Citrus Sinensis ID: 003482

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------

MCTHGTIEEAFCVSPGKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPERLLDISSDAPSLSRGSSGMSDDMESSPPAQLSELDENATLKSKKMSHNTLMALIKFLQKKRSSIIEKATAEGTEEVVLDAVGDNFTSHDSTRFKKSSKGRGTIPMYSGAREMAAILDTALLQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEESKSNQSQDEHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQNTTIPKAGSVTAVKVKGGRTTKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRQSENLQVKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFRDSQSMKAVAKGSPLRKR

ccccccccccccccccccccEEEEEEccEEEEEcccccccccccccccccccEEEEEccEEEEEccccEEEEEccccccEEEEEEEccccccccccccEEEcccccEEEEccccHHHHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHcccccccccccHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHHcccccccHHHHHHHHHHcccHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccccHHHccccHHHHHHHHcccccccHHHHHHHHHHHHHHccccHHHHHccccccHHHHHHHHHcccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHcHHHHHHHHHHHHHcccccHHHHHcccccccccHHHHHHHHHcccHHHHHHHHHHHHccHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHccccccccccccHHHHHccccccHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccHHHHHHcccccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEcccccccccccccccccEEEEccccEEEEcccccccccccccccccccccc

ccccccccccccccccccccEEEEcccccEEEEEcccccccccccccccccHEEEEcccEEEEEccccEEEEEEcccccEEEEEEccccEEEEEcccEEEEEcccEEEEEEcccHHHHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccHHHHHHHcHHHccccccccccccHHccccccccccccccccccccccccccHHcccccccccHHcccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHccHcHHHHHHcccccccHHHHHHHHHHHccHHHHHHHHHccccHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHccccccHHHHHHHHHHHHccHHHcEEEEccccccHHHHHHHHHHccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHcHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccccccccccHHHHHHHHHccccccccccHHHHHHHHHHccccccHHHHHcHcccccccccccHHHHHHHHHHccccccccHHHHHHHccccccccccHHHHHHHHHHHHHcHHcccHHHHHHHccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEccccccccccccccccEEEEEccccEEEEEEEccccccccccccccccccc

mcthgtieeafcvspgkreSVFSDMMENIGVFVdqngkllqadricwseapIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSifglfpvplgaQIVQLTASGDFEEALALCkllppedasLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALslypsivlpkttvvpeperlldissdapslsrgssgmsddmessppaqlseldenatlkskkmSHNTLMALIKFLQKKRSSIIEKATAEGTEEVVLDAvgdnftshdstrfkksskgrgtipmysGAREMAAILDTALLQALLLTGQSSAALELLkglnycdvKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEesksnqsqdehtqkfnpeSIIEYLkplcgtdpmLVLEFSMLVLescptqtielFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQqkwdekayspTRKKLLSALESisgynpevllkrlpadaLYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYesiahqpsgkssgnIYLTLLQIYlnprrttkNFEKQITNLVSsqnttipkagsVTAVkvkggrttkkiasiegaedmrmspsstdsgrsdgdaeefseegdstiMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRqsenlqvkdELYNQRKTVVKITSDsmcslcskkigtsvfavypngktIVHFVCFrdsqsmkavakgsplrkr

mcthgtieeafcvspgKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLpkttvvpeperlldissdapslsRGSSGMSDDMESSPPAQLSELDENATLKSKKMSHNTLMALIKFLQKKRSSIIEKAtaegteevvldavgdnftshdstrfkksskgrgtiPMYSGAREMAAILDTALLQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEesksnqsqdehtqkfnPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIahqpsgkssgnIYLTLLQIYLNPRRTTKNFEKQITNLvssqnttipkagsvtavkvkggrttkkiasiegaedmrmspsstdsgrsdGDAEEfseegdstiMIDQVLDLLSQRWDRINGAQalkllpretKLQNLLPFLEPLLRKSSEAHRNLSVIkslrqsenlqvkdelynqRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVcfrdsqsmkavakgsplrkr

MCTHGTIEEAFCVSPGKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPERLLDISSDAPslsrgssgmsddmessPPAQLSELDENATLKSKKMSHNTLMALIKFLQKKRSSIIEKATAEGTEEVVLDAVGDNFTSHDSTRFKKSSKGRGTIPMYSGAREMaaildtallqallltgqssaalELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEESKSNQSQDEHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQNTTIPKAGSVTAVKVKGGRTTKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKlqnllpflepllRKSSEAHRNLSVIKSLRQSENLQVKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFRDSQSMKAVAKGSPLRKR

********EAFCVSPGKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVV*****************************************************LMALIKFLQKK**SII*********EVVLDAV***********************MYSGAREMAAILDTALLQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLH**********************SIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQP**KSSGNIYLTLLQIYLNPRRTTKNFEKQITNLV*************************************************************TIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLL***********************VKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFR*****************

********EAFCVSPGKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCK*************EGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPERLLDI************************************SKKMSHNTLMALIKFLQKKRSSIIEKATAEGTEEVVLDAVGDNFTSHDSTRFK**************AREMAAILDTALLQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEESKSNQSQDEHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWY************AYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIA***SGKSSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQNTTIPKAGSVTAV*V***R*TKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSE**RNLSVIKSLRQSENLQVKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFV********************

MCTHGTIEEAFCVSPGKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPERLLDISSD**********************LSELDENATLKSKKMSHNTLMALIKFLQKKRSSIIEKATAEGTEEVVLDAVGDNFTSH************GTIPMYSGAREMAAILDTALLQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVE*************KFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQNTTIPKAGSVTAVKVKGGRTTKKIASIEGA*************************GDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRQSENLQVKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFRDSQS*************

*****TIEEAFCVSPGKRESVFSDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVLQNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLRAAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKT*********************************************T**SKKMSHNTLMALIKFLQKKRSSIIEKATA******************************GTIPMYSGAREMAAILDTALLQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEESK******EHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQ****SSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQNTTIPKAGSVTAVKVKGGRTTKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRQSENLQVKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFRD****************

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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		816	2.2.26 [Sep-21-2011]
Q8R5L3		886	Vam6/Vps39-like protein O	yes	no	0.784	0.722	0.266	2e-54
Q96JC1		886	Vam6/Vps39-like protein O	yes	no	0.780	0.718	0.267	2e-52
Q3UR70		860	Transforming growth facto	no	no	0.736	0.698	0.238	7e-21
Q8WUH2		860	Transforming growth facto	no	no	0.623	0.591	0.261	2e-19
A4IG72		863	Transforming growth facto	no	no	0.593	0.560	0.260	6e-19
A7MB11		859	Transforming growth facto	no	no	0.587	0.557	0.253	6e-18
O13955		905	Vacuolar morphogenesis pr	yes	no	0.613	0.553	0.243	3e-17
Q07468		1049	Vacuolar morphogenesis pr	yes	no	0.305	0.237	0.235	1e-08

>sp\|Q8R5L3\|VPS39_MOUSE Vam6/Vps39-like protein OS=Mus musculus GN=Vps39 PE=2 SV=1	Back alignment and function desciption

 Score =  214 bits (546), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 213/798 (26%), Positives = 369/798 (46%), Gaps = 158/798 (19%)

Query: 27  ENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVL 86
           +++ V +++ G   Q   + W++ P+A+  Q PY +A+LPR VE+R+L  P  L+Q+I L
Sbjct: 223 DDLTVVLNEEGICTQKCALNWTDIPVAMEHQPPYIVAVLPRYVEIRTLE-PRLLVQSIEL 281

Query: 87  QNVRHLIPS-SNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASL 145
           Q  R +    SN + VA  + ++ L PVP+  QI QL     FE AL L ++   +D S 
Sbjct: 282 QRPRFITSGGSNIIYVASNHFVWRLIPVPMATQIQQLLQDKQFELALQLAEM---KDDSD 338

Query: 146 RAAKEGSIHIR--FAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPE 203
              ++   HI+  +A  LF    ++E+M+ F     D T+ + LYP + LP      +  
Sbjct: 339 SEKQQQIHHIKNLYAFNLFCQKRFDESMQVFAKLGTDPTHVMGLYPDL-LPT-----DYR 392

Query: 204 RLLDISSDAPSLSRGSSGMSDDMESSPPAQLSELDENATLKSKKMSHNTLMALIKFLQKK 263
           + L   +  P+LS                  +EL++         +H   +ALI +L +K
Sbjct: 393 KQLQYPNPLPTLSG-----------------AELEK---------AH---LALIDYLTQK 423

Query: 264 RSSIIEKATAEGTEEVVLDAVGDNFTSHDSTRFKKSSKGRGTIPMYSGAREMAAILDTAL 323
           RS +++K                N + H S+    S    GT P     +++  I+DT L
Sbjct: 424 RSQLVKKL---------------NDSDHQSS---TSPLMEGT-PTIKSKKKLLQIIDTTL 464

Query: 324 LQALLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHE 383
           L+  L T  +  A  L    N+C ++  E +L+K + Y+ L+ LY+    H +AL++L  
Sbjct: 465 LKCYLHTNVALVAPLLRLENNHCHIEESEHVLKKAHKYSELIILYEKKGLHEKALQVL-- 522

Query: 384 LVEESK-SNQSQDEHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLS 442
            V++SK +N     H      E  ++YL+ L   +  L+  +S+ VL   P   +++F  
Sbjct: 523 -VDQSKKANSPLKGH------ERTVQYLQHLGTENLHLIFSYSVWVLRDFPEDGLKIFTE 575

Query: 443 G-----NIPADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWY 497
                 ++P D V ++L +   ++   YLE ++ + E +      N ++Q+Y  +V    
Sbjct: 576 DLPEVESLPRDRVLNFLIENFKALAIPYLEHIIHVWEET-GSQFHNCLIQLYCEKVQSLM 634

Query: 498 SDL---------SAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAI 548
            D                +       R+KLL  LE  S Y+P  L+   P D L EERA+
Sbjct: 635 KDYLLSLPTGKSPVPAGEEGGELGEYRQKLLMFLEISSHYDPGRLICDFPFDGLLEERAL 694

Query: 549 LLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPR 608
           LLG+M +HE AL +YVH L   ++A  YC + Y+      + + + ++YL+LL++YL+P 
Sbjct: 695 LLGRMGKHEQALFIYVHVLKDTKMAKEYCHKHYDQ-----NKEGNKDVYLSLLRMYLSP- 748

Query: 609 RTTKNFEKQITNLVSSQNTTIPKAGSVTAVKVKGGRTTKKIASIEGA-EDMRMSPSSTDS 667
                                P    +  +K++     +  A+++ A + + +  S  D+
Sbjct: 749 ---------------------PSIHCLGPIKLE---LLEPQANLQAALQVLELHYSKLDT 784

Query: 668 GRSDGDAEEFSEEGDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLL 727
            ++       ++  D  I +++VL+  +Q+  R N             L+NLL       
Sbjct: 785 TKAINLLPANTQINDIRIFLEKVLEENAQK-KRFNQV-----------LKNLL------- 825

Query: 728 RKSSEAHRNLSVIKSLRQSENLQVKDE--LYNQRKTVVKITSDSMCSLCSKKIGTSVFAV 785
                             +E L+V++E  L+ Q K +  IT + +C +C KKIG S FA 
Sbjct: 826 -----------------HAEFLRVQEERILHQQVKCI--ITEEKVCMVCKKKIGNSAFAR 866

Query: 786 YPNGKTIVHFVCFRDSQS 803
           YPNG  +VH+ C ++  S
Sbjct: 867 YPNG-VVVHYFCSKEVNS 883

May play a role in clustering and fusion of late endosomes and lysosomes.
Mus musculus (taxid: 10090)

>sp\|Q96JC1\|VPS39_HUMAN Vam6/Vps39-like protein OS=Homo sapiens GN=VPS39 PE=1 SV=2	Back alignment and function description

>sp\|Q3UR70\|TGFA1_MOUSE Transforming growth factor-beta receptor-associated protein 1 OS=Mus musculus GN=Tgfbrap1 PE=2 SV=1	Back alignment and function description

>sp\|Q8WUH2\|TGFA1_HUMAN Transforming growth factor-beta receptor-associated protein 1 OS=Homo sapiens GN=TGFBRAP1 PE=1 SV=1	Back alignment and function description

>sp\|A4IG72\|TGFA1_DANRE Transforming growth factor-beta receptor-associated protein 1 homolog OS=Danio rerio GN=tgfbrap1 PE=2 SV=1	Back alignment and function description

>sp\|A7MB11\|TGFA1_BOVIN Transforming growth factor-beta receptor-associated protein 1 OS=Bos taurus GN=TGFBRAP1 PE=2 SV=1	Back alignment and function description

>sp\|O13955\|VAM6_SCHPO Vacuolar morphogenesis protein 6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=vam6 PE=3 SV=1	Back alignment and function description

>sp\|Q07468\|VAM6_YEAST Vacuolar morphogenesis protein 6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=VAM6 PE=1 SV=1	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		816
224134292		1008	predicted protein [Populus trichocarpa]	0.968	0.783	0.832	0.0
297735158		924	unnamed protein product [Vitis vinifera]	0.968	0.854	0.830	0.0
225430766		1006	PREDICTED: vam6/Vps39-like protein [Viti	0.968	0.785	0.830	0.0
255561166		972	conserved hypothetical protein [Ricinus	0.927	0.778	0.810	0.0
449462842		996	PREDICTED: vam6/Vps39-like protein-like	0.952	0.780	0.8	0.0
449517638		996	PREDICTED: LOW QUALITY PROTEIN: vam6/Vps	0.952	0.780	0.796	0.0
356496767		989	PREDICTED: vam6/Vps39-like protein-like	0.959	0.791	0.778	0.0
356538190		989	PREDICTED: vam6/Vps39-like protein-like	0.958	0.790	0.773	0.0
297798238		1000	hypothetical protein ARALYDRAFT_490975 [	0.966	0.789	0.75	0.0
240256190		1000	Vacuolar sorting protein 39 [Arabidopsis	0.966	0.789	0.744	0.0

>gi\|224134292\|ref\|XP_002327802.1\| predicted protein [Populus trichocarpa] gi\|222836887\|gb\|EEE75280.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1340 bits (3469), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 658/790 (83%), Positives = 726/790 (91%)

Query: 27   ENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEVRSLRVPYALIQTIVL 86
            +NIGVFVDQNGK LQA++ICWSEAP  V+IQK YAI+LLPRR+E+RSLRVPY+LIQ  VL
Sbjct: 219  DNIGVFVDQNGKHLQAEKICWSEAPSLVVIQKSYAISLLPRRIEIRSLRVPYSLIQAFVL 278

Query: 87   QNVRHLIPSSNAVVVALENSIFGLFPVPLGAQIVQLTASGDFEEALALCKLLPPEDASLR 146
            QNVRHLI S+NA++VAL NS+  LFPVPLGAQIVQLTASG+FEEALALCKLLPPED++LR
Sbjct: 279  QNVRHLIESNNAIIVALSNSVRALFPVPLGAQIVQLTASGNFEEALALCKLLPPEDSNLR 338

Query: 147  AAKEGSIHIRFAHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPERLL 206
            AAKEGSIHIR+AHYLFD GSYEEAMEHFLASQVDI Y LSLYPSIVLPKT++VPE E+L+
Sbjct: 339  AAKEGSIHIRYAHYLFDNGSYEEAMEHFLASQVDIIYVLSLYPSIVLPKTSLVPEREKLI 398

Query: 207  DISSDAPSLSRGSSGMSDDMESSPPAQLSELDENATLKSKKMSHNTLMALIKFLQKKRSS 266
            DIS DAP LSRGS G+SD ME SPP  LS+ DE++ L+SKKMSHNTLMALIK+LQK+R  
Sbjct: 399  DISQDAPYLSRGSCGLSDIMEPSPPIHLSDFDEHSALESKKMSHNTLMALIKYLQKRRFG 458

Query: 267  IIEKATAEGTEEVVLDAVGDNFTSHDSTRFKKSSKGRGTIPMYSGAREMAAILDTALLQA 326
            I+EKATAEGT+EVVLDAVGDN+  +DS RFKKS+KGRG I + SGAREMAAILDTALLQA
Sbjct: 459  IVEKATAEGTDEVVLDAVGDNYGPYDSNRFKKSNKGRGNIAINSGAREMAAILDTALLQA 518

Query: 327  LLLTGQSSAALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVE 386
            LLLTGQ+SAALELLKGLNYCD+KICEEILQK NHYTALLELYK NA HREALKLLH+LVE
Sbjct: 519  LLLTGQTSAALELLKGLNYCDLKICEEILQKWNHYTALLELYKCNAMHREALKLLHQLVE 578

Query: 387  ESKSNQSQDEHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIP 446
            ESKSNQS+ E   KF PESI+EYLKPLC TDPMLVLEFSMLVLESCPTQTIEL LSGNIP
Sbjct: 579  ESKSNQSKPELNPKFKPESIVEYLKPLCWTDPMLVLEFSMLVLESCPTQTIELLLSGNIP 638

Query: 447  ADLVNSYLKQYSPSMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKW 506
            ADLVNSYLKQ++PSMQGRYLELML MNEN ISGNLQNEMVQIYLSEVLDW+++L+AQ+KW
Sbjct: 639  ADLVNSYLKQHAPSMQGRYLELMLVMNENGISGNLQNEMVQIYLSEVLDWHAELNAQEKW 698

Query: 507  DEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHK 566
            DEKAYSPTR KLLSALESISGYNPE LLKRLPADALYEERA+LLGKMNQHELALSLYVHK
Sbjct: 699  DEKAYSPTRNKLLSALESISGYNPEALLKRLPADALYEERALLLGKMNQHELALSLYVHK 758

Query: 567  LCVPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQN 626
            L VP+LAL+YCDRVYES AH PS KSSGNIYLTLLQIYLNPR+TT NFEK+ITNLVS QN
Sbjct: 759  LHVPDLALSYCDRVYESAAHLPSAKSSGNIYLTLLQIYLNPRKTTMNFEKRITNLVSFQN 818

Query: 627  TTIPKAGSVTAVKVKGGRTTKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIM 686
            T +PK  SVT VK KGGR TKKIA+IEGAED+R+SPS TDS RSDGDA+EF +EG STIM
Sbjct: 819  TNVPKVSSVTPVKAKGGRATKKIAAIEGAEDLRVSPSGTDSSRSDGDADEFGDEGGSTIM 878

Query: 687  IDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRQS 746
            +D+VLDLLS+RWDRINGAQALKLLPRETKLQNLLPFL PLL+KSSEA+RNLSVIKSLRQS
Sbjct: 879  LDEVLDLLSKRWDRINGAQALKLLPRETKLQNLLPFLGPLLKKSSEAYRNLSVIKSLRQS 938

Query: 747  ENLQVKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFRDSQSMKA 806
            ENLQV+DE+YN+RKTVVKITSD+ CSLC+KKIGTSVFAVYPNGKTIVHFVCF+DSQS+KA
Sbjct: 939  ENLQVRDEMYNRRKTVVKITSDTTCSLCNKKIGTSVFAVYPNGKTIVHFVCFKDSQSIKA 998

Query: 807  VAKGSPLRKR 816
            VAKGS LRKR
Sbjct: 999  VAKGSALRKR 1008

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297735158\|emb\|CBI17520.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225430766\|ref\|XP_002267514.1\| PREDICTED: vam6/Vps39-like protein [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255561166\|ref\|XP_002521595.1\| conserved hypothetical protein [Ricinus communis] gi\|223539273\|gb\|EEF40866.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|449462842\|ref\|XP_004149149.1\| PREDICTED: vam6/Vps39-like protein-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449517638\|ref\|XP_004165852.1\| PREDICTED: LOW QUALITY PROTEIN: vam6/Vps39-like protein-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356496767\|ref\|XP_003517237.1\| PREDICTED: vam6/Vps39-like protein-like [Glycine max]	Back alignment and taxonomy information

>gi\|356538190\|ref\|XP_003537587.1\| PREDICTED: vam6/Vps39-like protein-like [Glycine max]	Back alignment and taxonomy information

>gi\|297798238\|ref\|XP_002867003.1\| hypothetical protein ARALYDRAFT_490975 [Arabidopsis lyrata subsp. lyrata] gi\|297312839\|gb\|EFH43262.1\| hypothetical protein ARALYDRAFT_490975 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|240256190\|ref\|NP_195381.6\| Vacuolar sorting protein 39 [Arabidopsis thaliana] gi\|20466826\|gb\|AAM20730.1\| unknown protein [Arabidopsis thaliana] gi\|332661279\|gb\|AEE86679.1\| Vacuolar sorting protein 39 [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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		816
pfam10367		109	pfam10367, Vps39_2, Vacuolar sorting protein 39 do	8e-41
pfam10366		105	pfam10366, Vps39_1, Vacuolar sorting protein 39 do	2e-30
pfam00780		266	pfam00780, CNH, CNH domain	3e-11
pfam00637		143	pfam00637, Clathrin, Region in Clathrin and VPS	2e-05
pfam00637		143	pfam00637, Clathrin, Region in Clathrin and VPS	0.002
smart00299		140	smart00299, CLH, Clathrin heavy chain repeat homol	0.002

>gnl\|CDD\|150957 pfam10367, Vps39_2, Vacuolar sorting protein 39 domain 2	Back alignment and domain information

 Score =  145 bits (367), Expect = 8e-41
 Identities = 51/110 (46%), Positives = 73/110 (66%), Gaps = 1/110 (0%)

Query: 691 LDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRQSENLQ 750
           LDLL++  +RI+ A  L LLP +  LQ L  FLE  LR S+E  R   V+K+L ++ENLQ
Sbjct: 1   LDLLNKHGERIDPASVLDLLPDDVPLQLLESFLERALRNSTEQKREAQVVKNLLKAENLQ 60

Query: 751 VKDELYNQRKTVVKITSDSMCSLCSKKIGTSVFAVYPNGKTIVHFVCFRD 800
           V++EL   R   V++T +S+C++C K++G SVF VYPNG  +VH+ C   
Sbjct: 61  VEEELLKLRSRHVRVTEESVCAVCHKRLGNSVFVVYPNG-VVVHYGCADR 109

This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11. Length = 109

>gnl\|CDD\|220718 pfam10366, Vps39_1, Vacuolar sorting protein 39 domain 1	Back alignment and domain information

>gnl\|CDD\|216115 pfam00780, CNH, CNH domain	Back alignment and domain information

>gnl\|CDD\|216037 pfam00637, Clathrin, Region in Clathrin and VPS	Back alignment and domain information

>gnl\|CDD\|216037 pfam00637, Clathrin, Region in Clathrin and VPS	Back alignment and domain information

>gnl\|CDD\|128594 smart00299, CLH, Clathrin heavy chain repeat homology	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		816
KOG2063		877	consensus Vacuolar assembly/sorting proteins VPS39	100.0
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	100.0
KOG2066		846	consensus Vacuolar assembly/sorting protein VPS41	100.0
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	99.96
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	99.91
PF10366		108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	99.86
smart00299		140	CLH Clathrin heavy chain repeat homology.	99.58
PF00637		143	Clathrin: Region in Clathrin and VPS; InterPro: IP	99.34
PF00780		275	CNH: CNH domain; InterPro: IPR001180 Based on sequ	98.99
smart00036		302	CNH Domain found in NIK1-like kinases, mouse citro	98.58
KOG0985		1666	consensus Vesicle coat protein clathrin, heavy cha	98.44
PF05131		147	Pep3_Vps18: Pep3/Vps18/deep orange family; InterPr	97.94
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	97.81
KOG0985		1666	consensus Vesicle coat protein clathrin, heavy cha	97.58
KOG2079		1206	consensus Vacuolar assembly/sorting protein VPS8 [	97.51
KOG2066		846	consensus Vacuolar assembly/sorting protein VPS41	97.34
PF00637		143	Clathrin: Region in Clathrin and VPS; InterPro: IP	97.21
KOG4305		1029	consensus RhoGEF GTPase [Signal transduction mecha	97.16
smart00299		140	CLH Clathrin heavy chain repeat homology.	97.14
COG5422		1175	ROM1 RhoGEF, Guanine nucleotide exchange factor fo	96.96
PLN03081		697	pentatricopeptide (PPR) repeat-containing protein;	95.6
PF10366		108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	94.74
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	93.59
PLN03218		1060	maturation of RBCL 1; Provisional	93.51
PRK11447		1157	cellulose synthase subunit BcsC; Provisional	93.22
PF09943		101	DUF2175: Uncharacterized protein conserved in arch	92.96
COG4847		103	Uncharacterized protein conserved in archaea [Func	91.72
PF14559		68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	91.22
PLN03218		1060	maturation of RBCL 1; Provisional	90.83
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	90.63
KOG2076		895	consensus RNA polymerase III transcription factor	90.33
PLN03077		857	Protein ECB2; Provisional	89.94
PRK11447		1157	cellulose synthase subunit BcsC; Provisional	89.59
PF14446		54	Prok-RING_1: Prokaryotic RING finger family 1	88.29
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	87.16
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	87.14
PLN03077		857	Protein ECB2; Provisional	86.58
KOG1920		1265	consensus IkappaB kinase complex, IKAP component [	86.12
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	85.44
PRK11788		389	tetratricopeptide repeat protein; Provisional	85.05
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	84.9
PLN03081		697	pentatricopeptide (PPR) repeat-containing protein;	84.08
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	83.48
PF14762		374	HPS3_Mid: Hermansky-Pudlak syndrome 3, middle regi	83.46
PRK10747		398	putative protoheme IX biogenesis protein; Provisio	81.78
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	81.32
PF13525		203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	81.3
smart00132		39	LIM Zinc-binding domain present in Lin-11, Isl-1,	81.22
PF13512		142	TPR_18: Tetratricopeptide repeat	80.63
PF13371		73	TPR_9: Tetratricopeptide repeat	80.48

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

Probab=100.00  E-value=9.1e-92  Score=810.06  Aligned_cols=664  Identities=37%  Similarity=0.544  Sum_probs=551.7

Q ss_pred             CCCcccccccCC------cccccccc-----cccccceEEEEcCCCccccCCCccccCCCceEEeeCcEEEEecCCceEE
Q 003482            3 THGTIEEAFCVS------PGKRESVF-----SDMMENIGVFVDQNGKLLQADRICWSEAPIAVIIQKPYAIALLPRRVEV   71 (816)
Q Consensus         3 ~~g~~~~lf~~~------~p~~~~~~-----~~~~d~~gvfv~~~G~~~~~~~i~w~~~p~~v~~~~PYli~l~~~~ieV   71 (816)
                      .+|....+|+++      +|++.++.     +.++|++|||||.+|.+..++|+.|+..|.+|++.+||+|++.++.|||
T Consensus       185 ~~~~~~~~~~s~~~~~s~~P~I~~l~~~~~ll~~kd~~gv~vd~~G~~~~~~~l~ws~~P~~v~~~~PYlIa~~~~~veI  264 (877)
T KOG2063|consen  185 SKGVGPNLFPSSMDNESRKPLIKSLSDQSELLLGKDNIGVVVDLNGIIAQRGTLVWSEVPLSVVVESPYLIALLDRSVEI  264 (877)
T ss_pred             CCccccceeeeccccccCCCeEEEecCCceEEEccCceEEEEecCCcccCCCceEecccchhhcccCceEEEEccccEEE
Confidence            367888889887      58888875     5699999999999999867999999999999999999999999999999


Q ss_pred             EEccCCCcceeEe-eeCCceeeeecCCcEE-EecCCcEEEeccCC-HHHHHHHHHhcCCHHHHHHHhhhCCCcchHHHHh
Q 003482           72 RSLRVPYALIQTI-VLQNVRHLIPSSNAVV-VALENSIFGLFPVP-LGAQIVQLTASGDFEEALALCKLLPPEDASLRAA  148 (816)
Q Consensus        72 ~sl~~~~~~vQti-~l~~~~~l~~~~~~v~-v~s~~~I~~l~~~~-~~~qi~~Ll~~~~~eeAl~L~~~~~~~d~~~~~~  148 (816)
                      |+.. +++++|+| +++.+..+++++++++ +++.+.+|+|.|+| +..||++|+...+|++|++|++.... ..+.+..
T Consensus       265 ~s~~-~~qlvQSI~~~~~~~~l~s~~~~i~~~~~~s~v~~L~p~~~~~~qi~~lL~~k~fe~ai~L~e~~~~-~~p~~~~  342 (877)
T KOG2063|consen  265 RSKL-DGQLVQSITPLSNGRSLLSAHNGIIFVASLSNVWILVPVSNFEKQIQDLLQEKSFEEAISLAEILDS-PNPKEKR  342 (877)
T ss_pred             Eecc-CHHHhhccccccccceeeecCCcEEEEEeccceEEEEeccchHHHHHHHHHhhhHHHHHHHHhccCC-CChHHHH
Confidence            9996 88999999 9999988887766655 55559999999999 99999999999999999999998753 3344444


Q ss_pred             hHHHHHHHH-HHHHhcCCCHHHHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCCCCCCCC
Q 003482          149 KEGSIHIRF-AHYLFDTGSYEEAMEHFLASQVDITYALSLYPSIVLPKTTVVPEPERLLDISSDAPSLSRGSSGMSDDME  227 (816)
Q Consensus       149 ~~~~i~~~~-a~~Lf~~~~f~~A~~~f~~~~~dP~~vi~LFp~l~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~  227 (816)
                      .+..++.++ |+.+|.+++|++||.+|.++.+||+.||+|||+++|..... .   .+....+.                
T Consensus       343 ~i~~~~~l~~a~~lf~q~~f~ea~~~F~~~~~d~~~vi~lfP~l~p~~~~~-~---~~~~~vp~----------------  402 (877)
T KOG2063|consen  343 QISCIKILIDAFELFLQKQFEEAMSLFEKSEIDPRHVISLFPDLLPSENSS-I---EFTGVVPI----------------  402 (877)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHhhccChHHHHHhchhhcCCcccc-c---ceeeeccC----------------
Confidence            567777777 89999999999999999999999999999999997644421 0   11111110                


Q ss_pred             CCCCCCCCcchhhhhhhhhhhhHHHHHHHHHHHHHHhHHHHHhhhccCchhHhhhcccCCCCCCCcccccccCCCCCCCC
Q 003482          228 SSPPAQLSELDENATLKSKKMSHNTLMALIKFLQKKRSSIIEKATAEGTEEVVLDAVGDNFTSHDSTRFKKSSKGRGTIP  307 (816)
Q Consensus       228 ~~~~~~l~~~~~~~~le~~~~~~~a~~~L~~yL~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  307 (816)
                        +.+.+..++        ..  .|..+++.||+..|+...++.+......          +    +.+++   ...+..
T Consensus       403 --~~~~~~~~~--------~v--~a~l~~~~ylt~~r~~~~~~l~~~~m~~----------~----~~~~~---~~~s~~  453 (877)
T KOG2063|consen  403 --RAPELRGGD--------LV--PAVLALIVYLTQSRREENKKLNKYKMLY----------M----NYFKN---TLISEL  453 (877)
T ss_pred             --chhhhccCc--------cc--chhhhhhhHhHHHHHHHHHHHHHhhhhH----------H----hhhhc---cCcchh
Confidence              000111111        11  3556899999998887655443221110          0    00000   001111


Q ss_pred             CcccHHHHHHHHHHHHHHHHHhcCCchhHHhhhcCCC-cccHHHHHHHHHhcCCHHHHHHHHHHhccHHHHHHHHHHHHh
Q 003482          308 MYSGAREMAAILDTALLQALLLTGQSSAALELLKGLN-YCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVE  386 (816)
Q Consensus       308 ~~~~~~~~~~~vDT~Llk~yl~~~~~~~l~~ll~~~n-~c~~~~~~~~L~~~~~~~~L~~Ly~~~g~~~~AL~ll~~l~~  386 (816)
                      ...+...++++|||+|||||+++++ ....+++|.+| +|++++++.+|+++++|.+|+.||+.+|+|++||++|+++++
T Consensus       454 ~~~~~~~~~~~IDttLlk~Yl~~n~-~~v~~llrlen~~c~vee~e~~L~k~~~y~~Li~LY~~kg~h~~AL~ll~~l~d  532 (877)
T KOG2063|consen  454 LKSDLNDILELIDTTLLKCYLETNP-GLVGPLLRLENNHCDVEEIETVLKKSKKYRELIELYATKGMHEKALQLLRDLVD  532 (877)
T ss_pred             hccchHHHHHHHHHHHHHHHHhcCc-hhhhhhhhccCCCcchHHHHHHHHhcccHHHHHHHHHhccchHHHHHHHHHHhc
Confidence            2234567899999999999999986 46779998876 999999999999999999999999999999999999999998


Q ss_pred             hhc-CCCCcccccccCChHHHHHHhcccCCCChHHHHHhHHhhhhhCcccccccccc------CCCChHHHHHHHhhcCh
Q 003482          387 ESK-SNQSQDEHTQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLS------GNIPADLVNSYLKQYSP  459 (816)
Q Consensus       387 ~~~-~d~~~~~~~~~~~~~~~i~yL~~L~~~~~~li~~y~~wll~~~p~~~i~if~~------~~l~~~~Vl~~L~~~~~  459 (816)
                      +.. .|.     ....+++.+++||++++.++.++||+|+.|+++++|+.|++||++      +++++++|++||.+..+
T Consensus       533 ~~~~~d~-----~~~~~~e~ii~YL~~l~~~~~~Li~~y~~wvl~~~p~~gi~Ift~~~~~~~~sis~~~Vl~~l~~~~~  607 (877)
T KOG2063|consen  533 EDSDTDS-----FQLDGLEKIIEYLKKLGAENLDLILEYADWVLNKNPEAGIQIFTSEDKQEAESISRDDVLNYLKSKEP  607 (877)
T ss_pred             ccccccc-----chhhhHHHHHHHHHHhcccchhHHHHHhhhhhccCchhheeeeeccChhhhccCCHHHHHHHhhhhCc
Confidence            763 333     233467889999999999999999999999999999999999998      35999999999999999


Q ss_pred             hhHHHHHHHHHhhhcCCCCchhHHHHHHHHHHHHHH-HhhhhhhhhccCc-ccchHHHHHHHHHHhhhCCCChHHHhccC
Q 003482          460 SMQGRYLELMLAMNENSISGNLQNEMVQIYLSEVLD-WYSDLSAQQKWDE-KAYSPTRKKLLSALESISGYNPEVLLKRL  537 (816)
Q Consensus       460 ~~~~~YLE~li~~~~~~~~~~~h~~Li~lYl~~l~~-~~~~~~~~~~~~~-~~~~~~r~kL~~fL~~s~~Yd~~~~L~~~  537 (816)
                      .+.+.||||+|.+++ ..+..|||.|+.+|++.+.+ ...+    +++++ .+.. +|+||+.||+.|+.|+++.+|..+
T Consensus       608 ~l~I~YLE~li~~~~-~~~~~lht~ll~ly~e~v~~~~~~~----~kg~e~~E~~-~rekl~~~l~~s~~Y~p~~~L~~~  681 (877)
T KOG2063|consen  608 KLLIPYLEHLISDNR-LTSTLLHTVLLKLYLEKVLEQASTD----GKGEEAPETT-VREKLLDFLESSDLYDPQLLLERL  681 (877)
T ss_pred             chhHHHHHHHhHhcc-ccchHHHHHHHHHHHHHHhhccCch----hccccchhhh-HHHHHHHHhhhhcccCcchhhhhc
Confidence            999999999998763 45789999999999999984 2111    11111 1111 599999999999999999999999


Q ss_pred             CCCchhHHHHHHHhhcccHHHHHHHHHHhcCCHHHHHHHHHHhhhhccCCCCCCCCccHHHHHHHHhcCCCCCchhhhhh
Q 003482          538 PADALYEERAILLGKMNQHELALSLYVHKLCVPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNFEKQ  617 (816)
Q Consensus       538 ~~~~l~~e~a~Ll~rlg~h~~AL~ilv~~L~D~~~Ae~YC~~~~~~~~~~~~~~~~~~l~~~Ll~~yl~~~~~~~~~~~~  617 (816)
                      +.+.|++|+++++||+|+|++||+||++.|+|+++|+.||..+|+.      +..+.++|.+||++|+.+..+   +   
T Consensus       682 ~~~~l~ee~aill~rl~khe~aL~Iyv~~L~d~~~A~~Yc~~~y~~------~~~~~~~y~~lL~~~l~~~~d---~---  749 (877)
T KOG2063|consen  682 NGDELYEERAILLGRLGKHEEALHIYVHELDDIDAAESYCLPQYES------DKTNKEIYLTLLRIYLNPIHD---Y---  749 (877)
T ss_pred             cchhHHHHHHHHHhhhhhHHHHHHHHHHHhcchhHHHHHHHHhccC------CCcccHHHHHHHHHHhcchhh---c---
Confidence            9999999999999999999999999999999999999999999972      245789999999999986221   0   


Q ss_pred             hhhcccCCCCCCCCCCCccceeccCCccccchhhhcccccccCCCCCCCCCCCCCCcccccccCCchhcHHHHHHHHhhc
Q 003482          618 ITNLVSSQNTTIPKAGSVTAVKVKGGRTTKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLLSQR  697 (816)
Q Consensus       618 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lL~~~  697 (816)
                                                                                    .++    .-.++.+|++|
T Consensus       750 --------------------------------------------------------------~~~----~~~il~~l~~h  763 (877)
T KOG2063|consen  750 --------------------------------------------------------------KSG----PLYILNFLQKH  763 (877)
T ss_pred             --------------------------------------------------------------ccc----chhhhhHHHhh
Confidence                                                                          000    24677799999


Q ss_pred             cCCCCHHHHhhcCCCccchhhhHHHHHHHHHhHHHHHHHHHHHHHHHHhhhHHHHHHHHhcccceEEECCCCcCCcCCCc
Q 003482          698 WDRINGAQALKLLPRETKLQNLLPFLEPLLRKSSEAHRNLSVIKSLRQSENLQVKDELYNQRKTVVKITSDSMCSLCSKK  777 (816)
Q Consensus       698 ~~~ld~~~vL~~LP~~~~l~~l~~fL~~~lr~~~~~~r~~~i~~~l~~~~~~~~~~el~~~~s~~v~I~~~~~C~vC~k~  777 (816)
                      ++++|+..|+++||++|++..+.+|+.+.||...+.+|+.++.+++++++++...+++.+.++.+++|+.+..|.+|.|+
T Consensus       764 ~~r~d~~~~~~~Lp~~~sl~~~~~~l~~~Lr~~~~~~r~~q~~~~l~q~E~~~~~~~l~~~~s~~~~l~~~~~C~~C~k~  843 (877)
T KOG2063|consen  764 ADRLDLAQVLKLLPDDISLKDLCSFLSKLLRKRFEALRTTQVQKSLLQAELLPSTEELNKLRSSKIQLNDESLCSICEKR  843 (877)
T ss_pred             hhhcCHHHHHHhCCccCcHhHHHHHHHHHHHHHHHhcchhHHHHHHHHHhhcchHHHHHHhhcceEEEchhhHhHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCceEEEccCCCeEEEeccCCCccchhccc
Q 003482          778 IGTSVFAVYPNGKTIVHFVCFRDSQSMKAVA  808 (816)
Q Consensus       778 l~~~~f~v~p~g~~v~H~~C~~~~~~~~~~~  808 (816)
                      ||.++|++|||| +++|++|+++.|+...+.
T Consensus       844 i~~s~f~ryp~g-~lvh~~C~~~~q~~~~~~  873 (877)
T KOG2063|consen  844 IGTSVFVRYPNG-ILVHLSCAKDLQGSKAVK  873 (877)
T ss_pred             hcCeeEEECCCC-cEEEEEeechhccccccC
Confidence            999999999999 999999999988775543

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1	Back alignment and domain information

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1	Back alignment and domain information

>smart00299 CLH Clathrin heavy chain repeat homology	Back alignment and domain information

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>PF00780 CNH: CNH domain; InterPro: IPR001180 Based on sequence similarities a domain of homology has been identified in the following proteins []: Citron and Citron kinase	Back alignment and domain information

>smart00036 CNH Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2	Back alignment and domain information

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF05131 Pep3_Vps18: Pep3/Vps18/deep orange family; InterPro: IPR007810 This region is found in a number of proteins identified as being involved in Golgi function and vacuolar sorting	Back alignment and domain information

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG2079 consensus Vacuolar assembly/sorting protein VPS8 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>KOG4305 consensus RhoGEF GTPase [Signal transduction mechanisms]	Back alignment and domain information

>smart00299 CLH Clathrin heavy chain repeat homology	Back alignment and domain information

>COG5422 ROM1 RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]	Back alignment and domain information

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional	Back alignment and domain information

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1	Back alignment and domain information

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B	Back alignment and domain information

>PLN03218 maturation of RBCL 1; Provisional	Back alignment and domain information

>PRK11447 cellulose synthase subunit BcsC; Provisional	Back alignment and domain information

>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function	Back alignment and domain information

>COG4847 Uncharacterized protein conserved in archaea [Function unknown]	Back alignment and domain information

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A	Back alignment and domain information

>PLN03218 maturation of RBCL 1; Provisional	Back alignment and domain information

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A	Back alignment and domain information

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]	Back alignment and domain information

>PLN03077 Protein ECB2; Provisional	Back alignment and domain information

>PRK11447 cellulose synthase subunit BcsC; Provisional	Back alignment and domain information

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1	Back alignment and domain information

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A	Back alignment and domain information

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A	Back alignment and domain information

>PLN03077 Protein ECB2; Provisional	Back alignment and domain information

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]	Back alignment and domain information

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein	Back alignment and domain information

>PRK11788 tetratricopeptide repeat protein; Provisional	Back alignment and domain information

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional	Back alignment and domain information

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A	Back alignment and domain information

>PF14762 HPS3_Mid: Hermansky-Pudlak syndrome 3, middle region	Back alignment and domain information

>PRK10747 putative protoheme IX biogenesis protein; Provisional	Back alignment and domain information

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A	Back alignment and domain information

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

>PF13512 TPR_18: Tetratricopeptide repeat	Back alignment and domain information

>PF13371 TPR_9: Tetratricopeptide repeat	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		816
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-16
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-11
1xi4_A		1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	9e-11

>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 = 82.6 bits (203), Expect = 3e-16
 Identities = 95/656 (14%), Positives = 191/656 (29%), Gaps = 203/656 (30%)

Query: 154 HIRFAHYLFDTG----SYEEAMEHFLASQV---DITYALSLYPSIVLPKTTV-----VPE 201
           H    H  F+TG     Y++ +  F  + V   D        P  +L K  +       +
Sbjct: 1   HHHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQD-MPKSILSKEEIDHIIMSKD 59

Query: 202 PE----RLLDISSDAPSLSRGSSGMSDDMESSPPAQLSELDENATLKSKKMSHNTLMALI 257
                 RL         LS+    +   +E         L  N         +  LM+ I
Sbjct: 60  AVSGTLRLFWTL-----LSKQEEMVQKFVEEV-------LRIN---------YKFLMSPI 98

Query: 258 KFLQKKRSSIIEKATAEGTEEVVLDAVGDNFTSHDSTRFKKSSKGRGTIPMYSGAREMAA 317
           K  Q++ S +         +   L      F  ++ +R +   K                
Sbjct: 99  KTEQRQPSMMTRMYI---EQRDRLYNDNQVFAKYNVSRLQPYLK---------------- 139

Query: 318 ILDTALLQA-----LLL-----TGQSSAALELLK----------GLNYCDVKIC---EEI 354
            L  ALL+      +L+     +G++  AL++             + + ++K C   E +
Sbjct: 140 -LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198

Query: 355 LQK-KNHYTALLELYKSNARHREALKLLHELVEESKSN--QSQD--------------EH 397
           L+  +     +   + S + H   +KL    ++       +S+               + 
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258

Query: 398 TQKFNPE----------SIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLS--GNI 445
              FN             + ++L     T   L      L     P +   L L      
Sbjct: 259 WNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT----PDEVKSLLLKYLDCR 314

Query: 446 PADLVNSYLKQYSP---SMQGRYLELMLAMNEN--SISGNLQNEMVQIYLSEVLD----- 495
           P DL    +   +P   S+    +   LA  +N   ++ +    +++  L  VL+     
Sbjct: 315 PQDLPRE-VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL-NVLEPAEYR 372

Query: 496 -WYSDLSAQQKWDEKAYSPTRKKLLSALESISGYNPEVLLKRLPADALYEERAILLGKMN 554
             +  LS                       I    P +LL  +  D +  +  +++ K++
Sbjct: 373 KMFDRLSVFPP-SAH---------------I----PTILLSLIWFDVIKSDVMVVVNKLH 412

Query: 555 Q---------------HELALSL--------YVHKLCVP--ELALAYC---------DR- 579
           +                 + L L         +H+  V    +   +          D+ 
Sbjct: 413 KYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472

Query: 580 VYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNF-EKQITNLVSSQNTTIPKAGSVTAV 638
            Y  I H                ++L+ R     F E++I +  ++ N +     ++  +
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFR-----FLEQKIRHDSTAWNASGSILNTLQQL 527

Query: 639 KVKGGRTTKKIASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLL 694
           K             E               R      +F  + +  ++  +  DLL
Sbjct: 528 KFYKPYICDNDPKYE---------------RLVNAILDFLPKIEENLICSKYTDLL 568

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

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A Length = 1630	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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		816
d1b89a_		336	a.118.1.3 (A:) Clathrin heavy chain proximal leg s	1e-05

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]} Length = 336	Back information, alignment and structure


class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 30/247 (12%), Positives = 69/247 (27%), Gaps = 47/247 (19%)

Query: 338 ELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEESKSNQSQDEH 397
           E + G N   ++   +    +  Y A   LY + +        L  L             
Sbjct: 7   EFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLG------------ 54

Query: 398 TQKFNPESIIEYLKPLCGTDPMLVLEFSMLVLESCPTQTIELFLSGNIP-ADLVNSYLKQ 456
                 ++ ++  +           E     ++    +  ++     +  AD +   +  
Sbjct: 55  ----EYQAAVDGARKA--NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINY 108

Query: 457 YSPSMQGRYLELML----AMNENSISGNLQNEMVQIYLSEVLDWYSDLSAQQKWDEKAYS 512
           Y    +G + EL+     A+        +  E+  +Y                       
Sbjct: 109 YQD--RGYFEELITMLEAALGLERAHMGMFTELAILYSKFK------------------- 147

Query: 513 PTRKKLLSALESISG-YNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLCVPE 571
              +K+   LE      N   +L+      L+ E   L  K  +++ A+   ++      
Sbjct: 148 --PQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAW 205

Query: 572 LALAYCD 578
               + D
Sbjct: 206 KEGQFKD 212

PyMOL of d1b89a_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		816
d1b89a_		336	Clathrin heavy chain proximal leg segment {Cow (Bo	99.91
d1b89a_		336	Clathrin heavy chain proximal leg segment {Cow (Bo	99.44
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	89.04
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	87.99
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	87.87
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	87.86
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	87.0
d1rutx3		31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	86.3
d1zbpa1		264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	83.91
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	81.5

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.91  E-value=9.2e-23  Score=156.57  Aligned_cols=273  Identities=16%  Similarity=0.154  Sum_probs=214.2

Q ss_pred             HHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             68865137995158999999986398799999999800599999999998740017877321003689378999720169
Q 003482          335 AALELLKGLNYCDVKICEEILQKKNHYTALLELYKSNARHREALKLLHELVEESKSNQSQDEHTQKFNPESIIEYLKPLC  414 (816)
Q Consensus       335 ~l~~ll~~~n~c~~~~~~~~L~~~~~~~~L~~Ly~~~g~~~~AL~ll~~l~~~~~~d~~~~~~~~~~~~~~~i~yL~~L~  414 (816)
                      .+..|++++|+|++.++.+.|.+.+.|.+++.+|...+++++++.+|.++.+                .+.+++++++. 
T Consensus         4 ~~e~fl~~~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d~~rl~~~~v~l~~----------------~~~avd~~~k~-   66 (336)
T d1b89a_           4 ELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGE----------------YQAAVDGARKA-   66 (336)
T ss_dssp             HHTTTTTCC----------------CTTTHHHHHHHTTCHHHHHHHHHTTTC----------------HHHHHHHHHHH-
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHCC----------------HHHHHHHHHHC-
T ss_conf             6999875898578999999998787799999999867899999999970315----------------99999999880-


Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCCC-CCCCHHHH---HHHHHH-CCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             9985889995786542086231012344-78896789---999841-092018889999886102777801499999999
Q 003482          415 GTDPMLVLEFSMLVLESCPTQTIELFLS-GNIPADLV---NSYLKQ-YSPSMQGRYLELMLAMNENSISGNLQNEMVQIY  489 (816)
Q Consensus       415 ~~~~~li~~~~~wll~~~p~~~i~if~~-~~l~~~~V---l~~L~~-~~~~l~~~YLE~li~~~~~~~~~~~h~~L~~lY  489 (816)
                       ...+++.++..++++.++....++... ..+.++.+   +...+. .....++.|||..+..  ...+..+|++|+.+|
T Consensus        67 -~~~~~~k~~~~~l~~~~e~~la~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~--~~~~~~~~~~L~~ly  143 (336)
T d1b89a_          67 -NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL--ERAHMGMFTELAILY  143 (336)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--TTCCHHHHHHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCCCHHHHHHHHHHH
T ss_conf             -88999999999997272878999999875357887899999998769859999999999757--744467999999999


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH-HCCCCHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCC
Q ss_conf             99999774332221013721011879999999753-08999578960089985038999997200209999999999509
Q 003482          490 LSEVLDWYSDLSAQQKWDEKAYSPTRKKLLSALES-ISGYNPEVLLKRLPADALYEERAILLGKMNQHELALSLYVHKLC  568 (816)
Q Consensus       490 l~~i~~~~~~~~~~~~~~~~~~~~~r~kL~~fL~~-s~~Yd~~~~L~~i~~~~l~~E~aiL~~rlg~h~~AL~ilv~~L~  568 (816)
                      ...                     .+.|++.||+. |+.||+++++..|....+++|.++||+|+|+|++|+.+++....
T Consensus       144 ak~---------------------~~~kl~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~  202 (336)
T d1b89a_         144 SKF---------------------KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPT  202 (336)
T ss_dssp             HTT---------------------CHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTT
T ss_pred             HHH---------------------CHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHCCH
T ss_conf             986---------------------94999999986023599999999988748749999999855879999999997654


Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCC
Q ss_conf             97899999998601035899999976479999998549997750234433200367788888888754100048865200
Q 003482          569 VPELALAYCDRVYESIAHQPSGKSSGNIYLTLLQIYLNPRRTTKNFEKQITNLVSSQNTTIPKAGSVTAVKVKGGRTTKK  648 (816)
Q Consensus       569 D~~~Ae~YC~~~~~~~~~~~~~~~~~~l~~~Ll~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  648 (816)
                      |...++.|+.-....        ..+++|...+..||+..                                        
T Consensus       203 ~~~~~~~f~e~~~k~--------~N~e~~~~~i~~yL~~~----------------------------------------  234 (336)
T d1b89a_         203 DAWKEGQFKDIITKV--------ANVELYYRAIQFYLEFK----------------------------------------  234 (336)
T ss_dssp             TTCCHHHHHHHHHHC--------SSTHHHHHHHHHHHHHC----------------------------------------
T ss_pred             HHHHHHHHHHHHHCC--------CCHHHHHHHHHHHHHCC----------------------------------------
T ss_conf             456699999999724--------78699999999999759----------------------------------------


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCHHHHHHHHHHCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             12100011135799988899999985433335871230999999981015999987884019986454306999999999
Q 003482          649 IASIEGAEDMRMSPSSTDSGRSDGDAEEFSEEGDSTIMIDQVLDLLSQRWDRINGAQALKLLPRETKLQNLLPFLEPLLR  728 (816)
Q Consensus       649 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lL~~~~~~ld~~~vL~lLP~~~~l~~l~~fL~~~lr  728 (816)
                                                            +..+.++|...+..+|+..+++.++....|..+.+||.....
T Consensus       235 --------------------------------------p~~i~~lL~~v~~~~d~~r~V~~~~k~~~l~li~p~Le~v~~  276 (336)
T d1b89a_         235 --------------------------------------PLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQN  276 (336)
T ss_dssp             --------------------------------------GGGHHHHHHHHGGGCCHHHHHHHHHHTTCTTTTHHHHHHHHT
T ss_pred             --------------------------------------HHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             --------------------------------------999999999856579989999999853880779999999998


Q ss_pred             HHHHHH
Q ss_conf             579999
Q 003482          729 KSSEAH  734 (816)
Q Consensus       729 ~~~~~~  734 (816)
                      .+....
T Consensus       277 ~n~~~v  282 (336)
T d1b89a_         277 HNNKSV  282 (336)
T ss_dssp             TCCHHH
T ss_pred             CCHHHH
T ss_conf             180999

PyMOL of d1b89a_

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}	Back information, alignment and structure

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}	Back information, alignment and structure

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}	Back information, alignment and structure