=48.4

Q ss_pred             CCHHHHHHHHHhhhhC---CCCCHHHHHHHHHHcCCCcccccccccccHHHHhh
Q psy17256         67 FTEEQLQVLQANFQLD---SNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKK  117 (768)
Q Consensus        67 ~t~~Ql~~Le~~F~~~---~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k~  117 (768)
                      |+.+|+.+|+..|..+   +||+..++++||..+||++.+|++||||+|++.|+
T Consensus         5 ft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            9999999999999765   79999999999999999999999999999998875

>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=99.20  E-value=3.6e-12  Score=101.29  Aligned_cols=56  Identities=23%  Similarity=0.335  Sum_probs=51.8

Q ss_pred             CCCCccCCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHcCCCcccccccccccHHHHh
Q psy17256         61 KRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  116 (768)
Q Consensus        61 rr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~vqvWFqNrRak~k  116 (768)
                      |++|+.|+.+|+.+|+..|..   ++||+..++.+||..+||+..+|++||+|+|++..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            456788999999999999985   89999999999999999999999999999998864

>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=99.18  E-value=8.6e-13  Score=103.72  Aligned_cols=54  Identities=24%  Similarity=0.350  Sum_probs=49.8

Q ss_pred             ccccccHHHHHHHhhcccc-CCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        702 VRTTFTEEQLQVLQANFQL-DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       702 ~Rt~~s~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      .++.++.++..+||..|.. ++||+..+++.||.++||++++|++||||||+++|
T Consensus         4 ~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           4 DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            4667888899999999986 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=99.15  E-value=3.7e-12  Score=100.64  Aligned_cols=53  Identities=28%  Similarity=0.480  Sum_probs=49.0

Q ss_pred             cccHHHHHHHhhccccC---CCCCHHHHHHHHHHhCCCCCccccccccchhHHHhh
Q psy17256        705 TFTEEQLQVLQANFQLD---SNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH  757 (768)
Q Consensus       705 ~~s~~Ql~~Le~~F~~~---~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~kk~  757 (768)
                      +|+.+|+..|+..|..+   +||+..+++.||..+||++.+|++||||+|+|.|+.
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            49999999999999764   799999999999999999999999999999998763

>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=99.10  E-value=1e-11  Score=98.62  Aligned_cols=56  Identities=23%  Similarity=0.335  Sum_probs=51.4

Q ss_pred             ccccccccHHHHHHHhhcccc---CCCCCHHHHHHHHHHhCCCCCccccccccchhHHH
Q psy17256        700 KRVRTTFTEEQLQVLQANFQL---DSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQK  755 (768)
Q Consensus       700 rr~Rt~~s~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~lgls~~~V~vWFQNrRak~k  755 (768)
                      ++.|+.|+.+++.+|+..|..   ++||+..++..||..+||+..||++||+|+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            455778999999999999975   88999999999999999999999999999998864

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=2.8e-11  Score=83.87  Aligned_cols=34  Identities=32%  Similarity=0.633  Sum_probs=32.6

Q ss_pred             hhhhhcccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        610 ICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       610 ~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ||+++|+++|++|+++|.+.  +|.|+++.||++||
T Consensus         2 DY~~~fapkC~~C~~~I~g~--~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           2 DFLAMFSPKCGGCNRPVLEN--YLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCSCBCTTTCCBCCSS--CEEETTEEECTTTC
T ss_pred             cHHHHhChhhhhcCCcccch--heeecCCccCcccC
Confidence            69999999999999999976  99999999999998

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=3.3e-09  Score=73.51  Aligned_cols=36  Identities=28%  Similarity=0.551  Sum_probs=34.9

Q ss_pred             hhhhhcccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        610 ICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       610 ~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ||.+.|+++|.+|+++|.+++..|++.++.||.+||
T Consensus         2 Cy~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           2 CTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            689999999999999999999999999999999998

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=7.4e-09  Score=69.42  Aligned_cols=34  Identities=21%  Similarity=0.596  Sum_probs=32.5

Q ss_pred             hhhhhcccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        610 ICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       610 ~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ||.++|+++|..|+++|..+  .+.+.++.||.+||
T Consensus         2 CyE~kfa~~C~~Ckk~It~G--GvtY~dqpWHkeCF   35 (35)
T d2cuqa2           2 CYENKFAPRCARCSKTLTQG--GVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCSSCCCTTTCCCCCSC--CEESSSSEECTTTC
T ss_pred             chHHHHHHHHhhcCCccccC--ceeecCCcchhhhC
Confidence            69999999999999999987  89999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.42  E-value=4.3e-08  Score=68.73  Aligned_cols=34  Identities=32%  Similarity=0.567  Sum_probs=32.5

Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceecccC
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      .||.++||.+|..|++.|.+.  ||.|.++.||++|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~--V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGE--VVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSC--CEEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeee--eeEecCcccCCCC
Confidence            689999999999999999977  9999999999998

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.31  E-value=7.5e-08  Score=63.26  Aligned_cols=29  Identities=45%  Similarity=0.957  Sum_probs=27.8

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ..|++|++.|.+.|+||+|++++||..||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            47999999999999999999999999998

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.06  E-value=5.5e-07  Score=59.35  Aligned_cols=34  Identities=24%  Similarity=0.469  Sum_probs=31.5

Q ss_pred             hhhhhhcccccccCCCCCCCCcceeeecCceecccC
Q psy17256        609 LICFRSFGAKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       609 ~~y~~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      +||+.+||..|.+|...|.+.  +|.|.+..||++|
T Consensus         1 kdYw~kfge~C~~C~~~itGp--vMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTGP--FMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCSC--CBCCTTCCBCTTS
T ss_pred             CcHHHHHHHHhhhhHhhcccc--eeeecccccCCCC
Confidence            369999999999999988866  9999999999998

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.98  E-value=1e-06  Score=59.19  Aligned_cols=28  Identities=36%  Similarity=0.768  Sum_probs=26.0

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ..+|..|+++|.  |.+++|+|+.||+.||
T Consensus         8 lEkC~~C~~~I~--driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPIL--DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCC--SCCEEETTEEECTTTC
T ss_pred             HHHHHHhchHHH--HHHHHHhCCCCCCCCC
Confidence            469999999999  5699999999999998

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=1.5e-06  Score=61.98  Aligned_cols=28  Identities=21%  Similarity=0.370  Sum_probs=26.1

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      .++|++|+++|.+.  ++.|+|+.||++||
T Consensus        18 ~P~C~~C~~pI~g~--~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGP--FLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSC--EEEETTEEECTTTC
T ss_pred             CeeccccCCcccCc--eeeecCCccCcCCC
Confidence            57899999999976  99999999999998

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=3.7e-06  Score=54.64  Aligned_cols=30  Identities=23%  Similarity=0.323  Sum_probs=26.3

Q ss_pred             hhcccccccCCCCCCCCcceeeecCceecccC
Q psy17256        613 RSFGAKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       613 ~~f~~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      +++.++|+.|++||.+.  ++.|+|+.||++.
T Consensus         2 kmg~p~C~~C~~PI~~~--~vtAlgk~WHpEH   31 (31)
T d1u5sb1           2 SMGVPICGACRRPIEGR--VVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCCEETTTTEECCSC--EECCTTSBEETTT
T ss_pred             CcCCcchhhcCCchhhh--HhhhhccccCCCC
Confidence            35778999999999965  9999999999873

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.59  E-value=1.7e-05  Score=49.00  Aligned_cols=27  Identities=22%  Similarity=0.609  Sum_probs=26.0

Q ss_pred             cccCCCCCCCCcceeeecCceecccCc
Q psy17256        619 CSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       619 C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      |..|.+.|.++..-|+..|+.||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            889999999999999999999999998

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.44  E-value=9.1e-06  Score=55.64  Aligned_cols=33  Identities=27%  Similarity=0.559  Sum_probs=29.7

Q ss_pred             ccccccccccCCCCceEeecCccccccccccccc
Q psy17256        645 FACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       645 F~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      |+|..|+++| .+..|++.+|++||+.||.++..
T Consensus         1 F~C~~C~~~f-~~~~F~e~~G~pYCe~~Y~~lFA   33 (35)
T d1g47a2           1 FVCAQCFQQF-PEGLFYEFEGRKYCEHDFQMLFA   33 (35)
T ss_dssp             CCCTTTCCCC-GGGCSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCcCCC-CCCCeEEECCEecChHhHHhhcC
Confidence            8999999999 46779999999999999998764

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.42  E-value=2.9e-05  Score=47.88  Aligned_cols=27  Identities=22%  Similarity=0.551  Sum_probs=25.9

Q ss_pred             cccCCCCCCCCcceeeecCceecccCc
Q psy17256        619 CSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       619 C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      |..|.+.|.++..-|+..|+.||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            889999999999999999999999998

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=5.3e-05  Score=50.32  Aligned_cols=28  Identities=29%  Similarity=0.629  Sum_probs=25.0

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ..|++|++.|..+ ..+.|+++.||.+||
T Consensus         9 ~~CagCg~eik~g-QaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHG-QSLLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSS-CCEEETTEEECTTTC
T ss_pred             ccccccchhhhCC-ceeeeeecceeeeeC
Confidence            4899999999876 567899999999998

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.13  E-value=3.7e-05  Score=50.79  Aligned_cols=30  Identities=23%  Similarity=0.544  Sum_probs=26.7

Q ss_pred             cccccccccCCCCceEeecCccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLEL  676 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~  676 (768)
                      +|..|.+++ .+..|++.+|+|||+.||.++
T Consensus         1 VC~~C~~PF-~~~~Fy~~~g~PyCe~HyH~~   30 (32)
T d1x3ha2           1 VCGDCFTSF-STGSFFELDGRPFCELHYHHR   30 (32)
T ss_dssp             BCSSSCCBS-CSSCCEESSSCEECHHHHHHH
T ss_pred             CcCccCCcC-CCCCeEeECCccchHHhhhhh
Confidence            599999999 567799999999999999864

>d1x62a2 g.39.1.3 (A:8-42) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.00021  Score=46.86  Aligned_cols=27  Identities=37%  Similarity=0.742  Sum_probs=25.2

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      +.|..|+.+|.+.  ++.++++.+|++||
T Consensus         9 p~CdkCg~GIVG~--~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVGV--FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCSS--CEECSSCEECTTTT
T ss_pred             ccccccCCCcEeE--EEEeccccCCCCCC
Confidence            6899999999977  99999999999998

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.91  E-value=0.00019  Score=46.53  Aligned_cols=28  Identities=29%  Similarity=0.643  Sum_probs=24.4

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ..|++|+++|... .++.+.+..||..|.
T Consensus         3 ~~CaGC~~~I~DR-flL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADR-FLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCS-EEEEETTEEECGGGC
T ss_pred             cccCCCCCccchh-hhhccchhhhhhhhC
Confidence            4799999999964 678899999999984

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.90  E-value=0.00024  Score=45.86  Aligned_cols=27  Identities=30%  Similarity=0.667  Sum_probs=23.7

Q ss_pred             cccccCCCCCCCCcceeeecCceecccC
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      ..|++|+++|... +++.|.+..||..|
T Consensus         4 ~~CaGC~~~I~DR-flL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDR-YFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSS-EEEECSSSEECTTT
T ss_pred             cccCCCCCcchHH-HHHHHHHHHHhcCC
Confidence            4799999999964 67889999999988

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.88  E-value=0.00011  Score=48.06  Aligned_cols=33  Identities=24%  Similarity=0.678  Sum_probs=30.5

Q ss_pred             ccccccccccCCCCceEeecCccccccccccccc
Q psy17256        645 FACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       645 F~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      |+|..|.+++ -|...+.+.|..||+.||.++.+
T Consensus         1 FvCA~CekPF-~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPF-LGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBC-SSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCcc-CCchhhhhcCchHHHHHHHHHhc
Confidence            8999999999 78999999999999999998765

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.80  E-value=0.00012  Score=48.04  Aligned_cols=31  Identities=32%  Similarity=0.830  Sum_probs=28.1

Q ss_pred             cccccccccCCCCceEeecCcccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      +|..|..+| .|++|.+++++|||-.||.++.
T Consensus         1 ~C~~C~~~L-~GQry~~rd~~PyC~~Cf~~lf   31 (32)
T d2d8za2           1 VCTACRKQL-SGQRFTARDDFAYCLNCFCDLY   31 (32)
T ss_dssp             BCSSSCCBC-TTSCCEESSSSEECHHHHHHHT
T ss_pred             CcccCCccc-cCceeeecCCCeehHHhhHhhc
Confidence            488999999 8999999999999999998754

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.73  E-value=0.00036  Score=44.06  Aligned_cols=27  Identities=22%  Similarity=0.561  Sum_probs=23.6

Q ss_pred             cccCCCCCCC--CcceeeecCceecccCc
Q psy17256        619 CSKCCRGIAS--SDWVRKARDHVYHLACF  645 (768)
Q Consensus       619 C~~C~~~I~~--~e~~~~a~~~~~H~~CF  645 (768)
                      |++|.+||.+  +...+...+..||.+||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            8999999976  45678889999999998

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.62  E-value=0.00042  Score=48.54  Aligned_cols=28  Identities=46%  Similarity=0.806  Sum_probs=25.6

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      .+.|..|+.+|.+-  ++.++|+.+|++||
T Consensus        18 LP~CdkCg~GIVG~--~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGA--VVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSC--CEESSSCEECTTTC
T ss_pred             CccccccCCCcEEE--EEEeccccCCCCCC
Confidence            36889999999977  99999999999998

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.59  E-value=0.00023  Score=46.03  Aligned_cols=31  Identities=26%  Similarity=0.716  Sum_probs=28.1

Q ss_pred             cccccccccCCCCceEeecCcccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      +|..|+++| .|+.|..++.++||..||.++.
T Consensus         1 vCt~Ck~~L-aGqrFTSrde~pYC~~Cfg~Lf   31 (32)
T d2cuqa1           1 VCTGCQTPL-AGQQFTSRDEDPYCVACFGELF   31 (32)
T ss_dssp             BCSSSCCBC-TTCCEEECSSSEEEHHHHHHHT
T ss_pred             CccccCccc-cCCccccCCCCccHHHHhHhhc
Confidence            589999999 8999999999999999997654

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.47  E-value=0.0007  Score=42.65  Aligned_cols=27  Identities=26%  Similarity=0.599  Sum_probs=23.6

Q ss_pred             cccCCCCCCC--CcceeeecCceecccCc
Q psy17256        619 CSKCCRGIAS--SDWVRKARDHVYHLACF  645 (768)
Q Consensus       619 C~~C~~~I~~--~e~~~~a~~~~~H~~CF  645 (768)
                      |.+|.+||.+  +..++...+..||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            8899999976  55678889999999998

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.45  E-value=0.00031  Score=47.84  Aligned_cols=34  Identities=12%  Similarity=-0.169  Sum_probs=26.2

Q ss_pred             EEEeccccccccccccccccccccccCCCCcceeecccccccccchhhhhhhccc
Q psy17256        563 TEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGA  617 (768)
Q Consensus       563 ~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~  617 (768)
                      |+|+.|+.++.                 ...+|+++|++    ||+.||+++|+|
T Consensus         1 F~C~~C~~~f~-----------------~~~F~e~~G~p----YCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFP-----------------EGLFYEFEGRK----YCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCG-----------------GGCSEEETTEE----ECHHHHHHHCCC
T ss_pred             CCCCCCcCCCC-----------------CCCeEEECCEe----cChHhHHhhcCC
Confidence            67888985433                 24579999999    556999999986

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.36  E-value=0.00011  Score=52.20  Aligned_cols=33  Identities=15%  Similarity=-0.006  Sum_probs=30.0

Q ss_pred             cCCccccchhhhhhhhhhHHHHHhhcccccccccccceE
Q psy17256        525 TDGALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRT  563 (768)
Q Consensus       525 ~~G~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~  563 (768)
                      +.|..+|.|..|.++|.++++.++|+      .||++||
T Consensus        13 p~~~r~P~C~~C~~pI~g~~vtAlgk------~WHPEhF   45 (45)
T d2dara2          13 PAGKRTPMCAHCNQVIRGPFLVALGK------SWHPEEF   45 (45)
T ss_dssp             CTTTCCCBBSSSCCBCCSCEEEETTE------EECTTTC
T ss_pred             CCCCCCeeccccCCcccCceeeecCC------ccCcCCC
Confidence            34677888999999999999999999      9999997

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.24  E-value=0.001  Score=42.70  Aligned_cols=29  Identities=21%  Similarity=0.679  Sum_probs=26.6

Q ss_pred             cccccccccCCCCceEeecCccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYL  674 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~  674 (768)
                      +|+.|..+|.+|+.|...+|.+||+.+..
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~p   29 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDRP   29 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGCC
T ss_pred             CcccccccccCCceeEEecCEEEEecCCc
Confidence            58999999999999999999999998854

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.20  E-value=0.0013  Score=40.36  Aligned_cols=27  Identities=22%  Similarity=0.624  Sum_probs=24.0

Q ss_pred             cccCCCCCCCCcceeeecCceecccCc
Q psy17256        619 CSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       619 C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      |..|.+||.+...-+...+..||..||
T Consensus         1 c~ecrkpigad~ke~h~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHYKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEETTEEEETTTC
T ss_pred             CccccCCcCcchHHhhccccccccccC
Confidence            788999999876678888999999998

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.18  E-value=0.00015  Score=49.52  Aligned_cols=30  Identities=3%  Similarity=-0.058  Sum_probs=27.7

Q ss_pred             ccccchhhhhhhhhhHHHHHhhcccccccccccceE
Q psy17256        528 ALHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRT  563 (768)
Q Consensus       528 ~~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~  563 (768)
                      ..+|.|..|.++|.+.++.++|+      .||++||
T Consensus         6 ~fapkC~~C~~~I~g~~v~Al~~------~wHpeCF   35 (35)
T d1x3ha1           6 MFSPKCGGCNRPVLENYLSAMDT------VWHPECF   35 (35)
T ss_dssp             CCSCBCTTTCCBCCSSCEEETTE------EECTTTC
T ss_pred             HhChhhhhcCCcccchheeecCC------ccCcccC
Confidence            46788999999999999999999      9999997

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.18  E-value=0.00061  Score=43.53  Aligned_cols=29  Identities=34%  Similarity=0.831  Sum_probs=26.7

Q ss_pred             cccccccccCCCCceEeecCcccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLE  675 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e  675 (768)
                      +|..|+..| .|+.|+..+.+.||+.||..
T Consensus         1 vC~tC~~kL-RGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQL-RGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBC-TTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCcee-cCCcceEeeccccccceeee
Confidence            589999999 89999999999999999964

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.12  E-value=0.00087  Score=42.52  Aligned_cols=28  Identities=25%  Similarity=0.685  Sum_probs=24.6

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      +.|+.|++.+.+.|. +.-+|+.||..||
T Consensus         3 ~~CaRC~k~VYp~Ek-l~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEK-VNCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGC-CCSSSSCCCGGGC
T ss_pred             CcccccCCccccHHH-hhhhHHHHhhccC
Confidence            689999999998654 6789999999998

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.96  E-value=0.0021  Score=38.68  Aligned_cols=27  Identities=30%  Similarity=0.682  Sum_probs=23.3

Q ss_pred             cccCCCCCCCCcceeeecCceecccCc
Q psy17256        619 CSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       619 C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      |.+|++-+.+..-.+.|++.+||+.||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            889999887755568899999999998

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.94  E-value=0.00086  Score=42.77  Aligned_cols=29  Identities=31%  Similarity=0.783  Sum_probs=26.7

Q ss_pred             cccccccccCCCCceEeecCcccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLE  675 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e  675 (768)
                      +|..|.++| .|..|..++++.||.+||..
T Consensus         1 vC~~C~K~L-ag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKL-AGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBC-TTSCEEECSSCEEEHHHHHH
T ss_pred             Ccccccchh-cCceeEEecceEEEeeeecc
Confidence            589999999 89999999999999999964

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.87  E-value=0.0018  Score=41.26  Aligned_cols=26  Identities=31%  Similarity=0.684  Sum_probs=24.0

Q ss_pred             cccccCCCCCCCCcceeeecCceecccC
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      .-|..|.+.|.+.  |++|.++.||+.|
T Consensus         6 sgC~~C~~~ItGk--VLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGR--VLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSC--CBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhh--hhhccccccCCCC
Confidence            4689999999987  9999999999998

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.83  E-value=0.0012  Score=42.61  Aligned_cols=30  Identities=30%  Similarity=0.659  Sum_probs=25.3

Q ss_pred             cccccccccCCCCceEeecCcccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      +|..|+..| .| +|..++|.|||+.||...+
T Consensus         1 kC~~C~~vL-~g-EYm~kdG~PyCe~DY~~~F   30 (31)
T d2dj7a1           1 KCQTCSVIL-TG-EYISKDGVPYCESDYHAQF   30 (31)
T ss_dssp             BCSSSCCBC-SS-CCEEETTEEECTTHHHHHT
T ss_pred             CccccCccc-cc-eeecCCCCcccHHHHHHhc
Confidence            588999999 45 4888999999999998654

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.45  E-value=0.0036  Score=42.23  Aligned_cols=29  Identities=24%  Similarity=0.689  Sum_probs=25.1

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      ..+|..|++.+..-|. +.|.|+.||..||
T Consensus         7 ~~kC~~C~K~VY~~E~-~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMER-LLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSE-EECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeee-EecCCeehhhccC
Confidence            3599999999988655 6799999999998

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.40  E-value=0.0017  Score=42.40  Aligned_cols=32  Identities=31%  Similarity=0.677  Sum_probs=28.9

Q ss_pred             ccccccccccCCCCceEeec-Cccccccccccc
Q psy17256        645 FACEACKRQLSTGEEFALHE-DRVLCKSHYLEL  676 (768)
Q Consensus       645 F~C~~C~~~L~~G~~f~~~~-g~~~C~~~y~e~  676 (768)
                      |.|..|+.-+.+|+.|.+++ .++||..||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            78999999999999999988 689999999753

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.40  E-value=0.0005  Score=44.51  Aligned_cols=28  Identities=11%  Similarity=0.090  Sum_probs=24.5

Q ss_pred             ccc-chhhhhhhhhhHHHHHhhcccccccccccce
Q psy17256        529 LHL-EFHSFLKRIALVLSEKWKKMYGHVLSWLRVR  562 (768)
Q Consensus       529 ~g~-~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~  562 (768)
                      ||. .|..|.++|.++...++|+      .||++|
T Consensus         3 mg~p~C~~C~~PI~~~~vtAlgk------~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRVVNAMGK------QWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEECCSCEECCTTS------BEETTT
T ss_pred             cCCcchhhcCCchhhhHhhhhcc------ccCCCC
Confidence            444 4999999999999999999      999975

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=95.37  E-value=0.0027  Score=45.09  Aligned_cols=29  Identities=21%  Similarity=0.643  Sum_probs=25.3

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      +.+|..|++.+..-|.+ .+.|+.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~~-~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEKV-IGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSCE-EETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHHh-hcCCCccccCCC
Confidence            35899999999988764 689999999998

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=95.22  E-value=0.0016  Score=41.02  Aligned_cols=29  Identities=28%  Similarity=0.723  Sum_probs=25.3

Q ss_pred             ccccccccccCCCCceEeecCccccccccc
Q psy17256        645 FACEACKRQLSTGEEFALHEDRVLCKSHYL  674 (768)
Q Consensus       645 F~C~~C~~~L~~G~~f~~~~g~~~C~~~y~  674 (768)
                      |+|..|++.| .......++|.+||+.||.
T Consensus         1 frca~cgk~l-estt~adkdgeiyck~cya   29 (31)
T d1ibia2           1 FRCAKCGKSL-ESTTLTEKEGEIYCKGCYA   29 (31)
T ss_dssp             EECSSSCCEE-CSSCSEEETTEEECHHHHH
T ss_pred             CccccccCcc-ccceeeccCCcEEEeeeee
Confidence            7899999999 5566888899999999985

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.21  E-value=0.0049  Score=39.62  Aligned_cols=29  Identities=21%  Similarity=0.486  Sum_probs=24.6

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      .++|..|++++...|. +.++|+.||..|.
T Consensus         2 ~~~CprC~K~VYfaEk-~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEK-VSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTE-EEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHh-hccCCcccccccC
Confidence            4689999999998766 5688999999884

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.01  E-value=0.0054  Score=41.50  Aligned_cols=28  Identities=21%  Similarity=0.540  Sum_probs=24.7

Q ss_pred             cccccCCCCCCCCcceeeecCceecccCc
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      .+|..|++.+.+-|. +.|.|+.||..||
T Consensus         9 ~~C~~C~K~VY~~Er-l~a~g~~yHk~CF   36 (36)
T d2co8a2           9 DLCALCGEHLYVLER-LCVNGHFFHRSCF   36 (36)
T ss_dssp             CBCSSSCCBCCTTTB-CCBTTBCCBTTTC
T ss_pred             CcccccCCEEeeeeE-EEecCcEeccccC
Confidence            489999999988766 5799999999998

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.74  E-value=0.0033  Score=41.34  Aligned_cols=31  Identities=23%  Similarity=0.625  Sum_probs=26.8

Q ss_pred             cccccccccCCCCceEeec-Ccccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHE-DRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~-g~~~C~~~y~e~~  677 (768)
                      +|..|++.| +|..|.+.. +++||..||++..
T Consensus         1 tCvvC~~~L-DGvPFtvD~~n~i~Cv~DyHrkf   32 (33)
T d2dloa2           1 TCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKF   32 (33)
T ss_dssp             BCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHT
T ss_pred             CeeEcCccc-CCCcEEEcCCCCEeehhhhhhhc
Confidence            588999999 899999875 7999999998654

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.72  E-value=0.0037  Score=40.81  Aligned_cols=34  Identities=18%  Similarity=0.082  Sum_probs=26.2

Q ss_pred             EEEeccccccccccccccccccccccCCCCcceeecccccccccchhhhhhhccc
Q psy17256        563 TEFSILKAVSLRLRGTRQIVKPYGFDDGAGLMYIRVRILLKGRLSVLICFRSFGA  617 (768)
Q Consensus       563 ~~c~~c~~~~~~~~g~r~~~~~~~~~dg~~~~~~~~~~~~c~~yC~~~y~~~f~~  617 (768)
                      |+|+.|..+++   |.              ..|++.+..    ||+.+|+.+||.
T Consensus         1 FvCA~CekPF~---G~--------------rhyE~~g~a----yCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFL---GH--------------RHYERKGLA----YCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCS---SS--------------CCEEETTEE----ECHHHHHHHCSC
T ss_pred             CcccccCCccC---Cc--------------hhhhhcCch----HHHHHHHHHhcc
Confidence            67999987765   33              348889998    567999999974

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.49  E-value=0.0047  Score=43.27  Aligned_cols=33  Identities=33%  Similarity=0.769  Sum_probs=28.6

Q ss_pred             cccccccccCCCCceEeecCcccccccccccccC
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      +|..|+..|..| .|...+|.+||+.||.++...
T Consensus         1 rC~~C~~~Ls~~-~yas~~G~lYCkpHf~qLF~~   33 (42)
T d2d8ya2           1 RCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFKS   33 (42)
T ss_dssp             BCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSCC
T ss_pred             CcCcCCCCccCC-cchhhCCEeccHHHHHHHHHh
Confidence            599999999655 588889999999999988864

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.62  E-value=0.0079  Score=39.47  Aligned_cols=24  Identities=17%  Similarity=0.163  Sum_probs=18.1

Q ss_pred             CCCCcceeecccccccccchhhhhhhcc
Q psy17256        589 DGAGLMYIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       589 dg~~~~~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      ||.|+....++++    ||+.||+++|+
T Consensus        10 DGvPFtvD~~n~i----~Cv~DyHrkfA   33 (33)
T d2dloa2          10 DGIPFTVDATSQI----HCIEDFHRKFA   33 (33)
T ss_dssp             TTSCEECCTTCCC----EEHHHHHHHTT
T ss_pred             CCCcEEEcCCCCE----eehhhhhhhcC
Confidence            4556666666788    67899999986

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=93.42  E-value=0.016  Score=41.93  Aligned_cols=30  Identities=13%  Similarity=0.045  Sum_probs=23.9

Q ss_pred             cceeecccccccccchhhhhhhcccccccCCCCC
Q psy17256        593 LMYIRVRILLKGRLSVLICFRSFGAKCSKCCRGI  626 (768)
Q Consensus       593 ~~~~~~~~~~c~~yC~~~y~~~f~~~C~~C~~~I  626 (768)
                      ...++|+.+|    |..||-++|||++.+.+..-
T Consensus        13 t~~ehdg~~Y----Ck~CY~k~fGPKG~g~G~ga   42 (49)
T d1b8ta4          13 TLADKDGEIY----CKGCYAKNFGPKGFGFGQGA   42 (49)
T ss_dssp             SEEEETTEEE----EHHHHHHHTCCCCCCCCCCC
T ss_pred             cccccCCccc----chhhhhhccCCCccCcccCc
Confidence            3466888885    55999999999999988543

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.22  E-value=0.0097  Score=38.44  Aligned_cols=31  Identities=19%  Similarity=0.496  Sum_probs=25.7

Q ss_pred             cccccccccCCCCceEeecCcccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      .|+.|+.+| ....|+...|.+||+.||++-+
T Consensus         1 nCa~C~~sL-~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTM-AYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBC-SSSCBEESSSCEECHHHHHHHT
T ss_pred             CcccccccH-hhcceeeecCcEeHHHHHHHhc
Confidence            488999999 5566888889999999998643

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=92.76  E-value=0.021  Score=35.41  Aligned_cols=27  Identities=30%  Similarity=0.641  Sum_probs=22.6

Q ss_pred             cccccCCCCCCCCcceeeecCceecccC
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      .+|..|++.+.+.|.||-+ |+.||..|
T Consensus         2 d~CpRC~~~VyaAEkviGa-G~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGA-GKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESS-SSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcC-CCccccCC
Confidence            4799999999998888754 67899887

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=92.74  E-value=0.012  Score=37.66  Aligned_cols=29  Identities=34%  Similarity=0.770  Sum_probs=25.2

Q ss_pred             ccccccccCCCCceEeecCccccccccccc
Q psy17256        647 CEACKRQLSTGEEFALHEDRVLCKSHYLEL  676 (768)
Q Consensus       647 C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~  676 (768)
                      |..|.+.| +......+++.+||+.||...
T Consensus         2 C~~C~K~L-dStTva~h~~eiYCKsCygkk   30 (32)
T d1a7ia2           2 CMVCRKNL-DSTTVAIHDAEVYCKSCYGKK   30 (32)
T ss_dssp             CSSSCCEE-CSSCCEEETTEEECSHHHHHH
T ss_pred             chhhhhcc-CcceeeeecceEEehhhcccc
Confidence            88999999 566788999999999999654

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.52  E-value=0.02  Score=36.72  Aligned_cols=19  Identities=11%  Similarity=0.034  Sum_probs=14.9

Q ss_pred             ceeecccccccccchhhhhhhcc
Q psy17256        594 MYIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       594 ~~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      +.-+|+.+    ||+.||+.+||
T Consensus        13 Ym~kdG~P----yCe~DY~~~FG   31 (31)
T d2dj7a1          13 YISKDGVP----YCESDYHAQFG   31 (31)
T ss_dssp             CEEETTEE----ECTTHHHHHTT
T ss_pred             eecCCCCc----ccHHHHHHhcC
Confidence            45588888    55699999996

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=92.26  E-value=0.017  Score=41.74  Aligned_cols=33  Identities=21%  Similarity=0.534  Sum_probs=28.0

Q ss_pred             cccccccccCCCCceEeecCcccccccccccccC
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELVDG  679 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~~  679 (768)
                      +|..|++.|.++ ....+|+++||+.||......
T Consensus         1 KC~~C~k~Lds~-t~~ehdg~~YCk~CY~k~fGP   33 (49)
T d1b8ta4           1 RCAKCGKSLEST-TLADKDGEIYCKGCYAKNFGP   33 (49)
T ss_dssp             BCTTTCCBCCSS-SEEEETTEEEEHHHHHHHTCC
T ss_pred             ChhhcCCccCCC-cccccCCcccchhhhhhccCC
Confidence            589999999665 577799999999999887764

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.18  E-value=0.018  Score=37.29  Aligned_cols=31  Identities=16%  Similarity=0.528  Sum_probs=26.0

Q ss_pred             cccccccccCCCCceEeecCcccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      .|..|.+++ ....|..+++..||..||++..
T Consensus         1 ~C~~C~qPI-Gtksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           1 ICHRCQQPI-GTKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CCSSSCCCC-CSSSEEEETTEEEEHHHHHHHT
T ss_pred             CcccccCcc-cccccccCCCCceEeecchhhc
Confidence            488999999 3456999999999999998653

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.17  E-value=0.0041  Score=40.17  Aligned_cols=27  Identities=11%  Similarity=-0.132  Sum_probs=22.2

Q ss_pred             chhhhhhhhhhHHHHHhhcccccccccccceE
Q psy17256        532 EFHSFLKRIALVLSEKWKKMYGHVLSWLRVRT  563 (768)
Q Consensus       532 ~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~  563 (768)
                      .|++|.++|.++++.+...     ..||..|+
T Consensus         4 ~CaGC~~~I~DRflL~v~d-----r~WH~~CL   30 (30)
T d1rutx1           4 RCAGCGGKIADRFLLYAMD-----SYWHSRCL   30 (30)
T ss_dssp             BBTTTCCBCCCSEEEEETT-----EEECGGGC
T ss_pred             ccCCCCCccchhhhhccch-----hhhhhhhC
Confidence            5999999999998876643     29999885

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.79  E-value=0.027  Score=36.46  Aligned_cols=31  Identities=32%  Similarity=0.779  Sum_probs=25.0

Q ss_pred             cccccccccCCCCceEeecCcccccc-cccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKS-HYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~-~y~e~~  677 (768)
                      +|..|++.|..|. ...++|++||.. ||..++
T Consensus         1 kCekC~ktL~~G~-HaEH~gkPYC~~PCY~aLF   32 (33)
T d2cu8a2           1 KCERCSKTLTPGG-HAEHDGKPFCHKPCYATLF   32 (33)
T ss_dssp             BCSSSCCBCCTTS-CEEETTEEECTTTHHHHHS
T ss_pred             CchhcccccCCCC-ccccCCCcCcCcchHHhhc
Confidence            5889999997775 788999999965 886543

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.65  E-value=0.023  Score=36.62  Aligned_cols=31  Identities=19%  Similarity=0.491  Sum_probs=25.8

Q ss_pred             cccccccccCCCCceEeecCcccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELV  677 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~  677 (768)
                      .|..|.+++ ....|..+++..||..||+...
T Consensus         1 ~C~~C~qPI-GtkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           1 LCSGCEQPL-GSRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             BCTTTCCBT-TTSCEEEETTEEEEHHHHHHHT
T ss_pred             CcccccCcc-cccccccCCCcEEEEecccccc
Confidence            488999999 4456889999999999998653

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=91.25  E-value=0.057  Score=38.50  Aligned_cols=33  Identities=30%  Similarity=0.693  Sum_probs=28.1

Q ss_pred             cccccccccCCCCceEeecCcccc-cccccccccC
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLC-KSHYLELVDG  679 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C-~~~y~e~~~~  679 (768)
                      +|..|++.|.+| ....+++++|| +.||..++..
T Consensus         1 kC~~C~K~L~sg-~~aeHdg~pYC~k~CY~~~FGP   34 (48)
T d1imla2           1 KCEKCGKTLTSG-GHAEHEGKPYCNHPCYSAMFGP   34 (48)
T ss_dssp             BCTTTCCBCCTT-TEEEETTEEEETTTHHHHHSSC
T ss_pred             CchhcCcCcCCC-ChhhcCCcccccccchhhccCC
Confidence            589999999665 58899999999 7799988764

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.94  E-value=0.0064  Score=39.10  Aligned_cols=26  Identities=15%  Similarity=0.024  Sum_probs=21.4

Q ss_pred             cchhhhhhhhhhHHHHHh-hcccccccccccce
Q psy17256        531 LEFHSFLKRIALVLSEKW-KKMYGHVLSWLRVR  562 (768)
Q Consensus       531 ~~C~~c~k~Ia~~~~~~~-~~~~s~~~~wh~~~  562 (768)
                      ..|++|.++|.++++++. ++      .||..|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr------~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQ------YWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSS------EECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHH------HHhcCC
Confidence            459999999999987655 55      999875

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.58  E-value=0.0084  Score=39.75  Aligned_cols=29  Identities=10%  Similarity=0.013  Sum_probs=26.0

Q ss_pred             cccchhhhhhhhhhHHHHHhhcccccccccccceE
Q psy17256        529 LHLEFHSFLKRIALVLSEKWKKMYGHVLSWLRVRT  563 (768)
Q Consensus       529 ~g~~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~  563 (768)
                      .++.|..|.+.|....+.+.++      -||++||
T Consensus         7 fa~~C~~Ckk~It~GGvtY~dq------pWHkeCF   35 (35)
T d2cuqa2           7 FAPRCARCSKTLTQGGVTYRDQ------PWHRECL   35 (35)
T ss_dssp             SSCCCTTTCCCCCSCCEESSSS------EECTTTC
T ss_pred             HHHHHhhcCCccccCceeecCC------cchhhhC
Confidence            4677999999999999999999      6999997

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.39  E-value=0.0076  Score=40.15  Aligned_cols=26  Identities=8%  Similarity=-0.098  Sum_probs=24.5

Q ss_pred             chhhhhhhhhhHHHHHhhcccccccccccceE
Q psy17256        532 EFHSFLKRIALVLSEKWKKMYGHVLSWLRVRT  563 (768)
Q Consensus       532 ~C~~c~k~Ia~~~~~~~~~~~s~~~~wh~~~~  563 (768)
                      .|..|.++|.++++.+.|+      .||+.||
T Consensus        10 kC~~C~~~I~driLrA~Gk------~yHP~CF   35 (35)
T d2dloa1          10 KCATCSQPILDRILRAMGK------AYHPGCF   35 (35)
T ss_dssp             BCTTTCCBCCSCCEEETTE------EECTTTC
T ss_pred             HHHHhchHHHHHHHHHhCC------CCCCCCC
Confidence            4999999999999999999      8999987

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=90.18  E-value=0.06  Score=34.76  Aligned_cols=29  Identities=24%  Similarity=0.660  Sum_probs=23.5

Q ss_pred             ccccccCCCCCCCCcceeeecCceecccCc
Q psy17256        616 GAKCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       616 ~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      +.+|..|.+.+.-.|. +...|+.||..||
T Consensus         7 g~kcg~c~ktvy~aee-vqc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEE-VQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCC-EEETTEEECTTTC
T ss_pred             CceeccccceEeeeee-eeecCcccccccC
Confidence            5699999998875544 5578999999998

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.93  E-value=0.042  Score=35.89  Aligned_cols=21  Identities=14%  Similarity=0.048  Sum_probs=16.3

Q ss_pred             Ccceeecccccccccchhhhhhhcc
Q psy17256        592 GLMYIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       592 ~~~~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      +.+|+.++.+    ||+.+|+++.|
T Consensus        12 ~~Fy~~~g~P----yCe~HyH~~~G   32 (32)
T d1x3ha2          12 GSFFELDGRP----FCELHYHHRRG   32 (32)
T ss_dssp             SCCEESSSCE----ECHHHHHHHHS
T ss_pred             CCeEeECCcc----chHHhhhhhcC
Confidence            4579999999    45699998653

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.88  E-value=0.047  Score=34.63  Aligned_cols=28  Identities=21%  Similarity=0.581  Sum_probs=21.7

Q ss_pred             cccccccccCCCCceEeecCccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYL  674 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~  674 (768)
                      +|..|+.+|.... ++..++.+||+.|-.
T Consensus         1 vC~dCg~NLKqrG-~Ffv~~~lyCE~HAr   28 (31)
T d1x64a2           1 VCADCNLNLKQKG-YFFVEGELYCETHAR   28 (31)
T ss_dssp             CCSSSCCCTTTSC-CEEETTEEECHHHHH
T ss_pred             CccccccChhhcc-eEEeccEEeehhhhh
Confidence            5999999996544 445688999999854

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.67  E-value=0.083  Score=34.54  Aligned_cols=28  Identities=29%  Similarity=0.752  Sum_probs=25.8

Q ss_pred             cccccCCCCCCCCcceeeecCceecccC
Q psy17256        617 AKCSKCCRGIASSDWVRKARDHVYHLAC  644 (768)
Q Consensus       617 ~~C~~C~~~I~~~e~~~~a~~~~~H~~C  644 (768)
                      -.|..|+.+..+.|.++.-.|..||..|
T Consensus         8 ~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           8 ATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHccCCCchHHhhcCCCccccccC
Confidence            4789999999999999999999999987

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=89.32  E-value=0.12  Score=39.30  Aligned_cols=32  Identities=34%  Similarity=0.689  Sum_probs=27.0

Q ss_pred             cccccccccCCCCceEeecCccccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLELVD  678 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~~~  678 (768)
                      .|..|++.|.++ .+..+++++||+.||.....
T Consensus         1 ~C~~C~K~LdS~-~~~eh~~e~YCk~CY~k~fG   32 (65)
T d1b8ta2           1 LCMVCKKNLDST-TVAVHGDEIYCKSCYGKKYG   32 (65)
T ss_dssp             BCTTTCCBCCSS-SEEEETTEEEEHHHHHHHHS
T ss_pred             CchhcCCccCCC-ccccCCCcccchhhhccccC
Confidence            489999999554 58889999999999987664

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.92  E-value=0.054  Score=33.96  Aligned_cols=30  Identities=23%  Similarity=0.520  Sum_probs=24.6

Q ss_pred             cccccccccCCCCceEeecCccccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLEL  676 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e~  676 (768)
                      +|+.|++.+..| .|+.+....||..|++..
T Consensus         1 tcs~ckq~igsg-sffpkg~d~ycvtche~k   30 (32)
T d1x63a2           1 TCSNCKQVIGTG-SFFPKGEDFYCVTCHETK   30 (32)
T ss_dssp             CCSSSCCCCTTS-CEEEETTEEEEHHHHHHH
T ss_pred             Ccchhhhhcccc-cccCCCCcEEEEEeeccc
Confidence            588999999665 488888999999998754

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=88.67  E-value=0.11  Score=31.73  Aligned_cols=27  Identities=26%  Similarity=0.683  Sum_probs=22.1

Q ss_pred             ccccCCCCCCCCcceeeecCceecccCc
Q psy17256        618 KCSKCCRGIASSDWVRKARDHVYHLACF  645 (768)
Q Consensus       618 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF  645 (768)
                      +|..|.+.+.-.|. +...|+.||..||
T Consensus         2 kcg~c~ktvy~aee-vqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEE-VQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTE-EEETTEEEESSSE
T ss_pred             ccccccceEeeeee-eeecCceeccccC
Confidence            79999999875443 5678999999998

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.22  E-value=0.079  Score=34.18  Aligned_cols=21  Identities=5%  Similarity=-0.135  Sum_probs=15.5

Q ss_pred             Ccceeecccccccccchhhhhhhcc
Q psy17256        592 GLMYIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       592 ~~~~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      ..+..+++..    ||+.||.++|+
T Consensus        12 ksfipk~~~~----yCvpCyE~kfA   32 (32)
T d1x4ka1          12 KSFIPKDNQN----FCVPCYEKQHA   32 (32)
T ss_dssp             SSEEEETTEE----EEHHHHHHHTS
T ss_pred             cccccCCCCc----eEeecchhhcC
Confidence            3445577777    67899999986

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.22  E-value=0.076  Score=34.19  Aligned_cols=21  Identities=10%  Similarity=-0.113  Sum_probs=15.5

Q ss_pred             Ccceeecccccccccchhhhhhhcc
Q psy17256        592 GLMYIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       592 ~~~~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      ..+..+++.+    ||+.||.++|+
T Consensus        12 kSFip~~~~~----yCvpCYE~kfA   32 (32)
T d1wyha1          12 RSFVPDKGAH----YCVPCYENKFA   32 (32)
T ss_dssp             SCEEEETTEE----EEHHHHHHHTS
T ss_pred             cccccCCCcE----EEEeccccccC
Confidence            3445566677    67899999986

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.70  E-value=0.16  Score=33.94  Aligned_cols=30  Identities=20%  Similarity=0.705  Sum_probs=24.9

Q ss_pred             ccccccccccCCCCceEeecCccccccccc
Q psy17256        645 FACEACKRQLSTGEEFALHEDRVLCKSHYL  674 (768)
Q Consensus       645 F~C~~C~~~L~~G~~f~~~~g~~~C~~~y~  674 (768)
                      |+|..|.++|..|+.....+-+-.|..|-.
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs~   30 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCSL   30 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHHS
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcCC
Confidence            789999999988998887777778887754

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.79  E-value=0.2  Score=33.91  Aligned_cols=21  Identities=29%  Similarity=0.629  Sum_probs=12.9

Q ss_pred             cccccccccCCCCceEeecCc
Q psy17256        646 ACEACKRQLSTGEEFALHEDR  666 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~  666 (768)
                      .|+.|++.|..|++.++.++.
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~   21 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSS   21 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTE
T ss_pred             CcchhhccccccceeeecCCc
Confidence            056666666666666666653

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.80  E-value=0.19  Score=32.33  Aligned_cols=18  Identities=17%  Similarity=0.025  Sum_probs=10.8

Q ss_pred             eeecccccccccchhhhhhhcc
Q psy17256        595 YIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       595 ~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      .++.+.+|    |+.||.+.|+
T Consensus        15 VEE~g~lY----Ce~Cye~ffA   32 (32)
T d2dara1          15 VEEKGALY----CELCYEKFFA   32 (32)
T ss_dssp             EESSSCEE----CHHHHHHHTS
T ss_pred             eeecCcEe----HHHHHHHhcC
Confidence            44456774    5567777664

>d1x62a1 g.39.1.3 (A:43-73) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.90  E-value=0.06  Score=34.23  Aligned_cols=29  Identities=28%  Similarity=0.607  Sum_probs=21.7

Q ss_pred             cccccccccCCCCceEeecCcccccccccc
Q psy17256        646 ACEACKRQLSTGEEFALHEDRVLCKSHYLE  675 (768)
Q Consensus       646 ~C~~C~~~L~~G~~f~~~~g~~~C~~~y~e  675 (768)
                      .|..|+.+|.... ++..++.+||+.|-.+
T Consensus         1 vC~dCg~NLKqrG-~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKG-HFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHC-CEESSSCEECHHHHHH
T ss_pred             CccccccChhhcc-eEEeccEEehhhhhhh
Confidence            5899999996433 4456889999998643

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.50  E-value=0.22  Score=31.13  Aligned_cols=23  Identities=17%  Similarity=0.250  Sum_probs=17.6

Q ss_pred             CCCcceeecccccccccchhhhhhhcc
Q psy17256        590 GAGLMYIRVRILLKGRLSVLICFRSFG  616 (768)
Q Consensus       590 g~~~~~~~~~~~~c~~yC~~~y~~~f~  616 (768)
                      |.+.+|.++..+    ||+.|...+|+
T Consensus        10 gsgsffpkg~d~----ycvtche~kfa   32 (32)
T d1x63a2          10 GTGSFFPKGEDF----YCVTCHETKFA   32 (32)
T ss_dssp             TTSCEEEETTEE----EEHHHHHHHTS
T ss_pred             ccccccCCCCcE----EEEEeeccccC
Confidence            347788888888    67788888775

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.99  E-value=0.048  Score=37.01  Aligned_cols=29  Identities=14%  Similarity=-0.032  Sum_probs=24.7

Q ss_pred             cccchhhhhhhhh--hHHHHHhhcccccccccccceE
Q psy17256        529 LHLEFHSFLKRIA--LVLSEKWKKMYGHVLSWLRVRT  563 (768)
Q Consensus       529 ~g~~C~~c~k~Ia--~~~~~~~~~~~s~~~~wh~~~~  563 (768)
                      .++.|..|.++|.  ++-+.+.|+      +||..||
T Consensus         7 ~a~~C~~C~k~I~~G~k~veykg~------~WHe~CF   37 (37)
T d1x63a1           7 DSPKCKGCFKAIVAGDQNVEYKGT------VWHKDCF   37 (37)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSC------EEETTTC
T ss_pred             cCcccccCCCccCCCCeEeEeCCc------cchhccC
Confidence            5667999999995  577889998      9999997