Citrus Sinensis ID: 044351

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110------1120------1130------1140------1150------1160------1170--

MAPTRKSRSVNKRYANEVSPAKDVISPSKSKQKKKLSDKLGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDSERESNDASEMPRKSQKRKRAKVQLSASKEDISQSWSMAATGGCLSLLKRSRIDGNQPRAVKKRTPRFPVSYSQKKDDRDDYIPLNKKDRRSAVDANDDEVAHVAALALTEASQRGGSPQVSQSPHKKTEHGKSSPVQIWDKMFPPAETAHPDAREALNEEGCPEARILNRRPENGAYTRARKSLMDMEGVGTVEVHRKGKKFYRKKMKVEEVRNSLSDDEGEACSGTEEGLSSRKGKVGSEISNAKNDHLPLQMQRKRSKKLFFGDESTALNALQTLADLSLMLPDSTMESESSVQLKEERTAFDIDDKSSAPEETSTSHPKEKIKHLGPKEKALNTITEAEDIIPRKSKLGRYSGNDVETVAEVKEQPEPPNSMSKRKRKSVLSKKISNSEAVTDTHMTRTLESEAVAEEHNKFASKGKRTSQNSAQSKQWKPGRVLEGSSVNDQNRASIDLVAPTGQAPVASPASSPTKHQSRRKMDLKRKLSSKEMKFSENSLKTQPNKNSLSQEDRLLSMKEKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLKQYRESRVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLFASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAAYGQLCTVPQIQAREATVRALSEEALLMELKNTNNDILESQNGGESSLKDSEPLKKHIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQCNTHPESSRPSWPMHPANVKMLDNSHVSQESGSAVAEIVNGSRLKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDHIDKRQLTSDPRVSVIRSPEQVNGSLGHHNHFVSGTCDPQPTNNASGTKLQDVSDKNEAQIPSELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPTSI

ccccccccccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHccccccccccccHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccHHccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccEEEEcccccccHHHccccHHHHHHHHccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccEEEEEcccccccccccEEEEEcccEEEEEcccccccEEEccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHcccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccc

cccccccccEccccccccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHHHHHHccccccccHHHHHHHHHcccHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccEEEEccccccccccccccHHcccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHccccccccEEccccccccccccccccccccccccHcccccccccEEEcccccEEcccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccHHEHHHHHHHHcccHHHccccHHHHHHccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHcEEEEcHcHccccccEEEEEccccEEEEEcccccccEEcccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHEHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHccccc

maptrksrsvnkryanevspakdvispskskqkkklsdklgpqwskgELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAylslpegtASVVGLIAMMTDHynvmegsdseresndasemprksqKRKRAKVQLSASkedisqswsmaatGGCLSLLKrsridgnqpravkkrtprfpvsysqkkddrddyiplnkkdrrsavdandDEVAHVAALALTeasqrggspqvsqsphkktehgksspvqiwdkmfppaetahpdarealneegcpearilnrrpengayTRARKSLMDMEGVGTVEVHRKGKKFYRKKMKVEEVRNslsddegeacsgteeglssrkgkvgseisnakndhlplqmqrkrskklffgdeSTALNALQTLADLslmlpdstmesessvqlkeertafdiddkssapeetstshpkekikhlgpkekalNTITeaediiprksklgrysgndvetvaevkeqpeppnsmskrkRKSVLSKkisnseavtdtHMTRTLESEAVAEEHNKFaskgkrtsqnsaqskqwkpgrvlegssvndqnrasidlvaptgqapvaspassptkhqsrrkMDLKRKLSSKemkfsenslktqpnknslsQEDRLLSMKEKLsgclssnmvrrwcTFEWFYsaidypwfsnREFVEYLNHVglghiprltrVEWGVirsslgkprrlsKRFLHDEREKLKQYRESRviaihpktrelhdgsvltidhdkcrvqfdrpelgvefvmdidsmpsnpldnmpeALRRQISADKFSAISKELqvnghpnfgspmlfasdghlekapilpntlqkqakgdmnhalpqaKSLATDIVSAQQAAYgqlctvpqIQAREATVRALSEEALLMELKNtnndilesqnggesslkdsepLKKHIATVLVQLKEandqacgfrelCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQcnthpessrpswpmhpanvkmldnshvsqesgSAVAEIVNGSRLKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDhidkrqltsdprvsvirspeqvngslghhnhfvsgtcdpqptnnasgtklqdvsdkneaqipsELITSCVATLLMIQTcterhtpadVAQIIDSAvsslhpccpqnlpiYREIEMCMGRIKTQILALIPTSI

maptrksrsvnkryanevspakdvispskskqkkklsdklgpqwskgeLQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMegsdseresndasemprksqkrkrakvqlsaskedisqswsmaATGGCLSLLkrsridgnqpravkkrtprfpvsysqkkddrddyiplnkkdrrsavdanDDEVAHVAALALteasqrggspqvsqsphkktehgksspvqiWDKMFPPAETAHPDAREALneegcpearilnrrpengaYTRARkslmdmegvgtvevhrkgkkfyrkkmkveevrnslsddegeacsgteeglssrkgkvgseisnakndhlplqmqRKRSKKLFFGDESTALNALQTLADLSLMLPDSTMESESSVQLKEertafdiddkssapeetstshpkekikhlgpkekalntiteaediiprksklgrysgNDVETvaevkeqpeppnsmskrkrksvlskkisnseavtdthmtrtLESEAVAEEHNKfaskgkrtsqnsaqskqwkpgrvlegssvnDQNRASIDLVaptgqapvaspassptkhqsrrkmdlkrklsskemkfsenslktqpnknslsqEDRLLSMKEKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGvirsslgkprrlskrflhdereklkqyresrviaihpktrelhdgsvltidhdkcrvQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLFASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAAYGQLCTVPQIQAREATVRALSEEALLMELKNTNNDILESQNGGESSLKDSEPLKKHIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQCNTHPEssrpswpmHPANVKMLDNSHVSQESGSAVAEIVNGSRLKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDHIDKRQLTSDPRVSVIRSPEQVNGSLGHHNHFVSGTCDPQPTNNASGTKLQDVSDKNEAQIPSELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPTSI

MAPTRKSRSVNKRYANEVSPAKDVIspskskqkkklsdkLGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDSERESNDASEMPRKSQKRKRAKVQLSASKEDISQSWSMAATGGCLSLLKRSRIDGNQPRAVKKRTPRFPVSYSQKKDDRDDYIPLNKKDRRSAVDANDDEVAHVAALALTEASQRGGSPQVSQSPHKKTEHGKSSPVQIWDKMFPPAETAHPDAREALNEEGCPEARILNRRPENGAYTRARKSLMDMEGVGTVEVHRkgkkfyrkkmkVEEVRNSLSDDEGEACSGTEEGLSSRKGKVGSEISNAKNDHLPLQMQRKRSKKLFFGDESTALNALQTLADLSLMLPDSTMESESSVQLKEERTAFDIDDKSSAPEETSTSHPKEKIKHLGPKEKALNTITEAEDIIPRKSKLGRYSGNDVETVAEVKEQPEPPNsmskrkrksvlskkisNSEAVTDTHMTRTLESEAVAEEHNKFASKGKRTSQNSAQSKQWKPGRVLEGSSVNDQNRASIDLVAPTGQAPVASPASSPTKHQSRRKMDLKRKLSSKEMKFSENSLKTQPNKNSLSQEDRLLSMKEKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLKQYRESRVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLFASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAAYGQLCTVPQIQAREATVRALSEEALLMELKNTNNDILESQNGGESSLKDSEPLKKHIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQCNTHPESSRPSWPMHPANVKMLDNSHVSQESGSAVAEIVNGSRLKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDHIDKRQLTSDPRVSVIRSPEQVNGSLGHHNHFVSGTCDPQPTNNASGTKLQDVSDKNEAQIPSELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPTSI

**********************************************GELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNV***********************************************GCLSL********************************************************************************************************************************************************************************************************************************LNALQTL**************************************************************************************************************************************************************************************************************************************************GCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLG*******************YRESRVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDI*******************************************************************************ATDIVSAQQAAYGQLCTVPQIQAREATVR*************************************HIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVR*******************************************************************************************************************************************ELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALI****

***********************************************ELQRFYEAYRNYGKD******************LYNMNRAYLSLPEGTASVVGLIAM**************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************LSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLKQYRESRVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQIS***************************************************************************TVPQIQAREATVRALSEEALLMELK*********************PLKKHIATVLVQLKEANDQACGFRELCFGISCYL*****************************************************************************TMVDAAVKAM***********KIGEALD***********************************************************QIPSELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPTS*

************RYANE************************PQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVME************************************QSWSMAATGGCLSLLKRSRIDGNQPRAVKKRTPRFPVSYSQKKDDRDDYIPLNKKDRRSAVDANDDEVAHVAALALTE************************PVQIWDKMFPPAETAHPDAREALNEEGCPEARILNRRPENGAYTRARKSLMDMEGVGTVEVHRKGKKFYRKKMKVE****************************GSEISNAKNDHLPLQMQRKRSKKLFFGDESTALNALQTLADLSLMLPD***********KEERTAFDID******************KHLGPKEKALNTITEAEDIIPRKSKLGRYSGNDVETVAE******************************TDTHMTRTLESEA***************************GRVLEGSSVNDQNRASIDLVAPT***************************SSKEMKFSENSLKTQPNKNSLSQEDRLLSMKEKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLKQYRESRVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLFASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAAYGQLCTVPQIQAREATVRALSEEALLMELKNTNNDILES**********SEPLKKHIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVR************WPMHPANVKMLDNS*********VAEIVNGSRLKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDHIDKRQLTSDPRVSVIRSPEQVNGSLGHHNHFVSGTCDPQPTNNASGTKLQDVSDKNEAQIPSELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPTSI

*********************************KKLSDKLGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVM*****************************************************************KKRTPRFPVSYSQKK**********************DEVAHVAALALTEAS*******************************************************************************TVEVHRKGKKFYRKKMKVEEV*******************************************************STALNALQTLADLSLM*********************************************************************************************************************************************************************************************************************************DRLLSMKEKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLKQYRESRVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLFASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAAYGQLCTVPQIQAREATVRALSEEALLMELKNTNNDILESQNGGESSLKDSEPLKKHIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQCNTHPESSR***********************SAVAEIVNGSRLKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDHIDKRQLTSDPRVSVIRSPEQ************************************EAQIPSELITSCVATLLMIQTCTERHTPADVAQIIDSAVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPTSI

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		1172	2.2.26 [Sep-21-2011]
Q6A332		1132	Protein ALWAYS EARLY 3 OS	yes	no	0.883	0.915	0.397	0.0
Q6A333		1051	Protein ALWAYS EARLY 2 OS	no	no	0.723	0.806	0.477	0.0
Q6A331		971	Protein ALWAYS EARLY 1 OS	no	no	0.596	0.719	0.437	1e-159
Q5RHQ8		543	Protein lin-9 homolog OS=	yes	no	0.159	0.344	0.305	5e-14
Q5TKA1		542	Protein lin-9 homolog OS=	yes	no	0.120	0.260	0.323	2e-13
Q4R8N2		542	Protein lin-9 homolog OS=	N/A	no	0.120	0.260	0.323	2e-13
Q8C735		542	Protein lin-9 homolog OS=	yes	no	0.118	0.256	0.321	2e-13
P30630		644	Protein lin-9 OS=Caenorha	yes	no	0.107	0.195	0.333	2e-08

>sp\|Q6A332\|ALY3_ARATH Protein ALWAYS EARLY 3 OS=Arabidopsis thaliana GN=ALY3 PE=1 SV=1	Back alignment and function desciption

 Score =  731 bits (1886), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 491/1236 (39%), Positives = 679/1236 (54%), Gaps = 200/1236 (16%)

Query: 15   ANEVSPAKDVISPSKSKQKK-KLSDKLGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNR 73
            A  VSP KD  S SK+KQ+K KLSD LGPQWSK EL+RFYE YR +GK+WKKVA  V +R
Sbjct: 17   AKAVSPHKDEESMSKTKQRKRKLSDMLGPQWSKEELERFYEGYRKFGKEWKKVAGFVHSR 76

Query: 74   SAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEG-SDSERESNDASEMPRKSQ 132
            SAEMVEALY MN+AYLSLPEGTASVVGL AMMTDHY+V+ G SDSE+E+N+  E PR + 
Sbjct: 77   SAEMVEALYTMNKAYLSLPEGTASVVGLTAMMTDHYSVLHGGSDSEQENNEGIETPRSAP 136

Query: 133  KRKRAKV--QLSASKEDISQSWSMAATGGCLSLLKRSRIDGNQPRAVKKRTPRFPVSYSQ 190
            KR R K     S   E +S      ++ G +  LK+ R +   PRAV KRTPR P+SY+ 
Sbjct: 137  KRSRVKSSDHPSIGLEGLSDRLQFRSSSGFMPSLKKRRTE-TMPRAVGKRTPRIPISYTL 195

Query: 191  KKDDRDDYIPLNKKDRRSAVDANDDEVAHVAALALTEASQRGGSPQVSQSPHKKTEHGKS 250
            +KD R+ Y+   K+      D  DD++ H  ALAL EASQRGGS + S +P++K      
Sbjct: 196  EKDTRERYLSPVKRGLNQKGDDTDDDMEHEIALALAEASQRGGSTKNSHTPNRKA----- 250

Query: 251  SPVQIWDKMFPP---AETAHPDAREALN-------EEGCPEARILNRRPENGAYTRARKS 300
                   KM+PP    E    D   A+        E+   E  + +   +N  Y+  R  
Sbjct: 251  -------KMYPPDKKGERMRADIDLAIAKLHATDMEDVRCEPSLGSTEADNADYSGGRND 303

Query: 301  LMDMEGVGTVEVHRKGKKFYRKKMKVEEVRNSLSDDEGEACSGTEEG--LSSRKGKVGSE 358
            L   EG   VE  +KG+ +YR+++ ++E      +D  EACSGT+E   L +   K   E
Sbjct: 304  LTHGEGSSAVEKQQKGRTYYRRRVGIKE------EDAKEACSGTDEAPSLGAPDEKFEQE 357

Query: 359  ISNAKNDHLPLQMQRKRSKK-LFFGDESTALNALQTLADLSLMLPDSTMESESSVQLKEE 417
                K      ++ R++SKK LF  DE TA +AL TLADLSLM+P++  ++ESSVQ +E+
Sbjct: 358  -REGKALKFTYKVSRRKSKKSLFTADEDTACDALHTLADLSLMMPETATDTESSVQAEEK 416

Query: 418  RT--AFDIDDKSSAPEETSTSHPKEKIKHLGPKEKALNTITEAEDIIPRKSKLGRYSGND 475
            +   A+  D K + P   S             K  +L           R SK  RY  ND
Sbjct: 417  KAGEAYVSDFKGTDPASMS-------------KSSSL-----------RNSKQRRYGSND 452

Query: 476  VETVAEVKEQPEPPNSMSKRKRKSVLSKKISNS----EAVTDTHMTRTLESEAVAEEHNK 531
            +       E+  P +S+ +++R+  L  K+  +    E    + +     S+ + EE+ K
Sbjct: 453  L--CNPELERKSPSSSLIQKRRQKALPAKVRENVLKDELAASSQVIEPCNSKGIGEEY-K 509

Query: 532  FASKGKRTS--QNSAQSKQWKPGRVLEGSSVNDQNRASIDLVAPTGQAP----VASPASS 585
               +GKR++  +NS + K  K          +D   +S ++V     AP    +    + 
Sbjct: 510  PVGRGKRSASIRNSHEKKSAKS---------HDHTSSSNNIVEEDESAPSNAVIKKQVNL 560

Query: 586  PTKHQSRRKMDLKRKLSSKEMKFSENSLKTQPNKNSLSQEDRLLSMKEKLSGCLSSNMVR 645
            PTK +SRRK+  ++ L+  + K SE                      EK S C+SS   R
Sbjct: 561  PTKVRSRRKIVTEKPLTIDDGKISETI--------------------EKFSHCISSFRAR 600

Query: 646  RWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFL 705
            RWC FEWFYSAIDYPWF+ +EFVEYL+HVGLGH+PRLTRVEWGVIRSSLGKPRR S++FL
Sbjct: 601  RWCIFEWFYSAIDYPWFARQEFVEYLDHVGLGHVPRLTRVEWGVIRSSLGKPRRFSEQFL 660

Query: 706  HDEREKLKQYRES----------------------------RVIAIHPKTRELHDGSVLT 737
             +E+EKL  YR+S                            RVI +HPK+RE+HDG+VLT
Sbjct: 661  KEEKEKLYLYRDSVRKHYDELNTGMREGLPMDLARPLNVSQRVICLHPKSREIHDGNVLT 720

Query: 738  IDHDKCRVQFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKF---SAISKELQVN 794
            +DH + R+QFD PELGVEFV D + MP NPL+NMP +L R  +   +   + I +++   
Sbjct: 721  VDHCRYRIQFDNPELGVEFVKDTECMPLNPLENMPASLARHYAFSNYHIQNPIEEKMHER 780

Query: 795  GHPNF--GSPMLFASDGHLEKAPI--LPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAA 850
               +   G P L    GHL  +P   + N+L KQ K D++ + PQA+    D   A Q  
Sbjct: 781  AKESMLEGYPKLSCETGHLLSSPNYNISNSL-KQEKVDISSSNPQAQD-GVDEALALQLF 838

Query: 851  YGQLCTVPQIQAREATVRALSE--------EALLMELKNTNNDILESQ-NGGESSLKDSE 901
              Q  ++ QIQAREA V+ALSE        E +L ELK  N++++ESQ +G  ++LKDSE
Sbjct: 839  NSQPSSIGQIQAREADVQALSELTRALDKKELVLRELKCMNDEVVESQKDGHNNALKDSE 898

Query: 902  PLKKHIATVLVQLKEANDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALL 961
              KK  A VL QL E N+Q                                    S ALL
Sbjct: 899  SFKKQYAAVLFQLSEINEQV-----------------------------------SLALL 923

Query: 962  QVRQCNTHPES------SRPSWPMHPANVKMLDNSHVSQESGSAVAEIVNGSRLKAHTMV 1015
             +RQ NT+ E+       R S    P      ++++ S  +G  V+EIV  SR+KA  MV
Sbjct: 924  GLRQRNTYQENVPYSSIRRMSKSGEPDGQLTYEDNNASDTNGFHVSEIVESSRIKARKMV 983

Query: 1016 DAAVKAMSSVKEGEDAYTKIGEALDHIDKRQLTSDPRVSVIRSPEQVNGSLGHHNHFVSG 1075
              AV+A+  +++ E+    + EA+D ++  QL+ D           V  + G  +  +  
Sbjct: 984  YRAVQALELLRKDENNNVNMEEAIDFVNN-QLSIDQTEG-----SSVQQTQGGQDQRLPS 1037

Query: 1076 TCDPQPTNNASGTKLQDVSDKNEAQIPSELITSCVATLLMIQTCTERHTP-ADVAQIIDS 1134
            T +P  +  A+ + L +  D+N+ Q+PS+L++ C+ATLLMIQ CTER  P ++VAQ++DS
Sbjct: 1038 TPNPPSSTPANDSHL-NQPDQNDLQVPSDLVSRCIATLLMIQKCTERQFPPSEVAQVLDS 1096

Query: 1135 AVSSLHPCCPQNLPIYREIEMCMGRIKTQILALIPT 1170
            AV+SL PCC QNLPIY EI+ CMG I+ QILAL+P+
Sbjct: 1097 AVASLQPCCSQNLPIYTEIQKCMGIIRNQILALVPS 1132

Arabidopsis thaliana (taxid: 3702)

>sp\|Q6A333\|ALY2_ARATH Protein ALWAYS EARLY 2 OS=Arabidopsis thaliana GN=ALY2 PE=1 SV=1	Back alignment and function description

>sp\|Q6A331\|ALY1_ARATH Protein ALWAYS EARLY 1 OS=Arabidopsis thaliana GN=ALY1 PE=2 SV=2	Back alignment and function description

>sp\|Q5RHQ8\|LIN9_DANRE Protein lin-9 homolog OS=Danio rerio GN=lin9 PE=2 SV=1	Back alignment and function description

>sp\|Q5TKA1\|LIN9_HUMAN Protein lin-9 homolog OS=Homo sapiens GN=LIN9 PE=1 SV=1	Back alignment and function description

>sp\|Q4R8N2\|LIN9_MACFA Protein lin-9 homolog OS=Macaca fascicularis GN=LIN9 PE=2 SV=1	Back alignment and function description

>sp\|Q8C735\|LIN9_MOUSE Protein lin-9 homolog OS=Mus musculus GN=Lin9 PE=2 SV=2	Back alignment and function description

>sp\|P30630\|LIN9_CAEEL Protein lin-9 OS=Caenorhabditis elegans GN=lin-9 PE=1 SV=3	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1172
356533577		1126	PREDICTED: protein ALWAYS EARLY 2-like [	0.915	0.952	0.533	0.0
356574947		1120	PREDICTED: protein ALWAYS EARLY 2-like [	0.911	0.953	0.529	0.0
357441687		1139	Lin-9-like protein [Medicago truncatula]	0.918	0.944	0.535	0.0
296088361		1151	unnamed protein product [Vitis vinifera]	0.918	0.934	0.520	0.0
224125234		1007	predicted protein [Populus trichocarpa]	0.818	0.952	0.523	0.0
449432828		1161	PREDICTED: LOW QUALITY PROTEIN: protein	0.934	0.943	0.461	0.0
449495452		1161	PREDICTED: protein ALWAYS EARLY 3-like [	0.934	0.943	0.461	0.0
50540713		1251	expressed protein [Oryza sativa Japonica	0.923	0.864	0.434	0.0
108710016		1255	DIRP family protein, expressed [Oryza sa	0.923	0.862	0.433	0.0
108710017		1246	DIRP family protein, expressed [Oryza sa	0.916	0.861	0.428	0.0

>gi\|356533577\|ref\|XP_003535339.1\| PREDICTED: protein ALWAYS EARLY 2-like [Glycine max]	Back alignment and taxonomy information

 Score = 1118 bits (2891), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 652/1223 (53%), Positives = 805/1223 (65%), Gaps = 150/1223 (12%)

Query: 1    MAPTRKSRSVNKRYA--NEVSPAKDVISPSKSKQKK-KLSDKLGPQWSKGELQRFYEAYR 57
            MAPTRKSRSVNKR +  N+ SP KD ++ +KSKQ+K KL+DKLG QWSK EL+RFYEAYR
Sbjct: 1    MAPTRKSRSVNKRMSSSNDNSPEKDGVNSNKSKQRKRKLTDKLGSQWSKEELERFYEAYR 60

Query: 58   NYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDS 117
             YGKDWKKVAA VRNRS EMVEALY+MNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDS
Sbjct: 61   KYGKDWKKVAAVVRNRSTEMVEALYSMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDS 120

Query: 118  ERESNDASEMPRKSQKRKRAKVQLSASKEDISQSWSMAATGGCLSLLKRSRIDGNQ--PR 175
            ERESNDA    RK  KRKR KVQLS SK+   QS S+A++  CLS+LK+ R DG Q  P 
Sbjct: 121  ERESNDAPG-SRKPVKRKREKVQLSISKD---QSHSIASSDDCLSILKKRRFDGIQLKPH 176

Query: 176  AVKKRTPRFPVSYSQKKDDRDDYIPLNKKDRRSAVDANDDEVAHVAALALTEASQRGGSP 235
            AV KRTPR PV    KKDD ++Y+   ++  +S +DANDDEVAHV ALALTEA+QRGGSP
Sbjct: 177  AVGKRTPRVPV---YKKDDTENYVSPYRRSLKSTIDANDDEVAHVVALALTEAAQRGGSP 233

Query: 236  QVSQSPHKKTEHGKSSPVQIWDKMFPPAETAHPDAREALNEEGCPEARILNRRPENGAYT 295
            QVSQ+P ++ E  KSSP+Q W++    ++TA     +   ++   E  I +R  EN  Y 
Sbjct: 234  QVSQTPSRRVEQ-KSSPIQSWERKHQMSKTARAKFPDVSVDKEVLEGSIESRGAENEEYA 292

Query: 296  RARKSLMDMEGVGTVEVHRKGKKFYRKKMKVEEVRNSLSDDEGEACSGTEEGLS--SRKG 353
            +   SLMD EG+ T EV +K  +FYRK+ +V+ V N   DD GEACSGTEEGLS  S K 
Sbjct: 293  KDNSSLMDTEGIDTAEVFQKEGQFYRKRERVKNVGNHQLDDGGEACSGTEEGLSFNSLKE 352

Query: 354  KVGSEISNAKNDHLPLQMQRKRSKKLFFGDESTALNALQTLADLSLMLPDSTMESESSVQ 413
            KV  E++N K +    +  RKR+KKLFFGDE+ ALNALQTLADLSLM+P STMESESS+Q
Sbjct: 353  KVDIEVTNEKLEKFSPKSHRKRNKKLFFGDETPALNALQTLADLSLMMPISTMESESSIQ 412

Query: 414  LKEERTAFDIDDKSSAPEETSTSHPKEKIKHLGPKEKALNTITEAEDIIPRKSKLGRYSG 473
            LK ER   D +++S+ PE TSTSH + K+K+        + + + E +  ++SK G+   
Sbjct: 413  LKGERMVADKNNRSALPEATSTSHKRHKLKY--------SVVPKIEVLTSKESKTGKEPT 464

Query: 474  NDVETVAEVKEQPEPPNSMSKRKRKSVLSKKISNSEAVTDTHMTRTLESEAVAEEHNKFA 533
             D   ++E KE+    ++  KRKRKS+ SK  S   A  D++ +  L+ EA+ ++ NK  
Sbjct: 465  KDTNALSESKEKLPFADTAWKRKRKSMGSKVAS---AKLDSYPSGPLKDEAL-DDGNKPV 520

Query: 534  SKGKRTSQNSAQSKQWKPGRVLEGSSVNDQNRASIDLVAPTGQAPVASPASSPTKHQSRR 593
             KGK T Q     KQ K  +  E S  +DQ     DL   T + P+ +  S PTK Q +R
Sbjct: 521  VKGKHTDQAFTLPKQLKTVKSSESSLCSDQK----DLTVSTAEIPLLNEVSLPTK-QRKR 575

Query: 594  KMDLKRKLSSKEMKFSENSLKTQPNKNSLSQEDRLLSMKEKLSGCLSSNMVRRWCTFEWF 653
            KM L+R    KE K S+  LK+Q NK S        ++KEKLS CLSSNMVRRW  FEWF
Sbjct: 576  KMILQRTSLPKE-KSSDYILKSQSNKYS--------TLKEKLSSCLSSNMVRRWFVFEWF 626

Query: 654  YSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLK 713
            YSAIDYPWF+ REF+EYLNHVGLG+IPRLTRVEW VI+SSLGKPRR S+ FL +ER+KL+
Sbjct: 627  YSAIDYPWFAKREFMEYLNHVGLGNIPRLTRVEWSVIKSSLGKPRRFSEHFLCEERQKLE 686

Query: 714  QYRES----------------------------RVIAIHPKTRELHDGSVLTIDHDKCRV 745
            QYRES                             VIA+HPKTRE+HDGSVLT+D+DKCR+
Sbjct: 687  QYRESVRKHYTELRTGIRDGLPTDLAKPLYVGQHVIALHPKTREIHDGSVLTVDYDKCRI 746

Query: 746  QFDRPELGVEFVMDIDSMPSNPLDNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLF 805
            QFDRPELGVEFVMDID MP N  DNMPEALRR I +   S ++KE Q++G+ NFG     
Sbjct: 747  QFDRPELGVEFVMDIDCMPLNSSDNMPEALRRHIGSPISSFMNKEPQISGNSNFGG---- 802

Query: 806  ASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQAAYGQLCTVPQIQAREA 865
                                  +MNH+ P    +AT      QA   Q C V   QA+EA
Sbjct: 803  ---------------------CEMNHSSPVKAKVATVDNLCAQAGCAQPCKVTHHQAKEA 841

Query: 866  TVRALSE--------EALLMELKNTNNDILESQNGGESSLKDSEPLKKHIATVLVQLKEA 917
             ++A+SE        E LLMEL++ N+DILE++NG +  LKDSE  KKH ATVL+QLKEA
Sbjct: 842  DIQAVSELKHALDKKETLLMELRSANSDILENKNGID-CLKDSEVFKKHYATVLLQLKEA 900

Query: 918  NDQACGFRELCFGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQCNTHPESSRPSW 977
            +                                    Q S A+LQ+RQ NT+  +S PSW
Sbjct: 901  SG-----------------------------------QVSDAMLQLRQRNTYRGNSLPSW 925

Query: 978  --PMHPANV-----KMLDNSHVSQESGSAVAEIVNGSRLKAHTMVDAAVKAMSSVKEGED 1030
              P    NV      MLD+S ++QE GS V +++ GSRL+AH MVDAA +A+S  KEGED
Sbjct: 926  MKPQASFNVHDDLPSMLDSS-LTQELGSTVVQVIKGSRLRAHAMVDAAFQALSLAKEGED 984

Query: 1031 AYTKIGEALDHIDKRQLTSDPRVSVIRSPEQV--NGSLGHHNHFVSGTCDPQPTNNASGT 1088
            A+ KIG+ALD I+ +QL S  R+ VIRS EQV  NGS  H NH  SG  +P   N+ S  
Sbjct: 985  AFIKIGQALDSINHQQLASQSRLPVIRSQEQVNANGSFYHLNHSTSGVSEP-ILNDPSLP 1043

Query: 1089 KLQDVSDKNEAQIPSELITSCVATLLMIQTCTER-HTPADVAQIIDSAVSSLHPCCPQNL 1147
            K  + SDK + ++PS+LITSCVATL+MIQTCTER + PADVAQI+DSAV+SLHPCC QNL
Sbjct: 1044 KPHNCSDKFDTELPSDLITSCVATLIMIQTCTERQYPPADVAQILDSAVTSLHPCCSQNL 1103

Query: 1148 PIYREIEMCMGRIKTQILALIPT 1170
            PIYREI+MCMGRIKTQ+LALIPT
Sbjct: 1104 PIYREIQMCMGRIKTQMLALIPT 1126

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356574947\|ref\|XP_003555604.1\| PREDICTED: protein ALWAYS EARLY 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|357441687\|ref\|XP_003591121.1\| Lin-9-like protein [Medicago truncatula] gi\|355480169\|gb\|AES61372.1\| Lin-9-like protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|296088361\|emb\|CBI36806.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224125234\|ref\|XP_002319534.1\| predicted protein [Populus trichocarpa] gi\|222857910\|gb\|EEE95457.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449432828\|ref\|XP_004134200.1\| PREDICTED: LOW QUALITY PROTEIN: protein ALWAYS EARLY 3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449495452\|ref\|XP_004159845.1\| PREDICTED: protein ALWAYS EARLY 3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|50540713\|gb\|AAT77870.1\| expressed protein [Oryza sativa Japonica Group]	Back alignment and taxonomy information

>gi\|108710016\|gb\|ABF97811.1\| DIRP family protein, expressed [Oryza sativa Japonica Group]	Back alignment and taxonomy information

>gi\|108710017\|gb\|ABF97812.1\| DIRP family protein, expressed [Oryza sativa Japonica Group]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1172
TAIR\|locus:2143666		971	ALY1 "ALWAYS EARLY 1" [Arabido	0.273	0.330	0.417	5.4e-143
TAIR\|locus:2089438		1132	ALY3 "ALWAYS EARLY 3" [Arabido	0.363	0.376	0.418	8.4e-143
ZFIN\|ZDB-GENE-030131-1747		543	lin9 "lin-9 homolog (C. elegan	0.135	0.292	0.335	1.8e-13
RGD\|1591104		552	Lin9 "lin-9 homolog (C. elegan	0.137	0.291	0.329	6.9e-13
MGI\|MGI:1919818		542	Lin9 "lin-9 homolog (C. elegan	0.137	0.297	0.329	8.2e-13
DICTYBASE\|DDB_G0286665		999	lin9 "RmlC-like cupin family p	0.132	0.155	0.282	1.6e-12
UNIPROTKB\|F1MIQ3		541	LOC534587 "Uncharacterized pro	0.137	0.297	0.312	3.9e-12
UNIPROTKB\|Q5TKA1		542	LIN9 "Protein lin-9 homolog" [	0.137	0.297	0.317	5.7e-12
UNIPROTKB\|H0Y322		613	LIN9 "Protein lin-9 homolog" [	0.137	0.262	0.317	1.2e-11
UNIPROTKB\|C9J5J4		489	LIN9 "Protein lin-9 homolog" [	0.091	0.218	0.394	1.9e-11

TAIR\|locus:2143666 ALY1 "ALWAYS EARLY 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 587 (211.7 bits), Expect = 5.4e-143, Sum P(3) = 5.4e-143
 Identities = 142/340 (41%), Positives = 191/340 (56%)

Query:   381 FGDESTALNALQTLADLSLML-PDSTMESESSVQLKEERTAFDIDDKSSAPEETSTSHPK 439
             + D+   L AL+TLA++S  L P   +ESESS   +EER   ++D KS+  E  STSH +
Sbjct:   302 YSDDDDGLGALKTLAEMSASLAPAGLLESESSPHWEEERKTNNVDKKSNTLETVSTSHHR 361

Query:   440 EKIKHLGPKEKALNTITEAEDIIPRKSKLGRYSGNDVETVAEVKEQPEPPNXXXXXXXXX 499
             EK K  G ++  L+ I+  +   P KS      GN V ++ E++                
Sbjct:   362 EKAKQAGLEDNLLHAISAPDKRKP-KSVPESVDGN-VVSIEELR------TSSRKRKPKF 413

Query:   500 XXXXXXXNSEAVTDTHMTRTLESEAVAEEHNKFASKGKRTSQNSAQSKQWKPGRV-LEGS 558
                      E+  D  +  T ES  V  +  K   K +R+SQ  A  KQ K  +  +E S
Sbjct:   414 QVLDVVAPKESTQDKSLY-TKESAEV--DSLKTPVKARRSSQGPA--KQLKTAKTTVESS 468

Query:   559 SVNDQNRASIDLVAPTGQAPVASPASSPTKHQSRRKMDLKRKLSSKEMKFSENSLKTQPN 618
             S +D+     D V P  Q   + P + P K  +RRK+ LK+ L  +         K +  
Sbjct:   469 SASDKKITGPDAVVPATQVSASGPETLPQKPPNRRKISLKKSLQERAKSLETTHDKPRSF 528

Query:   619 KNSLSQEDRLLSMKEKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGH 678
             K  LS+ + L   +EKLS CLS  +VRRWC +EWFYSAIDYPWF+  EF +YLNHVGLGH
Sbjct:   529 KK-LSEHELL---QEKLSNCLSYPLVRRWCIYEWFYSAIDYPWFAKMEFTDYLNHVGLGH 584

Query:   679 IPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKLKQYRES 718
              PRLTRVEW VI+SSLG+PRRLS+RFL DER+KL++YRES
Sbjct:   585 APRLTRVEWSVIKSSLGRPRRLSQRFLQDERDKLQEYRES 624

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR\|locus:2089438 ALY3 "ALWAYS EARLY 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-1747 lin9 "lin-9 homolog (C. elegans)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

RGD\|1591104 Lin9 "lin-9 homolog (C. elegans)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:1919818 Lin9 "lin-9 homolog (C. elegans)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0286665 lin9 "RmlC-like cupin family protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MIQ3 LOC534587 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5TKA1 LIN9 "Protein lin-9 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|H0Y322 LIN9 "Protein lin-9 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|C9J5J4 LIN9 "Protein lin-9 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

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)
Q6A332	ALY3_ARATH	No assigned EC number	0.3972	0.8839	0.9151	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.XIII.940.1	hypothetical protein (1052 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		1172
pfam06584		109	pfam06584, DIRP, DIRP	3e-30
pfam00249		47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	4e-04
cd00167		45	cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-	8e-04
smart00717		49	smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII	0.002

>gnl\|CDD\|148285 pfam06584, DIRP, DIRP	Back alignment and domain information

 Score =  115 bits (289), Expect = 3e-30
 Identities = 40/67 (59%), Positives = 47/67 (70%), Gaps = 1/67 (1%)

Query: 653 FYSAIDYPWFSNREFVEYL-NHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREK 711
           FYSAID PWF + +FV YL  H  L H  RLTR EW +IR S+GKPRR S  FL +EREK
Sbjct: 1   FYSAIDKPWFEDNDFVRYLREHFPLLHTRRLTRAEWRLIRRSMGKPRRFSAAFLKEEREK 60

Query: 712 LKQYRES 718
           L++ RE 
Sbjct: 61  LERKREK 67

DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of fruit fly and mustard weed. Studies of lin-9 and aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway. Length = 109

>gnl\|CDD\|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain	Back alignment and domain information

>gnl\|CDD\|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains	Back alignment and domain information

>gnl\|CDD\|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1172
KOG1019		837	consensus Retinoblastoma pathway protein LIN-9/chr	100.0
PF06584		109	DIRP: DIRP; InterPro: IPR010561 DIRP (Domain in Rb	99.94
KOG1019		837	consensus Retinoblastoma pathway protein LIN-9/chr	99.94
PF00249		48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	98.22
smart00717		49	SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi	97.95
cd00167		45	SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do	97.91
TIGR01557		57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	97.63
PF13921		60	Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB:	97.34
PLN03212		249	Transcription repressor MYB5; Provisional	95.78
COG5259		531	RSC8 RSC chromatin remodeling complex subunit RSC8	94.8
PLN03091		459	hypothetical protein; Provisional	94.21
KOG1279		506	consensus Chromatin remodeling factor subunit and	92.48
COG5118		507	BDP1 Transcription initiation factor TFIIIB, Bdp1	91.56
KOG4468		782	consensus Polycomb-group transcriptional regulator	88.57
KOG4329		445	consensus DNA-binding protein [General function pr	88.49
KOG0457		438	consensus Histone acetyltransferase complex SAGA/A	87.85
PLN03212		249	Transcription repressor MYB5; Provisional	84.99
KOG0048		238	consensus Transcription factor, Myb superfamily [T	83.43
PLN03091		459	hypothetical protein; Provisional	81.42

>KOG1019 consensus Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]	Back alignment and domain information

Probab=100.00  E-value=6.3e-93  Score=824.36  Aligned_cols=800  Identities=39%  Similarity=0.455  Sum_probs=695.8

Q ss_pred             CCCCC--CcccccccccccCCCCCCCCCCchhhh-hhhhccccCCCCCHHHHHHHHHHHHHhCcCHHHHHHHHhc-ccHH
Q 044351            1 MAPTR--KSRSVNKRYANEVSPAKDVISPSKSKQ-KKKLSDKLGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRN-RSAE   76 (1172)
Q Consensus         1 Map~R--ksRsvnKr~~ne~s~~kd~~~~~k~k~-KrKlsD~lgp~WSkeEl~~Fyea~r~~GkdWkkva~~v~~-Rs~~   76 (1172)
                      |||.|  |++.+||+|+|+++|+++....+|.+| |||++|+|||||++.|+++||++|++||+.|+++++.++. |+.+
T Consensus         1 ~a~vRkrk~~~~~~~~~ndtsp~~~~~~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~   80 (837)
T KOG1019|consen    1 MAAVRKRKSKSVDKRFTNDTSPRYDSGSTSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSN   80 (837)
T ss_pred             CCcccccccccccccccccccccccccccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhh
Confidence            89999  899999999999999999999999999 9999999999999999999999999999999999999995 9999


Q ss_pred             HHHHHHHhcccccccCcccchhhhHHHhhccccccccCCCcccccCCCCCCcchhhhhhhhhh-cccCcccccccccccc
Q 044351           77 MVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDSERESNDASEMPRKSQKRKRAKV-QLSASKEDISQSWSMA  155 (1172)
Q Consensus        77 mV~aly~~~r~ylslpeg~as~~g~~a~mtdhy~~~~~s~se~es~~~~~~~~k~~kr~r~~~-~~~~~~~~~~~~~~~~  155 (1172)
                      ||++||.||+||+|+|+|++++.|+|+||||||.++.||.+++|++|+++..++..|++|+++ ..++..+.+.-.+.+.
T Consensus        81 ~vell~~~n~Ay~S~~~~~~si~G~~~~~t~~ys~~~gs~~~~e~~d~sE~e~k~~k~kr~~va~~~D~~eg~~l~n~~~  160 (837)
T KOG1019|consen   81 MVELLKAMNKAYLSLSEGTESILGLIEPMTDHYSVLEGSGPEGESNDASEKERKAIKRKRAKVAKRSDFDEGLRLTNEAK  160 (837)
T ss_pred             HHHHHHhhhcccccccccccccccccccCCCccchhcCCCCCCccchhhhhhHHHHHHHhhcccccccccccccchhhhc
Confidence            999999999999999999999999999999999999999999999999999999999999999 8888888888888889


Q ss_pred             ccCCccccccccccCCCCcccccccCCccccccccccCCcccCCCCccccccccccCCchhHHHHHHHHHHHHhhcCCCC
Q 044351          156 ATGGCLSLLKRSRIDGNQPRAVKKRTPRFPVSYSQKKDDRDDYIPLNKKDRRSAVDANDDEVAHVAALALTEASQRGGSP  235 (1172)
Q Consensus       156 S~~G~ls~lKk~~~~~~~p~aVGKRTPRvPV~~~~~kd~~e~~~~~~k~~~k~~~da~DDd~ah~~ALALteasqRGgSp  235 (1172)
                      +..||+++||+.++    -++.++++|++++-..+..+|...+.+|+.|..++. +.++            +++.||+. 
T Consensus       161 s~~~~~~~~~q~~~----~~~~k~~~~~~~~~~~~~aed~~~~s~~n~r~~~ql-~r~~------------~ksRr~~~-  222 (837)
T KOG1019|consen  161 SLSGHLWFFKQFRT----SQADKPTLKQFLVYKNQTAEDAPTLSRPNIRALWQL-DRRD------------GKSRRGSA-  222 (837)
T ss_pred             cccchHHHHHHHHh----hhhccccchhhhHHHhhhhhhhhhccchhhhhhhhh-hccc------------ccchhccc-
Confidence            99999999999997    478999999999999999999999999999999988 4444            67888887 


Q ss_pred             CccCCCccccccCCCCccccccccCCCCCCCCCcccccccccCCCcccccCCCCCCCccccchhccccccccccchhhcc
Q 044351          236 QVSQSPHKKTEHGKSSPVQIWDKMFPPAETAHPDAREALNEEGCPEARILNRRPENGAYTRARKSLMDMEGVGTVEVHRK  315 (1172)
Q Consensus       236 qvS~tP~rr~e~~~~Sp~q~~dkm~~~se~~~~k~~~s~~de~~~E~Sl~Sr~a~~g~y~rd~s~lm~~eG~g~~~~~~K  315 (1172)
                           |.++.+..+..|-+.++++.+..+-.+.+ ++++|.+.|    ..+....-|.-+++++.||+|++.|.++.   
T Consensus       223 -----~~f~~e~~E~~~~~~~~~~~~sr~~~~~~-~nss~~~~~----~~~i~~~l~~~~~~Ss~L~~~er~~~~~~---  289 (837)
T KOG1019|consen  223 -----PFFREELSEQIPKRERIKTSQSREKFSKL-KNSSMLRIG----PRSIPKPLGKPDRVSSLLMDMERMGLEEA---  289 (837)
T ss_pred             -----hhhHhHHhhhhHHHHhhhhhhhhcccCCC-CchHHhhhh----hhhcccccccCccchhhhhchhhcccccc---
Confidence                 89999888999999999998877766655 999999999    56677788999999999999999987654   


Q ss_pred             cccccccchhHHhhhcCCCccccccccccccCcccccCCcccccccccCCCCchhhhhhhcccccCCCcchhhHHHHHHH
Q 044351          316 GKKFYRKKMKVEEVRNSLSDDEGEACSGTEEGLSSRKGKVGSEISNAKNDHLPLQMQRKRSKKLFFGDESTALNALQTLA  395 (1172)
Q Consensus       316 ~k~~~~rk~kve~~~~~q~dD~~EAcSgteEg~s~~~~k~~~ev~~~k~~~~s~k~~~kRskklf~gde~salDAL~TLA  395 (1172)
                            |.++++.+.+++++|                                                  +|||++++|
T Consensus       290 ------kv~~~e~ae~sy~~d--------------------------------------------------~~~~~~~~a  313 (837)
T KOG1019|consen  290 ------KVVKDELAEGSYLDD--------------------------------------------------GLDALKLPA  313 (837)
T ss_pred             ------eeEeechhhhhhhhh--------------------------------------------------hhhhhccch
Confidence                  224566666666655                                                  499999999


Q ss_pred             Hhh-ccCCCCcccccchhhhhhhccccccCCCCCCCCcCCCCCchhhhcccCcchhhcccccccccccccccccCcccCC
Q 044351          396 DLS-LMLPDSTMESESSVQLKEERTAFDIDDKSSAPEETSTSHPKEKIKHLGPKEKALNTITEAEDIIPRKSKLGRYSGN  474 (1172)
Q Consensus       396 dlS-l~~P~~~~esess~q~kee~~~~~~d~k~~~p~~~s~~h~kek~k~~~~k~~~~~~~~~~~~~~~kksk~~k~~~~  474 (1172)
                      .++ +|+|...++||++.++++|+.+..+|.+++.++.+.++++..+..-...++...+.+...+   +++.|+.+.-..
T Consensus       314 e~~~s~~p~~~l~S~~~t~~~~~~s~~i~d~~ss~~~iv~~~~~~~~~nv~~~ke~L~~~l~a~~---~~k~k~~k~~s~  390 (837)
T KOG1019|consen  314 EESVSMLPGNRLESESSTHYKEERSGIIMDVNSSGFEIVETSPHIPKNNVSDTKELLDGKLRALS---KRKIKPSKPLST  390 (837)
T ss_pred             hhcccccccccchhhcccccccccccceeccCcCCceeeccCcCCccccchhhhhhhhhhhhhhh---hhcccccccccC
Confidence            999 9999999999999999999999999999999999999999988877777888888776664   567777777777


Q ss_pred             CcchhhhhccCCCCCCchhhcccccccccccccccccccccccccchhhhHhhhh-ccccccCcccccccccccccCCcc
Q 044351          475 DVETVAEVKEQPEPPNSMSKRKRKSVLSKKISNSEAVTDTHMTRTLESEAVAEEH-NKFASKGKRTSQNSAQSKQWKPGR  553 (1172)
Q Consensus       475 d~~~~~e~k~~~~~~~~~~krkrk~~~~~k~~~~e~~~~~~~~~~~~~~e~~~~~-~k~~~kgk~~~~~~~~~kq~k~~~  553 (1172)
                      |...++.....+.    +++++++ +.++++++ |..    +.++...++.+... .+..++|++..+..+. +|.++++
T Consensus       391 d~~~v~~~il~~l----s~~~~~~-v~D~et~~-ei~----q~~S~~~~~~~~~~e~~s~v~~~r~~~~~a~-~q~~t~~  459 (837)
T KOG1019|consen  391 DGVRVSVAILMDL----SRKRKLL-VLDVETPK-EIS----QSKSRNRGESTERLEKKSLVKGRRYSAVPAN-LQRLTKK  459 (837)
T ss_pred             CCccchhHHhhhh----cccCccc-cccccchh-hhh----cccccccccchhhhhhhhhhhhhhhhhhhHH-HHHhhhh
Confidence            7777777777754    3455555 77777763 322    22334444433333 5679999999999998 9999999


Q ss_pred             cccCC-ccccccccccccCCCCCCCCCCCCCCCCcccccccchhhccccchhhccccccccCCCCCCCCCchhHHHHHHH
Q 044351          554 VLEGS-SVNDQNRASIDLVAPTGQAPVASPASSPTKHQSRRKMDLKRKLSSKEMKFSENSLKTQPNKNSLSQEDRLLSMK  632 (1172)
Q Consensus       554 ~~e~s-~~~d~~~~~~~~~~p~~q~~~~~q~~lp~K~rSrRK~~~~k~l~~k~~~s~~~~~~~~~~~~~~s~~~~~~~~~  632 (1172)
                      ..+.+ +..|......|.+++..|+...+...++.|.+.+|++.+++++..+.+ +.|..+....+.+.+|.....  ++
T Consensus       460 i~~~~~l~~d~~~~~~d~~~~~~q~s~~~~~~~~Qk~~n~rd~elk~a~~e~~~-~~e~~h~~~~s~n~~Sq~~l~--~~  536 (837)
T KOG1019|consen  460 IGEESRLTRDKKELGADADIQPRQVSKSGPAFQEQKAPNIRDIELKNALQEKAL-SGEQDHHMYFSRNDLSQSELL--PK  536 (837)
T ss_pred             ccchhhhhhhhhhcccccccccchhcccchhhhhhhcchhHHHHHHhHHHHHHh-hcccchhhhccccchhHHHhc--ch
Confidence            99997 899999999999999999999999999999999999999999998875 456666666667777777665  78


Q ss_pred             HHHHhhccccccccceeeecccccCChhhhccchHHHHHHhcCCCCCCccchhhHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 044351          633 EKLSGCLSSNMVRRWCTFEWFYSAIDYPWFSNREFVEYLNHVGLGHIPRLTRVEWGVIRSSLGKPRRLSKRFLHDEREKL  712 (1172)
Q Consensus       633 ~rL~n~Lk~pkarRW~~~EwFYS~IDkp~F~~nEF~~~L~~~~l~~~~~LtR~EW~~IRr~mGKPRRfS~aFl~EER~kL  712 (1172)
                      .++.+|+..+...+||++||||+++|.+||..-+|..||.++++++++++++++|.+|-..+|.||  |..|..+||+.|
T Consensus       537 ~kre~c~~~~~~~vd~i~~~~~~~~~~l~~~k~~~Td~L~~v~lg~~p~~s~V~~~vl~~~lqepr--s~~~~~~er~~l  614 (837)
T KOG1019|consen  537 AKREECSSQAGRTVDHINEGFYSANPHLGFLKMEFTDYLNHVRLGGTPRLSAVEWSVLKSSLQEPR--STRILQEEREKL  614 (837)
T ss_pred             hHHHhhhccCchhHHHHHhHHhhcCcchhHHHhhhhhhhhccccccccchhhhhHHHHHHHhhcch--hhhhhhhHHHHH
Confidence            899999999999999999999999999999999999999999999999999999999999999999  999999999999


Q ss_pred             HhHhcc------------------------eEEEEcCCCCCccCceEEEEeCCceEEEecCCCCCeeeeccCcccCCCCC
Q 044351          713 KQYRES------------------------RVIAIHPKTRELHDGSVLTIDHDKCRVQFDRPELGVEFVMDIDSMPSNPL  768 (1172)
Q Consensus       713 E~~R~~------------------------kViA~hp~~r~L~dG~Vlavd~~~YrV~FDrpeLGv~~VpD~dvmp~~p~  768 (1172)
                      +.|++.                        -|=|.||.++++|||.|+++|++.|-|-|+  .||++.|||++|||++|+
T Consensus       615 q~yvE~~~k~~~~l~s~~~~~~~t~~~r~~d~~~s~p~t~e~~d~~~~~~~~n~~~~~~~--~~~a~~~~~q~~~~ln~~  692 (837)
T KOG1019|consen  615 QDYVESVRKTYHELRSEAGELLGTDLARKLDVGASHPKTREIHDGKILTVDHNKCNVLFD--KLGAELVMDQDCMPLNPL  692 (837)
T ss_pred             HHHHHhhhcchhhhhccccccccchhccccccccCCcchhhhhhhhhhhcccccCccchh--hhcccccchhhccccChh
Confidence            999998                        455789999999999999999999999999  899999999999999999


Q ss_pred             CCchHHHHHhhhhhhhhhhhhhhhhCCCCCCCCCccccCCCCCCCCCCCchhhhhhccccccccchhhhhhhhhHHHHHh
Q 044351          769 DNMPEALRRQISADKFSAISKELQVNGHPNFGSPMLFASDGHLEKAPILPNTLQKQAKGDMNHALPQAKSLATDIVSAQQ  848 (1172)
Q Consensus       769 e~~P~sl~~~~~~~kf~~~~~el~~nG~~~~~~~~l~sp~~~~~~~~~ls~~l~~qak~~~~e~~~~a~~~~~~av~~qq  848 (1172)
                      +.+|+.+++++  .++..+..|++++||.+.                                                 
T Consensus       693 ~dk~e~~~r~~--d~~~~~~~e~q~~g~~na-------------------------------------------------  721 (837)
T KOG1019|consen  693 EDKPEGLRRQI--DKCLEKEKEAQLGGHENA-------------------------------------------------  721 (837)
T ss_pred             hhhhhhhhhhh--hHHHHHHHHHHhCCCCCc-------------------------------------------------
Confidence            99999999998  777787777777775443                                                 


Q ss_pred             hhhcCccchhhHHHHHHHHHhhcHHHHHHHHHhhchHHHhhccCCCCccCCChHHHHHHHHHHHHHHHhhhhhccccchh
Q 044351          849 AAYGQLCTVPQIQAREATVRALSEEALLMELKNTNNDILESQNGGESSLKDSEPLKKHIATVLVQLKEANDQACGFRELC  928 (1172)
Q Consensus       849 ~~~~qP~~~~q~Q~keadI~aLsEeall~ELr~MNdEae~~~~~g~~~~k~se~Fqk~YA~VvlqL~e~N~~~~~~~~~~  928 (1172)
                                                                      +.+++-|+..|+.|.+|+.+.           
T Consensus       722 ------------------------------------------------~~~s~~~~~~~~~v~fq~~~~-----------  742 (837)
T KOG1019|consen  722 ------------------------------------------------GYSSLFRPDELENVEFQMNQQ-----------  742 (837)
T ss_pred             ------------------------------------------------CchhhcCchhHHHHHHHHHhc-----------
Confidence                                                            223455677888899998853           


Q ss_pred             cccccccccccccccccccccchhhhhHHHHHHHhhhccCCCCCCCCCCCCCCCcccccCCCcCccCCCCeeeeeeccch
Q 044351          929 FGISCYLSLQFHTLTWRRSLIDCFDMQASSALLQVRQCNTHPESSRPSWPMHPANVKMLDNSHVSQESGSAVAEIVNGSR 1008 (1172)
Q Consensus       929 ~~~~~~~~~~~~~~~~~~~~~~~~~~qvs~al~~lRqrnty~~n~~~~~~~~~~~~~~~~~~~~~~e~gs~v~eiv~~Sr 1008 (1172)
                                              +.|++-+|.-++||||--.+  ..-.--+..-.+..|....+|++.+|+|||.+|+
T Consensus       743 ------------------------~d~~~~~L~g~~q~~~~~~~--~~~~~E~~~~l~~qh~~~~~~~~~~~~eiv~~s~  796 (837)
T KOG1019|consen  743 ------------------------LDPEEPHLDGKVQHNTIEIQ--KLKLEEIQRELALQHLDDEEEMEPEMVEIVTQSK  796 (837)
T ss_pred             ------------------------cCchhhhhhhhhhccchHhh--hccccchhhHHHhhcCChhhhcCcchhhhhhhhH
Confidence                                    44599999999999992222  1111111122234489999999999999999999


Q ss_pred             hhHHHHHHHHHHHhhhccccchhHHHHHHHHhhcccccC
Q 044351         1009 LKAHTMVDAAVKAMSSVKEGEDAYTKIGEALDHIDKRQL 1047 (1172)
Q Consensus      1009 ~kA~~MVdaA~qA~s~~kege~~~~~i~~ald~i~~~~~ 1047 (1172)
                      .+|++|||+||||+++++|+|+....|+|||+   ++|+
T Consensus       797 i~a~kmvd~a~qaa~~~~~de~~~~~meea~~---~~~~  832 (837)
T KOG1019|consen  797 IEAQKMVDAAIQAASSTKEDEDVNLMMEEALE---EEQV  832 (837)
T ss_pred             HHHHHHHHHHHHHHHhhcccchhhHHHHHHHh---hhcc
Confidence            99999999999999999999999999999997   5544

>PF06584 DIRP: DIRP; InterPro: IPR010561 DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of Drosophila melanogaster and mustard weed	Back alignment and domain information

>KOG1019 consensus Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]	Back alignment and domain information

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins	Back alignment and domain information

>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains	Back alignment and domain information

>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains	Back alignment and domain information

>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class	Back alignment and domain information

>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A	Back alignment and domain information

>PLN03212 Transcription repressor MYB5; Provisional	Back alignment and domain information

>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]	Back alignment and domain information

>PLN03091 hypothetical protein; Provisional	Back alignment and domain information

>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]	Back alignment and domain information

>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]	Back alignment and domain information

>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]	Back alignment and domain information

>KOG4329 consensus DNA-binding protein [General function prediction only]	Back alignment and domain information

>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]	Back alignment and domain information

>PLN03212 Transcription repressor MYB5; Provisional	Back alignment and domain information

>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]	Back alignment and domain information

>PLN03091 hypothetical protein; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		1172
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
2ltp_A		89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	6e-10
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	5e-09
2cu7_A		72	KIAA1915 protein; nuclear protein, SANT domain, DN	8e-07
4a69_C		94	Nuclear receptor corepressor 2; transcription, hyd	3e-06
2eqr_A		61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	5e-06
2iw5_B		235	Protein corest, REST corepressor 1; oxidoreductase	8e-06
1x41_A		60	Transcriptional adaptor 2-like, isoform B; transcr	7e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

 Score = 71.4 bits (174), Expect = 2e-12
 Identities = 67/554 (12%), Positives = 149/554 (26%), Gaps = 168/554 (30%)

Query: 24  VISPSKSKQKKKLSDKLGPQWSKGE--LQRFYEAY--RNYGKDWKKVAAQVRNRSAEMVE 79
           ++S        +L   L    SK E  +Q+F E     NY   +     +   R   M+ 
Sbjct: 55  IMSKDAVSGTLRLFWTL---LSKQEEMVQKFVEEVLRINY--KFLMSPIKTEQRQPSMMT 109

Query: 80  ALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGSDSERESNDASEMPRKSQKRKRAKV 139
            +Y   R                               +R  ND     + +  R +  +
Sbjct: 110 RMYIEQR-------------------------------DRLYNDNQVFAKYNVSRLQPYL 138

Query: 140 QL-SASKEDISQSW----SMAATG-GCL--SLLKRSRIDGNQPRAVKKRTPRFPVSYSQK 191
           +L  A  E           +  +G   +   +    ++       +      F ++    
Sbjct: 139 KLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI------FWLNLKNC 192

Query: 192 KDDRDDYIPLNKKDRRSAVDANDDEVA-HVAALAL-TEASQRGGSPQVSQSPHKKT---- 245
                    L K   +  +D N    + H + + L   + Q      +   P++      
Sbjct: 193 NSPETVLEMLQKLLYQ--IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250

Query: 246 EHGKSSPVQIWDKMFPPAETAHPDAREALNEEGCPEARILNRRPENGAYTRARKSLMDME 305
            +       + +      +        A N   C   +IL         TR  K + D  
Sbjct: 251 LN-------VQNA-----KAW-----NAFN-LSC---KIL-------LTTR-FKQVTDFL 281

Query: 306 GVGTVEVHRKGKKFYRKKMKVEEVRNSLSDDEGEACSGTEEGLSSRKGKVGSEISNAKND 365
              T              + ++    +L+ DE       +  L            + +  
Sbjct: 282 SAAT-----------TTHISLDHHSMTLTPDE------VKSLLLK--------YLDCRPQ 316

Query: 366 HLPLQMQRKRSKKLFFGDESTALNALQTLADLSLMLPDSTMESESSVQLKEERTAFDIDD 425
            LP ++                 N    L+ ++  + D     ++   +  ++    I  
Sbjct: 317 DLPREVLT--------------TNPR-RLSIIAESIRDGLATWDNWKHVNCDKLTTII-- 359

Query: 426 KSSAPEETSTSHPKEKIKHLGPKE-----KALNTITEAEDI-IPRKSKLGRYSGNDVETV 479
           +SS             +  L P E       L ++       IP    L     + +++ 
Sbjct: 360 ESS-------------LNVLEPAEYRKMFDRL-SVFP-PSAHIPTIL-LSLIWFDVIKS- 402

Query: 480 AEVKEQPEPPNSMSKRKRKSVLSKKISNSEAVT--DTHMTRTLESEAVAEEHNKFASK-- 535
                  +    ++K  + S++ K+      ++    ++   ++ E     H        
Sbjct: 403 -------DVMVVVNKLHKYSLVEKQ-PKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454

Query: 536 GKRTSQNSAQSKQW 549
             +T  +      +
Sbjct: 455 IPKTFDSDDLIPPY 468

PyMOL of 1vt4

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens} Length = 89	Back alignment and structure

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens} Length = 79	Back alignment and structure

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 72	Back alignment and structure

>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A Length = 94	Back alignment and structure

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 61	Back alignment and structure

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B* Length = 235	Back alignment and structure

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 60	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		1172
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	98.63
2eqr_A		61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	98.59
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	98.59
2yqk_A		63	Arginine-glutamic acid dipeptide repeats protein;	98.51
2iw5_B		235	Protein corest, REST corepressor 1; oxidoreductase	98.43
2crg_A		70	Metastasis associated protein MTA3; transcription	98.06
2cu7_A		72	KIAA1915 protein; nuclear protein, SANT domain, DN	98.03
1wgx_A		73	KIAA1903 protein; MYB DNA-binding domain, human cD	97.95
4a69_C		94	Nuclear receptor corepressor 2; transcription, hyd	97.9
2elk_A		58	SPCC24B10.08C protein; hypothetical protein, struc	97.85
1x41_A		60	Transcriptional adaptor 2-like, isoform B; transcr	97.8
2yum_A		75	ZZZ3 protein, zinc finger ZZ-type-containing prote	97.74
2ltp_A		89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	96.81
2cqr_A		73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	97.5
1guu_A		52	C-MYB, MYB proto-oncogene protein; transcription,	97.49
2d9a_A		60	B-MYB, MYB-related protein B; DNA binding, structu	97.44
1gvd_A		52	MYB proto-oncogene protein; transcription, transcr	97.31
3osg_A		126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	97.27
2dim_A		70	Cell division cycle 5-like protein; MYB_DNA-bindin	97.22
2cqq_A		72	RSGI RUH-037, DNAJ homolog subfamily C member 1; m	97.22
2din_A		66	Cell division cycle 5-like protein; MYB_DNA-bindin	97.17
2llk_A		73	Cyclin-D-binding MYB-like transcription factor 1;	97.11
2k9n_A		107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	97.03
4eef_G		74	F-HB80.4, designed hemagglutinin binding protein;	97.02
1gv2_A		105	C-MYB, MYB proto-oncogene protein; transcription,	97.0
1w0t_A		53	Telomeric repeat binding factor 1; telomere, DNA-b	96.99
2cjj_A		93	Radialis; plant development, DNA-binding protein,	96.9
1h8a_C		128	AMV V-MYB, MYB transforming protein; transcription	96.78
1ity_A		69	TRF1; helix-turn-helix, telomeres, DNA binding, MY	96.67
3osg_A		126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	96.65
2k9n_A		107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	96.5
3sjm_A		64	Telomeric repeat-binding factor 2; human telomeric	96.48
3zqc_A		131	MYB3; transcription-DNA complex, DNA-binding prote	96.35
1gv2_A		105	C-MYB, MYB proto-oncogene protein; transcription,	96.34
1h8a_C		128	AMV V-MYB, MYB transforming protein; transcription	96.31
1h89_C		159	C-MYB, MYB proto-oncogene protein; transcription/D	96.27
1x58_A		62	Hypothetical protein 4930532D21RIK; MUS musculus a	95.83
3zqc_A		131	MYB3; transcription-DNA complex, DNA-binding prote	95.32
1h89_C		159	C-MYB, MYB proto-oncogene protein; transcription/D	95.2
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	95.02
2ckx_A		83	NGTRF1, telomere binding protein TBP1; nuclear pro	94.77
4b4c_A		211	Chromodomain-helicase-DNA-binding protein 1; chrom	94.48
1irz_A		64	ARR10-B; helix-turn-helix, DNA binding protein; NM	94.02
1ofc_X		304	ISWI protein; nuclear protein, chromatin remodelin	92.91
2aje_A		105	Telomere repeat-binding protein; DNA-binding, Trp,	91.94
2roh_A		122	RTBP1, telomere binding protein-1; plant, nucleus,	91.5
3hm5_A		93	DNA methyltransferase 1-associated protein 1; DNA	91.45
2juh_A		121	Telomere binding protein TBP1; helix, nucleus, nuc	90.36
2xb0_X		270	Chromo domain-containing protein 1; hydrolase, DNA	87.22
1ign_A		246	Protein (RAP1); RAP1,yeast,telomeres,homoeodomain,	86.56

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*	Back alignment and structure

Probab=98.63  E-value=1.7e-08  Score=115.59  Aligned_cols=66  Identities=18%  Similarity=0.361  Sum_probs=56.4

Q ss_pred             cCCCCCHHHHHHHHHHHHHhCcCHHHHHHHHhcccHHHHHHHHHhcccccccCcccchhhhHHHhhccccccccCC
Q 044351           40 LGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPEGTASVVGLIAMMTDHYNVMEGS  115 (1172)
Q Consensus        40 lgp~WSkeEl~~Fyea~r~~GkdWkkva~~v~~Rs~~mV~aly~~~r~ylslpeg~as~~g~~a~mtdhy~~~~~s  115 (1172)
                      ..++||.+|++.|+++|++||+||.+||..|++||+.||++.|..+|..|.|.+          |+-+|..-.+..
T Consensus       379 ~~~~WT~eE~~~f~~al~~yGkdw~~IA~~VgTKT~~Qvk~fy~~~kkr~~ld~----------il~e~e~~~~~~  444 (482)
T 2xag_B          379 CNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDE----------VLQEWEAEHGKE  444 (482)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHTTCHHHHHHHHSSCCHHHHHHHHHHTTTTTTHHH----------HHHHHHTC----
T ss_pred             cCCCCCHHHHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHHHHHHHhChHH----------HHHHHHHhhCCc
Confidence            467999999999999999999999999999999999999999999999999876          566664444433

PyMOL of 2xag

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens}	Back alignment and structure

>2yqk_A Arginine-glutamic acid dipeptide repeats protein; structure genomics, SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B*	Back alignment and structure

>2crg_A Metastasis associated protein MTA3; transcription factor, helix turn helix, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.3	Back alignment and structure

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A	Back alignment and structure

>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe}	Back alignment and structure

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens}	Back alignment and structure

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A	Back alignment and structure

>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A	Back alignment and structure

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A	Back alignment and structure

>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>2din_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens}	Back alignment and structure

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A	Back alignment and structure

>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin, fusion of virus membrane with membrane, membrane fusion, sialic acid, virion; HET: NAG BMA; 2.70A {Artificial gene}	Back alignment and structure

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A	Back alignment and structure

>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A	Back alignment and structure

>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3	Back alignment and structure

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3	Back alignment and structure

>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A	Back alignment and structure

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A	Back alignment and structure

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A	Back alignment and structure

>3sjm_A Telomeric repeat-binding factor 2; human telomeric repeat binding protein 2, telomere, telomeri homeodomain proteins amino acid sequence; HET: DNA; 1.35A {Homo sapiens} PDB: 1xg1_A 1vfc_A 1vf9_A 1w0u_A	Back alignment and structure

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}	Back alignment and structure

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A	Back alignment and structure

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3	Back alignment and structure

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C	Back alignment and structure

>1x58_A Hypothetical protein 4930532D21RIK; MUS musculus adult MALE testis cDNA, riken FULL-length enriched library, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}	Back alignment and structure

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C	Back alignment and structure

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*	Back alignment and structure

>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A	Back alignment and structure

>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens}	Back alignment and structure

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11	Back alignment and structure

>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A	Back alignment and structure

>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3	Back alignment and structure

>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa}	Back alignment and structure

>3hm5_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin, structural genomics consortium, SGC, activator, chromatin regulator; HET: DNA; 1.80A {Homo sapiens}	Back alignment and structure

>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa}	Back alignment and structure

>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A	Back alignment and structure

>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		1172
d1xc5a1		68	a.4.1.3 (A:413-480) Nuclear receptor corepressor 2	2e-07
d2iw5b1		65	a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Hu	3e-07
d2crga1		57	a.4.1.3 (A:8-64) Metastasis associated protein MTA	3e-04

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 68	Back information, alignment and structure


class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Nuclear receptor corepressor 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 10/68 (14%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 24 VISPSKSKQKKKLSDKLGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYN 83
          +  P K  + +++ +     WS+ E + F E +  + K++  +A+ +  ++       Y 
Sbjct: 4  MADPMKVYKDRQVMNM----WSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYY 59

Query: 84 MNRAYLSL 91
          + +   + 
Sbjct: 60 LTKKNENY 67

PyMOL of d1xc5a1

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]} Length = 65	Back information, alignment and structure

>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 57	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		1172
d2iw5b1		65	REST corepressor 1, CoREST {Human (Homo sapiens) [	98.83
d1xc5a1		68	Nuclear receptor corepressor 2 {Human (Homo sapien	98.54
d2cu7a1		65	MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960	98.29
d2crga1		57	Metastasis associated protein MTA3 {Mouse (Mus mus	98.19
d1x41a1		47	Transcriptional adaptor 2-like, TADA2L, isoform b	98.18
d2cjja1		63	Radialis {Garden snapdragon (Antirrhinum majus) [T	97.93
d1gv2a2		47	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	97.61
d2cqra1		60	DnaJ homolog subfamily C member 1 {Human (Homo sap	97.49
d1irza_		64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	97.28
d2cqqa1		59	DnaJ homolog subfamily C member 1 {Human (Homo sap	97.25
d1guua_		50	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	97.24
d1gvda_		52	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	96.72
d1w0ta_		52	DNA-binding domain of human telomeric protein, hTR	96.26
d1w0ua_		55	Telomeric repeat binding factor 2, TRF2 {Human (Ho	96.16
d1igna1		86	DNA-binding domain of rap1 {Baker's yeast (Sacchar	94.54
d1ofcx1		52	SANT domain of the nucleosome remodeling ATPase IS	93.24
d1ug2a_		95	2610100b20rik gene product {Mouse (Mus musculus) [	92.97
d2ckxa1		83	Telomere binding protein TBP1 {Tobacco (Nicotiana	91.77
d1wgxa_		73	Hypothetical protein C14orf106 (KIAA1903) {Human (	89.69

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: REST corepressor 1, CoREST
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.83  E-value=1.5e-09  Score=91.42  Aligned_cols=54  Identities=22%  Similarity=0.450  Sum_probs=50.3

Q ss_pred             cCCCCCHHHHHHHHHHHHHhCcCHHHHHHHHhcccHHHHHHHHHhcccccccCc
Q 044351           40 LGPQWSKGELQRFYEAYRNYGKDWKKVAAQVRNRSAEMVEALYNMNRAYLSLPE   93 (1172)
Q Consensus        40 lgp~WSkeEl~~Fyea~r~~GkdWkkva~~v~~Rs~~mV~aly~~~r~ylslpe   93 (1172)
                      ..++||.+|.+.|+++++.||++|.+||+.|++||..+|+.-|.+++.-+.+++
T Consensus         4 ~~~~WT~eE~~~f~~~~~~~G~~w~~Ia~~~~~kt~~q~~~~y~~~~k~~~~~~   57 (65)
T d2iw5b1           4 CNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDE   57 (65)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHSSCHHHHHHHHSSCCHHHHHHHHHHTTTTTTHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHhCchHHHHHHHcCCCCHHHHHHHHHHHHhhcCHHH
Confidence            568999999999999999999999999999999999999999999988777754

PyMOL of d2iw5b1

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]}	Back information, alignment and structure

>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1ofcx1 a.4.1.3 (X:799-850) SANT domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1ug2a_ a.4.1.3 (A:) 2610100b20rik gene product {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]}	Back information, alignment and structure

>d1wgxa_ a.4.1.3 (A:) Hypothetical protein C14orf106 (KIAA1903) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure