Citrus Sinensis ID: 042398

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420--
Protein Sequence
MGNIFAFLKQRNRSISISRISSSRSTSASANHRYPSMSKQASSVSTSGTSSAAASATPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQPSRGSTPVAETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA
Secondary Structure (PSIPRED)
cccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccHHHHHHHHHHHccccEEccEEEEEccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccEEcccccccccccHHHHHHHHHHHcccEEEccccccHHHHHHHHHHHHHcccccEEEEEEcccccccccccccccccHHHHHHHHHHHHcccccccEEEcccccccccccccccccccccccccEEEEEHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccEEEEEcccccccccHcccccccccccccccccccccccccEEEEcccHHHHHcccccHcccHHHHHHEccccHccccccHHHHHHHHHHHccccEEEEEEEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccEEEEcccccccccHHHHHHHHHHHHcccEEEcccccHHHHHHHHHHHHHHccccEEEEEEEEccEEEEccccccccccccHHHHHHHHHHHcccccEEEEEEcccccHHHHHHHcccccHHHccEEEEEcHHHHHcccccccHHHHHHHHHHHHHcHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccHHcccccccccccccccEEEEEEEc
Coil and Loop (DISEMBL)
MGNIFAFLKQRNRSisisrisssrstsasanhrypsmskqassvstsgtssaaasatpkeniISSARDKMKkkysfipdtfSSLEQVTAALRDSglessnlilgidftksnewtgkvsfnnrslhaigdtpnpyEKAITIIgktlapfdednlipcfgfgdatthdqevfsfhddhtpchgfEEVLACYRNIvpnlrlagptsyaPVVEAAMDIVEKSGGQYHVLVIIADgqvtrsvntgdgelssqEQKTIKSIVAASSYPLSIVLVgvgdgpwedmqkfddkiparefdnfqfvNFTAimsknatpsEKETAFALAALMEIPIQYKAAVELGImgrttgrakkiaprpppapysrralperqpsrgstpvaetqacpicltnakdlafgcghmtcrecgsrvsncpicrQRITNRLRLFA
Flexible Loop (DISEMBL)
mgnifaflkqrnrsisisrisssrstsasanhrypsmskqassvstsgtssaaasatpkeniissarDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSlhaigdtpnPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTgdgelssqeQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRttgrakkiaprpppapysrralperqpsrgstpvaeTQACPICLTNAKDLAFGCGHMTCRecgsrvsncpicrqritnrlrlfa
Low Complexity Region (SEG)
MGNIFAFLKQRNrsisisrisssrstsasaNHRYPSMSKQassvstsgtssaaasatPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGrakkiaprpppapysrralpERQPSRGSTPVAETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA
Disordered region (IsUnstruct)
***************************************************************************FIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTR****************IKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKN******ETAFALAALMEIPIQYKAAVELGIMGR*************************************QACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLR***
Disordered Region (DISOPRED)
*******************************************************************************TFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNT**********KTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQ**********TQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA
Disordered Region (DISEMBL)
MGNIFAFLKQRNRSISIS****************************************KENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVN************TIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGR************YSRRAL**************TQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA
Disordered Region (DISPRO)
*GNIF*FLKQRNRS************************KQASSVSTSGTSSAAASATPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNE******F*NRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGR************************************TQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGNIFAFLKQRNRSISISRISSSRSTSASANHRYPSMSKQASSVSTSGTSSAAASATPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQPSRGSTPVAETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	422	2.2.26 [Sep-21-2011]
Q9LY87	468	E3 ubiquitin-protein liga	no	no	0.890	0.803	0.595	1e-136
Q9SS90	489	E3 ubiquitin-protein liga	no	no	0.909	0.785	0.591	1e-132
Q09221	7705	Copine family protein 2 O	no	no	0.563	0.030	0.473	8e-65
Q96A23	557	Copine-4 OS=Homo sapiens	yes	no	0.476	0.360	0.340	2e-22
Q8BLR2	557	Copine-4 OS=Mus musculus	yes	no	0.476	0.360	0.340	2e-22
Q0VE82	557	Copine-7 OS=Mus musculus	no	no	0.516	0.391	0.330	3e-21
Q9UBL6	633	Copine-7 OS=Homo sapiens	no	no	0.483	0.322	0.336	8e-21
Q99829	537	Copine-1 OS=Homo sapiens	no	no	0.651	0.512	0.294	1e-20
Q5S1W2	586	Protein BONZAI 2 OS=Arabi	no	no	0.547	0.394	0.311	7e-20
Q7YXU4	600	Copine-A OS=Dictyostelium	no	no	0.573	0.403	0.282	2e-19

>sp|Q9LY87|RGLG2_ARATH E3 ubiquitin-protein ligase RGLG2 OS=Arabidopsis thaliana GN=RGLG2 PE=1 SV=1

 Score =  483 bits (1244), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 240/403 (59%), Positives = 294/403 (72%), Gaps = 27/403 (6%)

Query: 45  STSGTSSAAASATPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILG 104
           ST   S+ + SA P ++  S  + ++++KYS I D +SSLEQVT AL  +GLESSNLI+G
Sbjct: 67  STQPYSAPSYSAPPSQSYGSDNKKRLERKYSKISDDYSSLEQVTEALARAGLESSNLIVG 126

Query: 105 IDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATT 164
           IDFTKSNEWTG  SFN +SLH IG +PNPYE+AITIIG+TLA FDEDNLIPC+GFGDA+T
Sbjct: 127 IDFTKSNEWTGARSFNRKSLHFIGSSPNPYEQAITIIGRTLAAFDEDNLIPCYGFGDAST 186

Query: 165 HDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHV 224
           HDQ+VFSF+ +   C+GFEEVL+ Y+ IVP L+LAGPTS+AP+++ AM IVE+SGGQYHV
Sbjct: 187 HDQDVFSFNSEDRFCNGFEEVLSRYKEIVPQLKLAGPTSFAPIIDMAMTIVEQSGGQYHV 246

Query: 225 LVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDK 284
           LVIIADGQVTRSV+T +G+LS QEQKT+ +IV AS  PLSIVLVGVGDGPW+ M++FDD 
Sbjct: 247 LVIIADGQVTRSVDTENGQLSPQEQKTVDAIVQASKLPLSIVLVGVGDGPWDMMREFDDN 306

Query: 285 IPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAK 344
           IPAR FDNFQFVNFT IM+KN   S KET FAL+ALMEIP QYKA +EL ++GR  G   
Sbjct: 307 IPARAFDNFQFVNFTEIMAKNKAQSLKETEFALSALMEIPQQYKATIELNLLGRRNGYIP 366

Query: 345 KIAPRPPP---------APYSRRALPERQPSRGSTPV-----------------AETQAC 378
           +  P PPP         +P   R LP  +PS    P                  ++ Q C
Sbjct: 367 ERFPLPPPMRGGSSSYNSPKPSR-LPSFKPSVPPHPTEGYHVRSSPVPPPTSSASDNQLC 425

Query: 379 PICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
           PICL+N KD+AFGCGH TC ECG  +  CPICR  I  R++L+
Sbjct: 426 PICLSNPKDMAFGCGHQTCCECGPDLQMCPICRAPIQTRIKLY 468

E3 ubiquitin-protein ligase that mediates the formation of 'Lys-63'-linked multiubiquitin chains. Regulates apical dominance by acting on the auxin transport proteins abundance.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q9SS90|RGLG1_ARATH E3 ubiquitin-protein ligase RGLG1 OS=Arabidopsis thaliana GN=RGLG1 PE=1 SV=1

 Score =  473 bits (1217), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 236/399 (59%), Positives = 283/399 (70%), Gaps = 15/399 (3%)

Query: 38  SKQASSVSTSGTSSAAASAT---PKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDS 94
           S      S  G +SAA+      P      + R K  ++YS I D +SSL QV+ AL  +
Sbjct: 91  SSYGHQYSQEGYASAASQPNYPPPPSQSQVADRKKFDRRYSKISDNYSSLLQVSEALGRA 150

Query: 95  GLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLI 154
           GLESSNLI+GIDFTKSNEWTG  SFN +SLH + +TPNPYE+AITIIG+TLA FDEDNLI
Sbjct: 151 GLESSNLIVGIDFTKSNEWTGAKSFNRKSLHHLSNTPNPYEQAITIIGRTLAAFDEDNLI 210

Query: 155 PCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDI 214
           PC+GFGDA+THDQ+VFSF+ +   C+GFEEVLA YR IVP L+LAGPTS+AP++E AM +
Sbjct: 211 PCYGFGDASTHDQDVFSFYPEGRFCNGFEEVLARYREIVPQLKLAGPTSFAPIIEMAMTV 270

Query: 215 VEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGP 274
           VE+S GQYHVLVIIADGQVTRSV+T  G LS QEQKT+ +IV AS+ PLSIVLVGVGDGP
Sbjct: 271 VEQSSGQYHVLVIIADGQVTRSVDTEHGRLSPQEQKTVDAIVKASTLPLSIVLVGVGDGP 330

Query: 275 WEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELG 334
           W+ MQ+FDD IPAR FDNFQFVNFT IMSKN   S KET FAL+ALMEIP QYKA +EL 
Sbjct: 331 WDMMQEFDDNIPARAFDNFQFVNFTEIMSKNKDQSRKETEFALSALMEIPPQYKATIELN 390

Query: 335 IMGRTTGRAKKIAPRPPPAPYSRRA----LPERQPSRGSTPVA--------ETQACPICL 382
           ++G   G   +  P PPP           +P  +PS    P          + Q CPICL
Sbjct: 391 LLGVRNGNIPQRIPLPPPVQSGSSFSSSRIPNFEPSVPPYPFESKQMSSADDIQLCPICL 450

Query: 383 TNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
           +N K++AFGCGH TC ECG  +  CPICR  I  R++L+
Sbjct: 451 SNPKNMAFGCGHQTCCECGPDLKVCPICRAPIQTRIKLY 489

E3 ubiquitin-protein ligase that mediates the formation of 'Lys-63'-linked multiubiquitin chains. Regulates apical dominance by acting on the auxin transport proteins abundance.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q09221|CPNA2_CAEEL Copine family protein 2 OS=Caenorhabditis elegans GN=cpna-2 PE=2 SV=4

 Score =  248 bits (632), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 124/262 (47%), Positives = 167/262 (63%), Gaps = 24/262 (9%)

Query: 81   FSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTP-NPYEKAIT 139
            F +L+ +  A++ +GLE SNLI GID+TKSN + G+ +F+ R LH I     NPY++ I 
Sbjct: 7456 FKTLDDIVKAIKHAGLEYSNLIFGIDYTKSNFYQGERTFDKRPLHTIDPAEMNPYQQVIQ 7515

Query: 140  IIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSF---HDDHTPCHGFEEVLACYRNIVPNL 196
            I+GKTL+ FD D  IP +GFGD    D  +F+    +D    C+GFEEVL  Y  + P +
Sbjct: 7516 IVGKTLSSFDADGQIPAYGFGDEEFTDHGIFNIAERYDLEKDCNGFEEVLRVYNEVTPTI 7575

Query: 197  RLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIV 256
             ++GPT++ P+++ A++I  K    YH+LVI+ADGQVT             E+   K+I 
Sbjct: 7576 EMSGPTNFVPLIDRAIEIC-KEKHSYHILVIVADGQVT------------NEKINQKAIA 7622

Query: 257  AASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIM--SKNATPSEKETA 314
            AAS YPLSI++VGVGDGPW  M +FDD IP R FDNF FV+F  +M  + NA  S     
Sbjct: 7623 AASHYPLSIIMVGVGDGPWNMMGRFDDNIPKRLFDNFHFVDFHKVMFNAPNADAS----- 7677

Query: 315  FALAALMEIPIQYKAAVELGIM 336
            FAL ALMEIP QYKA  ELG++
Sbjct: 7678 FALNALMEIPDQYKAIKELGLL 7699

Caenorhabditis elegans (taxid: 6239)

>sp|Q96A23|CPNE4_HUMAN Copine-4 OS=Homo sapiens GN=CPNE4 PE=2 SV=1

 Score =  107 bits (266), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/244 (34%), Positives = 126/244 (51%), Gaps = 43/244 (17%)

Query: 103 LGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGD 161
           + IDFT SN   G    N+ SLH I    PN Y KA+  +G+    +D D + P FGFG 
Sbjct: 310 VAIDFTASN---GDPR-NSCSLHYIHPYQPNEYLKALVAVGEICQDYDSDKMFPAFGFGA 365

Query: 162 ------ATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE-----A 210
                   +HD  + +F++D+  C G + V+  Y++ +P L+L GPT+ AP+++     A
Sbjct: 366 RIPPEYTVSHDFAI-NFNEDNPECAGIQGVVEAYQSCLPKLQLYGPTNIAPIIQKVAKSA 424

Query: 211 AMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGV 270
           + +   K   QY +L+I+ DG +T   +T +            +IV AS  P+S+++VGV
Sbjct: 425 SEETNTKEASQYFILLILTDGVITDMADTRE------------AIVHASHLPMSVIIVGV 472

Query: 271 GDGPWEDMQKF--DDKI---PARE---FDNFQFVNFTAIMSKNATPSEKETAFALAALME 322
           G+  + DMQ    DD I   P  E    D  QFV F     K+A+P+    A A + L E
Sbjct: 473 GNADFSDMQMLDGDDGILRSPKGEPVLRDIVQFVPFRNF--KHASPA----ALAKSVLAE 526

Query: 323 IPIQ 326
           +P Q
Sbjct: 527 VPNQ 530

May function in membrane trafficking. Exhibits calcium-dependent phospholipid binding properties.

Homo sapiens (taxid: 9606)

>sp|Q8BLR2|CPNE4_MOUSE Copine-4 OS=Mus musculus GN=Cpne4 PE=1 SV=1

 Score =  107 bits (266), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/244 (34%), Positives = 126/244 (51%), Gaps = 43/244 (17%)

Query: 103 LGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGD 161
           + IDFT SN   G    N+ SLH I    PN Y KA+  +G+    +D D + P FGFG 
Sbjct: 310 VAIDFTASN---GDPR-NSCSLHYIHPYQPNEYLKALVAVGEICQDYDSDKMFPAFGFGA 365

Query: 162 ------ATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE-----A 210
                   +HD  + +F++D+  C G + V+  Y++ +P L+L GPT+ AP+++     A
Sbjct: 366 RIPPEYTVSHDFAI-NFNEDNPECAGIQGVVEAYQSCLPKLQLYGPTNIAPIIQKVAKSA 424

Query: 211 AMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGV 270
           + +   K   QY +L+I+ DG +T   +T +            +IV AS  P+S+++VGV
Sbjct: 425 SEETNTKEASQYFILLILTDGVITDMADTRE------------AIVHASHLPMSVIIVGV 472

Query: 271 GDGPWEDMQKF--DDKI---PARE---FDNFQFVNFTAIMSKNATPSEKETAFALAALME 322
           G+  + DMQ    DD I   P  E    D  QFV F     K+A+P+    A A + L E
Sbjct: 473 GNADFSDMQMLDGDDGILRSPKGEPVLRDIVQFVPFRNF--KHASPA----ALAKSVLAE 526

Query: 323 IPIQ 326
           +P Q
Sbjct: 527 VPNQ 530

May function in membrane trafficking. Exhibits calcium-dependent phospholipid binding properties.

Mus musculus (taxid: 10090)

>sp|Q0VE82|CPNE7_MOUSE Copine-7 OS=Mus musculus GN=Cpne7 PE=2 SV=1

 Score =  103 bits (256), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/266 (33%), Positives = 130/266 (48%), Gaps = 48/266 (18%)

Query: 103 LGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGD 161
           + IDFT SN        N+ SLH I    PN Y +A+  +G+    +D D      GFG 
Sbjct: 309 VAIDFTASN----GDPRNSCSLHHINPYQPNEYLRALVAVGEVCQDYDSDKRFSALGFGA 364

Query: 162 ATTHDQEV-----FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE--AAMDI 214
                 EV      +F+ +   C G + V+  Y+N +P ++L GPT+ AP++   A M  
Sbjct: 365 RIPPKYEVSHDFAINFNPEDDECEGIQGVVEAYQNCLPKVQLYGPTNVAPIISKVARMAA 424

Query: 215 VEKSGG---QYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVG 271
            E+S G   QY++L+I+ DG VT   +T +            +IV AS  P+S+++VGVG
Sbjct: 425 AEESTGEASQYYILLILTDGVVTDMSDTRE------------AIVRASHLPMSVIIVGVG 472

Query: 272 DGPWEDMQKF--DDKI-------PAREFDNFQFVNFTAIMSKNATPSEKETAFALAALME 322
           +  + DMQ    DD +       PA   D  QFV F  +  KNA+P+    A A   L E
Sbjct: 473 NADFTDMQILDGDDGVLRSPRGEPALR-DIVQFVPFREL--KNASPA----ALAKCVLAE 525

Query: 323 IP---IQYKAAVEL--GIMGRTTGRA 343
           +P   ++Y +  EL    +G  TG A
Sbjct: 526 VPKQVVEYYSHKELPPRSLGAQTGEA 551

May function in membrane trafficking. Exhibits calcium-dependent phospholipid binding properties.

Mus musculus (taxid: 10090)

>sp|Q9UBL6|CPNE7_HUMAN Copine-7 OS=Homo sapiens GN=CPNE7 PE=2 SV=1

 Score =  102 bits (253), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 121/247 (48%), Gaps = 43/247 (17%)

Query: 100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFG 158
           +  + IDFT SN        N+ SLH I    PN Y KA+  +G+    +D D      G
Sbjct: 382 HFTVAIDFTASN----GDPRNSCSLHYINPYQPNEYLKALVSVGEICQDYDSDKRFSALG 437

Query: 159 FGDATTHDQEV-----FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE--AA 211
           FG       EV      +F+ +   C G + V+  Y+N +P ++L GPT+ AP++   A 
Sbjct: 438 FGARIPPKYEVSHDFAINFNPEDDECEGIQGVVEAYQNCLPRVQLYGPTNVAPIISKVAR 497

Query: 212 MDIVEKSGG---QYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLV 268
           +   E+S G   QY++L+I+ DG VT   +T +            +IV AS  P+SI++V
Sbjct: 498 VAAAEESTGKASQYYILLILTDGVVTDMADTRE------------AIVRASRLPMSIIIV 545

Query: 269 GVGDGPWEDMQKF--DDKI-------PAREFDNFQFVNFTAIMSKNATPSEKETAFALAA 319
           GVG+  + DMQ    DD +       PA   D  QFV F  +  KNA+P+    A A   
Sbjct: 546 GVGNADFTDMQVLDGDDGVLRSPRGEPALR-DIVQFVPFREL--KNASPA----ALAKCV 598

Query: 320 LMEIPIQ 326
           L E+P Q
Sbjct: 599 LAEVPKQ 605

May function in membrane trafficking. Exhibits calcium-dependent phospholipid binding properties.

Homo sapiens (taxid: 9606)

>sp|Q99829|CPNE1_HUMAN Copine-1 OS=Homo sapiens GN=CPNE1 PE=1 SV=1

 Score =  100 bits (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 100/340 (29%), Positives = 151/340 (44%), Gaps = 65/340 (19%)

Query: 44  VSTSGTSSAAASATPKE-NIISSARDKMKKKYS----------FIPDTFSSLEQVTAALR 92
           + T  TS A   A P E   I   + + KK Y            +   +S L+ V    +
Sbjct: 224 IGTFHTSLAQLQAVPAEFECIHPEKQQKKKSYKNSGTIRVKICRVETEYSFLDYVMGGCQ 283

Query: 93  DSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTP-NPYEKAITIIGKTLAPFDED 151
                  N  +G+DFT SN   G  S +  SLH +  T  N Y  A+  +G  +  +D D
Sbjct: 284 ------INFTVGVDFTGSN---GDPS-SPDSLHYLSPTGVNEYLMALWSVGSVVQDYDSD 333

Query: 152 NLIPCFGFGDATTHDQEV-----FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAP 206
            L P FGFG     D +V      +F+  +  C G + ++  YR  +P +RL GPT++AP
Sbjct: 334 KLFPAFGFGAQVPPDWQVSHEFALNFNPSNPYCAGIQGIVDAYRQALPQVRLYGPTNFAP 393

Query: 207 VVE-----AAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSY 261
           ++      AA    + +  QY +L+++ DG VT              + T +++V AS+ 
Sbjct: 394 IINHVARFAAQAAHQGTASQYFMLLLLTDGAVT------------DVEATREAVVRASNL 441

Query: 262 PLSIVLVGVGDGPWEDMQKFD-DKIP-------AREFDNFQFVNFTAIMSKNATPSEKET 313
           P+S+++VGVG   +E M++ D D  P       A   D  QFV +     +NA P E   
Sbjct: 442 PMSVIIVGVGGADFEAMEQLDADGGPLHTRSGQAAARDIVQFVPYRRF--QNA-PRE--- 495

Query: 314 AFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPA 353
           A A   L E+P Q  +        R  G A  + P PP A
Sbjct: 496 ALAQTVLAEVPTQLVSYF------RAQGWA-PLKPLPPSA 528

May function in membrane trafficking. Exhibits calcium-dependent phospholipid binding properties.

Homo sapiens (taxid: 9606)

>sp|Q5S1W2|BON2_ARATH Protein BONZAI 2 OS=Arabidopsis thaliana GN=BON2 PE=1 SV=2

 Score = 98.6 bits (244), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 89/286 (31%), Positives = 131/286 (45%), Gaps = 55/286 (19%)

Query: 67  RDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNR---S 123
            D++ K   F+     +++        SG E  N ++ IDFT SN        N R   S
Sbjct: 312 EDRVLKSQLFVDKFTETVQHTFLEYLASGFEL-NFMVAIDFTASNG-------NPRLPDS 363

Query: 124 LHAIGDTP--NPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEV---FSFHDDHTP 178
           LH I  T   N Y++AI  +G+ L  +D D   P +GFG A   D  V   F+ +   T 
Sbjct: 364 LHYIDPTGRLNAYQRAIVEVGEVLQFYDSDKRFPAWGFG-ARPIDIPVSHCFNLNGSSTY 422

Query: 179 CH--GFEEVLACYRNIVPNLRLAGPTSYAPVVEAAM----DIVEKSGGQYHVLVIIADGQ 232
           C   G + ++  Y   + N+  AGPT + PV+ AA     D + +S  +Y+VL+II DG 
Sbjct: 423 CEVDGIQGIMNAYNGALFNVSFAGPTLFGPVINAAATIASDSLAQSAKKYYVLLIITDGV 482

Query: 233 VTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFD---------- 282
           +T              Q+T  SIV+AS  PLSI++VGVG   +++M+  D          
Sbjct: 483 IT------------DLQETRDSIVSASDLPLSILIVGVGGADYKEMEVLDGDKGEKLESS 530

Query: 283 -DKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQY 327
             +I +R  D  QFV    I     +  E       A L E+P Q+
Sbjct: 531 SGRIASR--DIVQFVALRDIQYGEVSVVE-------ALLAELPTQF 567

Negative regulator of cell death and defense responses. May repress a number of R genes and may have effects in promoting growth and development. May function in membrane trafficking and in fusion of vesicles with plasma membrane.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7YXU4|CPNA_DICDI Copine-A OS=Dictyostelium discoideum GN=cpnA PE=2 SV=1

 Score = 97.8 bits (242), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 82/290 (28%), Positives = 126/290 (43%), Gaps = 48/290 (16%)

Query: 61  NIISSARDKMKKKY----------SFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKS 110
           N+I+S + + K  Y          + I   ++ LE +    +       NLI+GID T S
Sbjct: 243 NVINSHKQEKKSGYKNSGTVSVSDAVIEREYNFLEYIMGGCQ------MNLIVGIDCTAS 296

Query: 111 NEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEV- 169
           N   G  +  N   +      N Y  AI  +G  + P+    LIP +GFG       EV 
Sbjct: 297 N---GDSNDPNSLHYKNAQGLNQYANAICSVGNVIVPYTTTPLIPVYGFGGIMPGQSEVS 353

Query: 170 ----FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQ---- 221
                + +  +T C G   VL CY + +  ++L GPT +AP++  A     +   Q    
Sbjct: 354 HCFPMTLNASNTLCCGVNGVLDCYYDNISKIQLHGPTYFAPLINMAARYASQGQSQSNQK 413

Query: 222 YHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKF 281
           Y +L+II DG++  + N            TI +IV +S  PLSI++VGVG+  + +M   
Sbjct: 414 YTILMIITDGEILDADN------------TIDAIVKSSGLPLSIIIVGVGNANFTNMNIL 461

Query: 282 DDKIPAREFDNFQ----FVNFTAIMSKNATPSEKETAFALAALMEIPIQY 327
           D    A +    +     V F A+      P+E     A   L EIP Q+
Sbjct: 462 DGDDAALQSGGVRAERDIVQFVAMRDYLNRPNE----LAAEVLREIPTQF 507

Required for cytokinesis, contractile vacuole function and development.

Dictyostelium discoideum (taxid: 44689)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	422
224112337	396	predicted protein [Populus trichocarpa]	0.917	0.977	0.776	0.0
359494663	450	PREDICTED: E3 ubiquitin-protein ligase R	0.978	0.917	0.690	1e-177
356526411	425	PREDICTED: E3 ubiquitin-protein ligase R	0.848	0.842	0.764	1e-168
356556700	417	PREDICTED: E3 ubiquitin-protein ligase R	0.848	0.858	0.764	1e-167
356528633	451	PREDICTED: E3 ubiquitin-protein ligase R	0.829	0.776	0.769	1e-167
297736098	5665	unnamed protein product [Vitis vinifera]	0.793	0.059	0.782	1e-165
224098822	342	predicted protein [Populus trichocarpa]	0.805	0.994	0.783	1e-164
242078093	408	hypothetical protein SORBIDRAFT_07g00270	0.947	0.980	0.641	1e-161
388518783	407	unknown [Medicago truncatula]	0.855	0.886	0.752	1e-160
357501221	390	E3 ubiquitin-protein ligase RGLG2 [Medic	0.829	0.897	0.734	1e-158

>gi|224112337|ref|XP_002316157.1| predicted protein [Populus trichocarpa] gi|222865197|gb|EEF02328.1| predicted protein [Populus trichocarpa]

 Score =  652 bits (1682), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 302/389 (77%), Positives = 347/389 (89%), Gaps = 2/389 (0%)

Query: 36  SMSKQASSVSTSGTSSAAASATPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSG 95
           S+S  A +  +  +S A  ++  K       +  +K+KYSFIPD FSSLEQVT ALR++G
Sbjct: 8   SLSNTARATGSDTSSQAKGTSQAKGGSKLEKKQSIKQKYSFIPDNFSSLEQVTTALREAG 67

Query: 96  LESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIP 155
           LESSNL++GIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAI+IIGKT+APFDEDNLIP
Sbjct: 68  LESSNLVVGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAISIIGKTMAPFDEDNLIP 127

Query: 156 CFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIV 215
           CFGFGDATTHDQEVFSFH DH+PCHGFEEVLACY+ IVPNLRL+GPTSY PV+EAA+DIV
Sbjct: 128 CFGFGDATTHDQEVFSFHSDHSPCHGFEEVLACYKKIVPNLRLSGPTSYGPVIEAAIDIV 187

Query: 216 EKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPW 275
           EKSGGQYHVL+IIADGQVTRSV+TGDGE+S QE++TIK+IV ASSYPLSI+LVGVGDGPW
Sbjct: 188 EKSGGQYHVLLIIADGQVTRSVDTGDGEMSPQEEQTIKAIVDASSYPLSIILVGVGDGPW 247

Query: 276 EDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGI 335
           EDM++FDDK+PAREFDNFQFVNFTAIMSKNAT SEKETAFALAALMEIP+QYKAAVE GI
Sbjct: 248 EDMKRFDDKLPAREFDNFQFVNFTAIMSKNATISEKETAFALAALMEIPLQYKAAVEFGI 307

Query: 336 MGRTTGRAKKIAPRPPPAPYSRRALPERQPSRGSTPVAE--TQACPICLTNAKDLAFGCG 393
           +GR+ G+AKKI PRPPP PYSRR + +R+P+  S+PV +  TQACPICLTN KDLAFGCG
Sbjct: 308 IGRSMGQAKKIVPRPPPVPYSRRPVLDREPTHVSSPVLDERTQACPICLTNRKDLAFGCG 367

Query: 394 HMTCRECGSRVSNCPICRQRITNRLRLFA 422
           HMTCR+CGSRVS+CPICR+ IT+R+RLFA
Sbjct: 368 HMTCRDCGSRVSSCPICRRPITSRIRLFA 396

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494663|ref|XP_002265556.2| PREDICTED: E3 ubiquitin-protein ligase RGLG2-like [Vitis vinifera]

 Score =  626 bits (1615), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 315/456 (69%), Positives = 353/456 (77%), Gaps = 43/456 (9%)

Query: 1   MGNIFAFLKQRNRSISISRISSS-RSTSASANH-----------RYPSMSKQASSVSTSG 48
           MGN F F ++R  S S+S I+ S R    S+N            RYP+ ++  SS    G
Sbjct: 1   MGNFFGFRRRRGNSRSVSSINGSFRINGDSSNSVVERRRAEVAARYPTTARSMSSEKEKG 60

Query: 49  TSSAAASATPKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFT 108
            +S A+SA         +      KYSFIPD FS++EQVT ALR+SGLESSNLI+GIDFT
Sbjct: 61  GASHASSAA--------STASKPNKYSFIPDNFSTIEQVTNALRESGLESSNLIIGIDFT 112

Query: 109 KSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQE 168
           KSNEWTGK SFNNRSLHAIGDTPNPYEKAI+IIGKTLAPFDEDNLIPCFGFGDATTHD E
Sbjct: 113 KSNEWTGKASFNNRSLHAIGDTPNPYEKAISIIGKTLAPFDEDNLIPCFGFGDATTHDSE 172

Query: 169 VFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVII 228
           VFSFHDD +PCHGFEEVLACY+ IVPNL+L+GPTSYAPVVEAA+DIVEKSGGQYHVLVII
Sbjct: 173 VFSFHDDRSPCHGFEEVLACYKRIVPNLQLSGPTSYAPVVEAAIDIVEKSGGQYHVLVII 232

Query: 229 ADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAR 288
           ADGQVTRSVN  D ELS QE+KTI SIV ASSYPLSI+LVGVGDGPW+DM+KFDDKIPAR
Sbjct: 233 ADGQVTRSVNANDKELSPQEEKTINSIVTASSYPLSIILVGVGDGPWDDMKKFDDKIPAR 292

Query: 289 EFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAP 348
            FDNFQFVNFTAIMSKNA+PSEKETAFALAALMEIPIQYKA VE GI+GR TG+AKK+ P
Sbjct: 293 GFDNFQFVNFTAIMSKNASPSEKETAFALAALMEIPIQYKATVEFGILGRVTGKAKKVVP 352

Query: 349 RPPPAPYSRRA---------------------LPERQPSR--GSTPVAETQACPICLTNA 385
           RPPPA Y+R A                     +P R PSR   +T     QACPICLT+ 
Sbjct: 353 RPPPASYARHAPPPYAMPYGMPSHQPSNLSSRMPSRMPSRQLSNTRDEGNQACPICLTSV 412

Query: 386 KDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
           KD+AFGCGHMTCREC S+VSNCPICR+ I NRLR++
Sbjct: 413 KDMAFGCGHMTCRECASKVSNCPICREPIRNRLRVY 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526411|ref|XP_003531811.1| PREDICTED: E3 ubiquitin-protein ligase RGLG2-like [Glycine max]

 Score =  596 bits (1537), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 276/361 (76%), Positives = 314/361 (86%), Gaps = 3/361 (0%)

Query: 65  SARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSL 124
           S +   K+KY+ IPD F++LEQVT ALR  GLESSNL+LGIDFTKSNEWTG VSFNN+SL
Sbjct: 64  SGKLSAKEKYALIPDNFTTLEQVTTALRKEGLESSNLVLGIDFTKSNEWTGSVSFNNKSL 123

Query: 125 HAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEE 184
           HAIG T NPYEKAI+IIGKTLAPFD+DNLIPCFGFGDATTHDQEVFSFH DH+PCHGFEE
Sbjct: 124 HAIGSTANPYEKAISIIGKTLAPFDDDNLIPCFGFGDATTHDQEVFSFHSDHSPCHGFEE 183

Query: 185 VLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGEL 244
           VLACY+ +VPNLRL+GPTSYAPV+EAA+DIVEKS GQ+HVLVI+ADGQVT S  +  GEL
Sbjct: 184 VLACYQKVVPNLRLSGPTSYAPVIEAAIDIVEKSHGQFHVLVIVADGQVTTSAASEHGEL 243

Query: 245 SSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSK 304
           S QE +TIK+IV ASSYPLSI+LVGVGDGPWEDM+KFDDKIPAR+FDNFQFVNFT IM+K
Sbjct: 244 SPQEARTIKAIVDASSYPLSIILVGVGDGPWEDMKKFDDKIPARDFDNFQFVNFTDIMTK 303

Query: 305 NATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQ 364
            ++PSEKETAFALAALMEIP QYKAA+EL ++GR TGR+ KI PRPPPAPYSR   P R 
Sbjct: 304 KSSPSEKETAFALAALMEIPFQYKAAIELELLGRATGRSNKIVPRPPPAPYSRLVPPARV 363

Query: 365 PSRGSTPVAETQ---ACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
            S   T + + +   AC ICLTN KDLAFGCGHMTCR+CGSR++NCPICRQRITNRLR+F
Sbjct: 364 LSNMPTFMDDERNQMACAICLTNKKDLAFGCGHMTCRDCGSRLTNCPICRQRITNRLRVF 423

Query: 422 A 422
           +
Sbjct: 424 S 424

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556700|ref|XP_003546661.1| PREDICTED: E3 ubiquitin-protein ligase RGLG2-like [Glycine max]

 Score =  595 bits (1535), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 276/361 (76%), Positives = 314/361 (86%), Gaps = 3/361 (0%)

Query: 65  SARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSL 124
           S +   K+KY+ IPD F++LEQVT ALR  GLESSNL+LGIDFTKSNEWTG VSFNNRSL
Sbjct: 56  SGKLSAKEKYALIPDNFTTLEQVTIALRKEGLESSNLVLGIDFTKSNEWTGSVSFNNRSL 115

Query: 125 HAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEE 184
           HAIG TPNPYEKAI+IIGKTLAPFD+DNLIPCFGFGDATTHDQEVFSFH D++PCHGFEE
Sbjct: 116 HAIGSTPNPYEKAISIIGKTLAPFDDDNLIPCFGFGDATTHDQEVFSFHSDNSPCHGFEE 175

Query: 185 VLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGEL 244
           VLACY+ IVPNLRL+GPTSYAPV+EAA+DIVEKS GQ+HVLVI+ADGQVT S  + DGEL
Sbjct: 176 VLACYQKIVPNLRLSGPTSYAPVIEAAIDIVEKSHGQFHVLVIVADGQVTTSAASEDGEL 235

Query: 245 SSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSK 304
           S QE +TIK+I  ASSYPLSI+LVGVGDGPWEDM+KFDDKIPAR+FDNFQFVNFT IM+K
Sbjct: 236 SPQEARTIKAIADASSYPLSIILVGVGDGPWEDMKKFDDKIPARDFDNFQFVNFTDIMAK 295

Query: 305 NATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQ 364
            ++PSEKE AFALAALMEIP QYKAA ELG++GR TGR+ KI PRPPPAPYS+   P R 
Sbjct: 296 KSSPSEKEAAFALAALMEIPFQYKAATELGLLGRATGRSNKIVPRPPPAPYSQLVPPARV 355

Query: 365 PSRGSTPVAETQ---ACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
            S   T + + +   AC ICLTN KDLAFGCGHMTCR+CGSR+++CPICRQRITNRLR+F
Sbjct: 356 LSNTPTFMDDERNQMACAICLTNKKDLAFGCGHMTCRDCGSRLTDCPICRQRITNRLRVF 415

Query: 422 A 422
           +
Sbjct: 416 S 416

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528633|ref|XP_003532904.1| PREDICTED: E3 ubiquitin-protein ligase RGLG2-like [Glycine max]

 Score =  593 bits (1528), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 270/351 (76%), Positives = 311/351 (88%), Gaps = 1/351 (0%)

Query: 72  KKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTP 131
           KKY+ I D FS+LEQVT ALR  GLESSNLILGIDFTKSNEWTG++SFN RSLHAIG TP
Sbjct: 101 KKYALIRDNFSTLEQVTTALRKEGLESSNLILGIDFTKSNEWTGRISFNKRSLHAIGSTP 160

Query: 132 NPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRN 191
           NPYEKAI+IIGKTLAPFD+DNLIPCFGFGDATTHDQEVFSFH DH+P HGFEEVLACY+ 
Sbjct: 161 NPYEKAISIIGKTLAPFDDDNLIPCFGFGDATTHDQEVFSFHSDHSPYHGFEEVLACYQK 220

Query: 192 IVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKT 251
           IVPNL+L+GPTSYAPV+EAA+DIVEK+ GQ+HVLVI+ADGQVTRSV+T DGELS QE+KT
Sbjct: 221 IVPNLKLSGPTSYAPVIEAAIDIVEKNRGQFHVLVIVADGQVTRSVDTSDGELSPQEEKT 280

Query: 252 IKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEK 311
           IK++V AS+YPL+IVLVGVGDGPWEDM+KFDDKIPAR++DNFQFVNFT IMSKN +PSEK
Sbjct: 281 IKAVVDASAYPLAIVLVGVGDGPWEDMRKFDDKIPARDYDNFQFVNFTEIMSKNISPSEK 340

Query: 312 ETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQPSRGSTP 371
           E AFALAALMEIP QYKA +E GI+GR TGRAK+I P+PPP PYSR A P    +  S  
Sbjct: 341 EAAFALAALMEIPFQYKATMEFGILGRVTGRAKRIVPKPPPVPYSRPA-PSINTAASSGD 399

Query: 372 VAETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA 422
                ACP+CLTNA+DLAFGCGHMTCRECG +++NCP+CR+RIT+RLR+++
Sbjct: 400 DQNQTACPVCLTNARDLAFGCGHMTCRECGHKLTNCPMCRERITSRLRVYS 450

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736098|emb|CBI24136.3| unnamed protein product [Vitis vinifera]

 Score =  587 bits (1513), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 280/358 (78%), Positives = 305/358 (85%), Gaps = 23/358 (6%)

Query: 87   VTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLA 146
            VT ALR+SGLESSNLI+GIDFTKSNEWTGK SFNNRSLHAIGDTPNPYEKAI+IIGKTLA
Sbjct: 5306 VTNALRESGLESSNLIIGIDFTKSNEWTGKASFNNRSLHAIGDTPNPYEKAISIIGKTLA 5365

Query: 147  PFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAP 206
            PFDEDNLIPCFGFGDATTHD EVFSFHDD +PCHGFEEVLACY+ IVPNL+L+GPTSYAP
Sbjct: 5366 PFDEDNLIPCFGFGDATTHDSEVFSFHDDRSPCHGFEEVLACYKRIVPNLQLSGPTSYAP 5425

Query: 207  VVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIV 266
            VVEAA+DIVEKSGGQYHVLVIIADGQVTRSVN  D ELS QE+KTI SIV ASSYPLSI+
Sbjct: 5426 VVEAAIDIVEKSGGQYHVLVIIADGQVTRSVNANDKELSPQEEKTINSIVTASSYPLSII 5485

Query: 267  LVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQ 326
            LVGVGDGPW+DM+KFDDKIPAR FDNFQFVNFTAIMSKNA+PSEKETAFALAALMEIPIQ
Sbjct: 5486 LVGVGDGPWDDMKKFDDKIPARGFDNFQFVNFTAIMSKNASPSEKETAFALAALMEIPIQ 5545

Query: 327  YKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRA---------------------LPERQP 365
            YKA VE GI+GR TG+AKK+ PRPPPA Y+R A                     +P R P
Sbjct: 5546 YKATVEFGILGRVTGKAKKVVPRPPPASYARHAPPPYAMPYGMPSHQPSNLSSRMPSRMP 5605

Query: 366  SR--GSTPVAETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
            SR   +T     QACPICLT+ KD+AFGCGHMTCREC S+VSNCPICR+ I NRLR++
Sbjct: 5606 SRQLSNTRDEGNQACPICLTSVKDMAFGCGHMTCRECASKVSNCPICREPIRNRLRVY 5663

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098822|ref|XP_002311280.1| predicted protein [Populus trichocarpa] gi|222851100|gb|EEE88647.1| predicted protein [Populus trichocarpa]

 Score =  583 bits (1504), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 268/342 (78%), Positives = 306/342 (89%), Gaps = 2/342 (0%)

Query: 83  SLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIG 142
           S+ QVT ALR++GLESSNLI+GIDFTKSNEWTGKVSFNNR LH IGDTPNPYEKAI+IIG
Sbjct: 1   SILQVTTALREAGLESSNLIVGIDFTKSNEWTGKVSFNNRCLHVIGDTPNPYEKAISIIG 60

Query: 143 KTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPT 202
            T++PFDEDNL+PCFGFGDATTHDQEVFSFH DH+PCHGFEEVL CY+ IVPNLRLAGPT
Sbjct: 61  NTMSPFDEDNLVPCFGFGDATTHDQEVFSFHGDHSPCHGFEEVLTCYKKIVPNLRLAGPT 120

Query: 203 SYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYP 262
           SY PV+EAA+DIV+KS GQYHVL+IIADGQVTRS N+ D ELS QE++TIK+IV ASSYP
Sbjct: 121 SYGPVIEAAIDIVQKSKGQYHVLIIIADGQVTRSDNSSDRELSPQEEQTIKAIVDASSYP 180

Query: 263 LSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALME 322
           LSI+LVGVGDGPWEDM++FDDKIP R+FDNFQFVNFT IM+K AT SEKE AFAL ALME
Sbjct: 181 LSIILVGVGDGPWEDMKRFDDKIPDRKFDNFQFVNFTEIMAKKATLSEKEAAFALTALME 240

Query: 323 IPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPERQPSRGSTPVAE--TQACPI 380
           IP QYKAAVE G++G +TGRAKKI PRPPP PYS R++  R+P+  S+PV +  TQACPI
Sbjct: 241 IPFQYKAAVEFGVIGCSTGRAKKIVPRPPPVPYSSRSVQCREPTNVSSPVLDERTQACPI 300

Query: 381 CLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLFA 422
           CLT+ KDLAFGCGHMTCR+CGSRVSNCPICRQ IT+R++LF+
Sbjct: 301 CLTDGKDLAFGCGHMTCRDCGSRVSNCPICRQPITSRMKLFS 342

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242078093|ref|XP_002443815.1| hypothetical protein SORBIDRAFT_07g002700 [Sorghum bicolor] gi|241940165|gb|EES13310.1| hypothetical protein SORBIDRAFT_07g002700 [Sorghum bicolor]

 Score =  574 bits (1480), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 275/429 (64%), Positives = 341/429 (79%), Gaps = 29/429 (6%)

Query: 1   MGNIFAFLKQRNRSISISRISSSRSTSASANHRYPSMSKQASSVSTSGTSSAAASATPKE 60
           MG +   L        + R S  R  +    +R+  +++Q S+      ++AAA+   ++
Sbjct: 1   MGGVLGAL--------LHRRSGGRPPAQGTRNRHLGLTRQPSTYD----ATAAAAGGHRK 48

Query: 61  NIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFN 120
            ++S       KKYS+IPDT++SL+QV AALR+ GLESSNLILGIDFTKSNEWTGK SF 
Sbjct: 49  AMLS-------KKYSYIPDTYTSLDQVAAALREQGLESSNLILGIDFTKSNEWTGKQSFG 101

Query: 121 NRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC 179
            +SLH I D  PNPYE+AI+IIGKTLAPFDEDNLIPCFGFGDATTHD  VFSFH D+TPC
Sbjct: 102 GQSLHRISDDAPNPYEQAISIIGKTLAPFDEDNLIPCFGFGDATTHDNNVFSFHRDNTPC 161

Query: 180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNT 239
           HGFEEVLACYR +VP+LRL+GPTS+AP+VEAA+DIV++SGGQYHVLVI+ADGQVTRSV+T
Sbjct: 162 HGFEEVLACYRTVVPHLRLSGPTSFAPIVEAAVDIVDRSGGQYHVLVIVADGQVTRSVDT 221

Query: 240 GDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFT 299
           GDG+LS QE++T+ SIV ASSYPLSIVLVGVGDGPW+DM++FDDK+PAR+FDNFQFVNFT
Sbjct: 222 GDGDLSPQEKRTVDSIVMASSYPLSIVLVGVGDGPWDDMRRFDDKLPARDFDNFQFVNFT 281

Query: 300 AIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRA 359
           +IMS+ AT  +KE+AFALAALME+PIQYKA +ELGI+GR+TG AK+++P PPP P ++R 
Sbjct: 282 SIMSRAATAQQKESAFALAALMEVPIQYKATMELGILGRSTGNAKRVSPAPPPLPNAQRQ 341

Query: 360 LPERQPSRGSTPVA------ETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQR 413
              R   RG++ V       + Q CPICLTNAKDLAFGCGHMTCRECG  ++ CPICRQ 
Sbjct: 342 SSLR---RGASNVGAAAAPRDDQVCPICLTNAKDLAFGCGHMTCRECGESLTRCPICRQP 398

Query: 414 ITNRLRLFA 422
           I ++LRL++
Sbjct: 399 IRSKLRLYS 407

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388518783|gb|AFK47453.1| unknown [Medicago truncatula]

 Score =  570 bits (1468), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 276/367 (75%), Positives = 311/367 (84%), Gaps = 6/367 (1%)

Query: 61  NIISSARDKM--KKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVS 118
           NI    + K+  K+KY+ IPD F++LEQVT+ALR  GLESSNLILGIDFTKSNEWTG+ S
Sbjct: 39  NIHLHGKKKLATKEKYALIPDNFTTLEQVTSALRHEGLESSNLILGIDFTKSNEWTGRSS 98

Query: 119 FNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP 178
           FNN+SLH+IG TPNPYEKAI+IIGKTLAPFD+DNLIPC GFGDATTHD EVFSFH D + 
Sbjct: 99  FNNKSLHSIGGTPNPYEKAISIIGKTLAPFDDDNLIPCLGFGDATTHDSEVFSFHADDSS 158

Query: 179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVN 238
           CHGFEEVLACY+ IVPNL L+GPTSYAPV+EAAMDIVEK+ GQ+HVLVI+ADGQVTR  N
Sbjct: 159 CHGFEEVLACYQKIVPNLSLSGPTSYAPVIEAAMDIVEKTHGQFHVLVIVADGQVTRYGN 218

Query: 239 TGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNF 298
              G+LS QE+KTIK+I  ASSYPLSIVLVGVGDGPWEDM+KFDDK+PAR+FDNFQFVNF
Sbjct: 219 NESGKLSPQEEKTIKAIADASSYPLSIVLVGVGDGPWEDMKKFDDKLPARDFDNFQFVNF 278

Query: 299 TAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRR 358
           T IMSK  +PS KE AFALAALMEIP QYKAA+ELG++GR TGRAKK+ PRPPPAPYSR 
Sbjct: 279 TDIMSKKISPSAKEAAFALAALMEIPFQYKAALELGLLGRATGRAKKMVPRPPPAPYSRH 338

Query: 359 ALPERQPSRGSTPVAETQ----ACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRI 414
             PE   SR  T   + Q     C ICLTN KDLAFGCGHMTCR+CGSR+S+CPICRQRI
Sbjct: 339 MPPEHFLSRMPTSSMDDQRNQMECAICLTNKKDLAFGCGHMTCRDCGSRLSDCPICRQRI 398

Query: 415 TNRLRLF 421
           TNRLR+F
Sbjct: 399 TNRLRVF 405

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357501221|ref|XP_003620899.1| E3 ubiquitin-protein ligase RGLG2 [Medicago truncatula] gi|355495914|gb|AES77117.1| E3 ubiquitin-protein ligase RGLG2 [Medicago truncatula]

 Score =  565 bits (1455), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 265/361 (73%), Positives = 302/361 (83%), Gaps = 11/361 (3%)

Query: 64  SSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRS 123
           SS   K  KKY  I D F++LEQV  ALR  GLESSNLILGIDFTKSNEWTG++SFN +S
Sbjct: 38  SSNTKKPLKKYDLIQDNFTTLEQVIVALRKEGLESSNLILGIDFTKSNEWTGQISFNKKS 97

Query: 124 LHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFE 183
           LHAIGDTPNPYEKAI+I+GKTLAPFDEDNLIPCFGFGDATTHDQEVFSFH DH+PCHGFE
Sbjct: 98  LHAIGDTPNPYEKAISIVGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHSDHSPCHGFE 157

Query: 184 EVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGE 243
           EVLACY+NIVPNL+L+GPTSYAPV+EAA+DIVEKS GQ+HVLVIIADGQVT+SV   D E
Sbjct: 158 EVLACYKNIVPNLKLSGPTSYAPVIEAAIDIVEKSHGQFHVLVIIADGQVTKSV---DNE 214

Query: 244 LSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMS 303
           +S QE+KTIK+I  AS YPL+IVLVGVGDGPWEDM+KFDDKIP R+FDNFQFVNFT IMS
Sbjct: 215 VSPQEKKTIKAIADASKYPLAIVLVGVGDGPWEDMEKFDDKIPTRDFDNFQFVNFTKIMS 274

Query: 304 KNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGRAKKIAPRPPPAPYSRRALPER 363
           KN + +EKE AFA+  LMEIP QYKA VE   +G  TGRAK+I P+P P PYSR A    
Sbjct: 275 KNTSAAEKEAAFAVNTLMEIPFQYKACVEFRKLGHVTGRAKRIVPKPSPVPYSRPA---- 330

Query: 364 QPSRGSTPVAETQA--CPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
                ST   + Q+  CP+CLTNAKDLAFGCGHMTCR+CGSR+ +CPICR RIT+RLR++
Sbjct: 331 --HSNSTTDDQNQSACCPVCLTNAKDLAFGCGHMTCRDCGSRLRHCPICRHRITSRLRVY 388

Query: 422 A 422
           +
Sbjct: 389 S 389

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	422
TAIR|locus:2206395	401	RGLG4 "RING DOMAIN LIGASE 4" [	0.829	0.872	0.690	1.8e-133
TAIR|locus:2145643	468	RGLG2 "RING domain ligase2" [A	0.672	0.606	0.690	2.8e-120
TAIR|locus:2008570	453	AT1G67800 [Arabidopsis thalian	0.644	0.600	0.709	7.6e-118
TAIR|locus:2084218	489	RGLG1 "RING domain ligase1" [A	0.860	0.742	0.601	6.4e-115
TAIR|locus:2160821	367	RGLG3 "RING DOMAIN LIGASE 3" [	0.630	0.724	0.669	3.4e-111
DICTYBASE|DDB_G0272196	284	DDB_G0272196 "copine family pr	0.590	0.876	0.509	4.7e-64
WB|WBGene00006495	1107	cpna-1 [Caenorhabditis elegans	0.580	0.221	0.440	3.8e-54
MGI|MGI:1921270	557	Cpne4 "copine IV" [Mus musculu	0.476	0.360	0.340	1e-22
MGI|MGI:2386621	536	Cpne1 "copine I" [Mus musculus	0.485	0.382	0.341	5.3e-21
MGI|MGI:2142747	557	Cpne7 "copine VII" [Mus muscul	0.514	0.389	0.338	6e-21

TAIR|locus:2206395 RGLG4 "RING DOMAIN LIGASE 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 1308 (465.5 bits), Expect = 1.8e-133, P = 1.8e-133
 Identities = 243/352 (69%), Positives = 288/352 (81%)

Query:    71 KKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDT 130
             KKKY+ IPD FSSL+QV+ ALR++GLESSNLILG+DFTKSNEWTGK SF+ + LHA+G+T
Sbjct:    50 KKKYALIPDRFSSLDQVSKALREAGLESSNLILGVDFTKSNEWTGKTSFDGKCLHALGET 109

Query:   131 PNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYR 190
              NPYEKAI +IG+TLAPFDEDNLIPCFGFGD+TTHD+EVF FH D++PCHGFEEVLACY+
Sbjct:   110 SNPYEKAIFVIGQTLAPFDEDNLIPCFGFGDSTTHDEEVFGFHSDNSPCHGFEEVLACYK 169

Query:   191 NIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQK 250
              I PNLRL+GPTSY P+++AA+DIVEK+ GQ+HVLVI+ADGQVTR  +  +GELS QE+ 
Sbjct:   170 RIAPNLRLSGPTSYGPLIDAAVDIVEKNNGQFHVLVIVADGQVTRGTDMAEGELSQQEKT 229

Query:   251 TIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSE 310
             TI +IV ASSY LSIVLVGVGDGPWEDM+KFDDKIP REFDNFQFVNFT IM++N+  S 
Sbjct:   230 TIDAIVNASSYALSIVLVGVGDGPWEDMRKFDDKIPKREFDNFQFVNFTEIMTRNSPESA 289

Query:   311 KETAFALAALMEIPIQYKAAVELGIMGRTTGXXXXXXXXXXXXXXXXXXXXERQPSRGST 370
             KETAFALAALMEIP QY+AA+EL ++G+ TG                    E  PS  S 
Sbjct:   290 KETAFALAALMEIPFQYQAAIELRLLGKQTGLAKTIVPRPPPIPYTPPTNAEL-PSTASP 348

Query:   371 PVAE-TQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
                E TQ+CPICLTN KD+AF CGHMTC +CGS++SNCPICR RITNRL+L+
Sbjct:   349 ASPEQTQSCPICLTNRKDVAFSCGHMTCGDCGSKISNCPICRVRITNRLKLY 400

GO:0005886 "plasma membrane" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006487 "protein N-linked glycosylation" evidence=RCA

GO:0006816 "calcium ion transport" evidence=RCA

GO:0009690 "cytokinin metabolic process" evidence=RCA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009611 "response to wounding" evidence=IMP

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IMP

GO:0042742 "defense response to bacterium" evidence=IMP

TAIR|locus:2145643 RGLG2 "RING domain ligase2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1028 (366.9 bits), Expect = 2.8e-120, Sum P(2) = 2.8e-120
 Identities = 196/284 (69%), Positives = 237/284 (83%)

Query:    58 PKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKV 117
             P ++  S  + ++++KYS I D +SSLEQVT AL  +GLESSNLI+GIDFTKSNEWTG  
Sbjct:    80 PSQSYGSDNKKRLERKYSKISDDYSSLEQVTEALARAGLESSNLIVGIDFTKSNEWTGAR 139

Query:   118 SFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHT 177
             SFN +SLH IG +PNPYE+AITIIG+TLA FDEDNLIPC+GFGDA+THDQ+VFSF+ +  
Sbjct:   140 SFNRKSLHFIGSSPNPYEQAITIIGRTLAAFDEDNLIPCYGFGDASTHDQDVFSFNSEDR 199

Query:   178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSV 237
              C+GFEEVL+ Y+ IVP L+LAGPTS+AP+++ AM IVE+SGGQYHVLVIIADGQVTRSV
Sbjct:   200 FCNGFEEVLSRYKEIVPQLKLAGPTSFAPIIDMAMTIVEQSGGQYHVLVIIADGQVTRSV 259

Query:   238 NTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVN 297
             +T +G+LS QEQKT+ +IV AS  PLSIVLVGVGDGPW+ M++FDD IPAR FDNFQFVN
Sbjct:   260 DTENGQLSPQEQKTVDAIVQASKLPLSIVLVGVGDGPWDMMREFDDNIPARAFDNFQFVN 319

Query:   298 FTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTG 341
             FT IM+KN   S KET FAL+ALMEIP QYKA +EL ++GR  G
Sbjct:   320 FTEIMAKNKAQSLKETEFALSALMEIPQQYKATIELNLLGRRNG 363

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009690 "cytokinin metabolic process" evidence=IGI;RCA

GO:0009850 "auxin metabolic process" evidence=IGI

GO:0005634 "nucleus" evidence=IDA

GO:0080148 "negative regulation of response to water deprivation" evidence=IGI

TAIR|locus:2008570 AT1G67800 [Arabidopsis thaliana (taxid:3702)]

 Score = 1026 (366.2 bits), Expect = 7.6e-118, Sum P(2) = 7.6e-118
 Identities = 193/272 (70%), Positives = 231/272 (84%)

Query:    70 MKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGD 129
             +++KYS I D + S+++VTAAL  +GLESSNLI+GID TKSNEWTG  SF  +SLH IG 
Sbjct:    83 LERKYSRIADNYRSIDEVTAALSHAGLESSNLIVGIDVTKSNEWTGARSFGRKSLHFIGT 142

Query:   130 TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACY 189
             TPNPY++AI+IIGKTL+ FDEDNLIPC+GFGDATTHDQ+VFSF+ + T C+GFEEVL CY
Sbjct:   143 TPNPYQQAISIIGKTLSVFDEDNLIPCYGFGDATTHDQDVFSFNPNDTYCNGFEEVLMCY 202

Query:   190 RNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQ 249
             R IVP LRL+GPTS+AP++E AM IVE+SGGQYHVL+IIADGQVTRSV+T +G  S QEQ
Sbjct:   203 REIVPQLRLSGPTSFAPIIERAMTIVEESGGQYHVLLIIADGQVTRSVDTDNGGFSPQEQ 262

Query:   250 KTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPS 309
             +TI +IV AS YPLSIVLVGVGDGPW+ M++FDD IPAR FDNFQFVNFT IMSKN  P+
Sbjct:   263 QTIDAIVRASEYPLSIVLVGVGDGPWDTMRQFDDNIPARAFDNFQFVNFTDIMSKNIDPA 322

Query:   310 EKETAFALAALMEIPIQYKAAVELGIMGRTTG 341
              KE  FAL+ALMEIP QYKA +ELG++G+ TG
Sbjct:   323 RKEAEFALSALMEIPSQYKATLELGLLGQRTG 354

GO:0005886 "plasma membrane" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009863 "salicylic acid mediated signaling pathway" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0045087 "innate immune response" evidence=RCA

TAIR|locus:2084218 RGLG1 "RING domain ligase1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1133 (403.9 bits), Expect = 6.4e-115, P = 6.4e-115
 Identities = 226/376 (60%), Positives = 272/376 (72%)

Query:    58 PKENIISSARDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKV 117
             P ++ ++  R K  ++YS I D +SSL QV+ AL  +GLESSNLI+GIDFTKSNEWTG  
Sbjct:   115 PSQSQVAD-RKKFDRRYSKISDNYSSLLQVSEALGRAGLESSNLIVGIDFTKSNEWTGAK 173

Query:   118 SFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHT 177
             SFN +SLH + +TPNPYE+AITIIG+TLA FDEDNLIPC+GFGDA+THDQ+VFSF+ +  
Sbjct:   174 SFNRKSLHHLSNTPNPYEQAITIIGRTLAAFDEDNLIPCYGFGDASTHDQDVFSFYPEGR 233

Query:   178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSV 237
              C+GFEEVLA YR IVP L+LAGPTS+AP++E AM +VE+S GQYHVLVIIADGQVTRSV
Sbjct:   234 FCNGFEEVLARYREIVPQLKLAGPTSFAPIIEMAMTVVEQSSGQYHVLVIIADGQVTRSV 293

Query:   238 NTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVN 297
             +T  G LS QEQKT+ +IV AS+ PLSIVLVGVGDGPW+ MQ+FDD IPAR FDNFQFVN
Sbjct:   294 DTEHGRLSPQEQKTVDAIVKASTLPLSIVLVGVGDGPWDMMQEFDDNIPARAFDNFQFVN 353

Query:   298 FTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIMGRTTGXXXXXXXXXXXXXXXX 357
             FT IMSKN   S KET FAL+ALMEIP QYKA +EL ++G   G                
Sbjct:   354 FTEIMSKNKDQSRKETEFALSALMEIPPQYKATIELNLLGVRNGNIPQRIPLPPPVQSGS 413

Query:   358 XXXXERQPS-RGSTP-----------VAETQACPICLTNAKDLAFGCGHMTCRECGSRVS 405
                  R P+   S P             + Q CPICL+N K++AFGCGH TC ECG  + 
Sbjct:   414 SFSSSRIPNFEPSVPPYPFESKQMSSADDIQLCPICLSNPKNMAFGCGHQTCCECGPDLK 473

Query:   406 NCPICRQRITNRLRLF 421
              CPICR  I  R++L+
Sbjct:   474 VCPICRAPIQTRIKLY 489

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009690 "cytokinin metabolic process" evidence=IGI;RCA

GO:0009850 "auxin metabolic process" evidence=IGI

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0080148 "negative regulation of response to water deprivation" evidence=IGI

TAIR|locus:2160821 RGLG3 "RING DOMAIN LIGASE 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 932 (333.1 bits), Expect = 3.4e-111, Sum P(2) = 3.4e-111
 Identities = 178/266 (66%), Positives = 219/266 (82%)

Query:    68 DKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAI 127
             +K  ++ S+I D FSSL+QV  +LR++GLESSNLILGIDFTKSNEWTG+ SFN +SLHAI
Sbjct:     5 NKRNQQPSYIADHFSSLDQVITSLREAGLESSNLILGIDFTKSNEWTGRYSFNRKSLHAI 64

Query:   128 GDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLA 187
             G   NPYEKAI+IIG+TL+PFDED+LIPCFGFGD TT DQ VFSF+ ++  C G E  + 
Sbjct:    65 GKRQNPYEKAISIIGRTLSPFDEDDLIPCFGFGDVTTRDQYVFSFYPENKSCDGLENAVK 124

Query:   188 CYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQ 247
              YR IVP+L+L+GPTS+APV++AA++IVE++  QYHVLVIIADGQVTR+ +   G LS Q
Sbjct:   125 RYREIVPHLKLSGPTSFAPVIDAAINIVEQNNMQYHVLVIIADGQVTRNPDVPLGRLSPQ 184

Query:   248 EQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNAT 307
             E+ T+ SI+AAS YPLSIVLVGVGDGPW+ M++FDD IP REFDNFQFVNFT IMS++  
Sbjct:   185 EEATMNSIMAASHYPLSIVLVGVGDGPWDTMKQFDDNIPHREFDNFQFVNFTKIMSEHKD 244

Query:   308 PSEKETAFALAALMEIPIQYKAAVEL 333
              ++KE AFALAALMEIP QYKA + L
Sbjct:   245 AAKKEAAFALAALMEIPFQYKATLSL 270

GO:0005886 "plasma membrane" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009690 "cytokinin metabolic process" evidence=RCA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009611 "response to wounding" evidence=IMP

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IMP

GO:0042742 "defense response to bacterium" evidence=IMP

DICTYBASE|DDB_G0272196 DDB_G0272196 "copine family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 136/267 (50%), Positives = 181/267 (67%)

Query:    71 KKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDT 130
             K K+  I D F SL++V  ALR +GLESSNLI+GID+TKSN W GK +F  + LH I   
Sbjct:    35 KVKFQPIKDKFQSLQEVQDALRTAGLESSNLIIGIDYTKSNTWNGKKTFGGKCLHDIQPG 94

Query:   131 P-NPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACY 189
               NPY++AI IIGKTL+ FD+DNL+P +GFGD+ T D+ VFSF  +  PC GF EVL  Y
Sbjct:    95 MLNPYQEAIEIIGKTLSVFDDDNLLPTYGFGDSRTTDKSVFSFTTER-PCFGFNEVLQKY 153

Query:   190 RNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQ 249
               I P + L+GPTS+AP++   ++I   +   YH+LVIIADG+V+  VN           
Sbjct:   154 NEITPLVSLSGPTSFAPIIRETINITAAAKA-YHILVIIADGEVS-VVN----------- 200

Query:   250 KTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPS 309
             +TIK+I  AS YP+SI+ +GVGDGPW+ M+KFDD +P R+FDNFQFV F   M+K     
Sbjct:   201 ETIKAIEEASKYPISIICIGVGDGPWDTMEKFDDDLPERQFDNFQFVPFHTTMAK---AE 257

Query:   310 EKETAFALAALMEIPIQYKAAVELGIM 336
              +E  FA+AAL EIP Q++   +LG++
Sbjct:   258 NREVDFAVAALQEIPEQFQYIKQLGLL 284

GO:0044351 "macropinocytosis" evidence=RCA

WB|WBGene00006495 cpna-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 569 (205.4 bits), Expect = 3.8e-54, P = 3.8e-54
 Identities = 114/259 (44%), Positives = 168/259 (64%)

Query:    82 SSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITI 140
             +SL+ ++ A+R +GLE++NLI GID+T SN++ G+ SF  RSLH I     NPY++ I+I
Sbjct:   845 TSLDSLSEAMRKAGLETTNLIFGIDYTASNKYQGEESFGGRSLHTIHPHVTNPYQQVISI 904

Query:   141 IGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAG 200
             +G+TLAPF     +  +GFGDA T D  VF+   +   C   +EVL  Y  + P + L+G
Sbjct:   905 LGRTLAPFAGQGRLGVYGFGDAKTGDWSVFNLKGEGGDCRSLDEVLNVYNTVTPTVALSG 964

Query:   201 PTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASS 260
             PT++AP++  AM+I +KS   YH+LVIIADGQVT             E+ T ++IV A  
Sbjct:   965 PTNFAPLIYQAMEICQKSR-DYHILVIIADGQVTN------------ERATRRAIVQACQ 1011

Query:   261 YPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAAL 320
             +PLSI++VGVGDGPW+ M+ FD+ +P R +DNF FV F  I+ K+    + +   A+ +L
Sbjct:  1012 HPLSIIVVGVGDGPWDMMRIFDESLPKRPWDNFHFVEFHEIVKKSTNMEDGDVKLAVQSL 1071

Query:   321 MEIPIQYKAAVELGIMGRT 339
             +EIP QY+   ELG++ R+
Sbjct:  1072 LEIPDQYRCICELGLLDRS 1090

GO:0016021 "integral to membrane" evidence=IEA

GO:0061199 "striated muscle contraction involved in embryonic body morphogenesis" evidence=IMP

MGI|MGI:1921270 Cpne4 "copine IV" [Mus musculus (taxid:10090)]

 Score = 270 (100.1 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 83/244 (34%), Positives = 126/244 (51%)

Query:   103 LGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGD 161
             + IDFT SN   G    N+ SLH I    PN Y KA+  +G+    +D D + P FGFG 
Sbjct:   310 VAIDFTASN---GDPR-NSCSLHYIHPYQPNEYLKALVAVGEICQDYDSDKMFPAFGFGA 365

Query:   162 ------ATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE-----A 210
                     +HD  + +F++D+  C G + V+  Y++ +P L+L GPT+ AP+++     A
Sbjct:   366 RIPPEYTVSHDFAI-NFNEDNPECAGIQGVVEAYQSCLPKLQLYGPTNIAPIIQKVAKSA 424

Query:   211 AMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGV 270
             + +   K   QY +L+I+ DG +T   +T +            +IV AS  P+S+++VGV
Sbjct:   425 SEETNTKEASQYFILLILTDGVITDMADTRE------------AIVHASHLPMSVIIVGV 472

Query:   271 GDGPWEDMQKFD--DKI---PARE---FDNFQFVNFTAIMSKNATPSEKETAFALAALME 322
             G+  + DMQ  D  D I   P  E    D  QFV F     K+A+P+    A A + L E
Sbjct:   473 GNADFSDMQMLDGDDGILRSPKGEPVLRDIVQFVPFRNF--KHASPA----ALAKSVLAE 526

Query:   323 IPIQ 326
             +P Q
Sbjct:   527 VPNQ 530

GO:0005515 "protein binding" evidence=IPI

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

MGI|MGI:2386621 Cpne1 "copine I" [Mus musculus (taxid:10090)]

 Score = 263 (97.6 bits), Expect = 5.3e-21, P = 5.3e-21
 Identities = 84/246 (34%), Positives = 123/246 (50%)

Query:   100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTP-NPYEKAITIIGKTLAPFDEDNLIPCFG 158
             N  +G+DFT SN   G  S  + SLH +  T  N Y  A+  +G  +  +D D L P FG
Sbjct:   284 NFTVGVDFTGSN---GDPSSPD-SLHYLSPTGVNEYLTALWSVGSVVQDYDSDKLFPAFG 339

Query:   159 FGDATTHDQEV-----FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE---- 209
             FG     D +V      +F+  +  C G + ++  YR  +P +RL GPT++AP++     
Sbjct:   340 FGAQVPPDWQVSHEFALNFNPSNPYCAGIQGIVDAYRQALPQVRLYGPTNFAPIINHVAR 399

Query:   210 -AAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLV 268
              AA    ++S  QY VL+++ DG VT      D E       T K++V AS  P+S+++V
Sbjct:   400 FAAQAAQQRSASQYFVLLLLTDGAVT------DVEA------TCKAVVDASKLPMSVIIV 447

Query:   269 GVGDGPWEDMQKFD-DKIPAREF-------DNFQFVNFTAIMSKNATPSEKETAFALAAL 320
             GVG   +E M++ D D  P R         D  QFV +     +NA P  +ET  A   L
Sbjct:   448 GVGGADFEVMEQLDADGGPLRTRSGEAAARDIVQFVPYRRF--QNA-P--RET-LAQTVL 501

Query:   321 MEIPIQ 326
              E+P Q
Sbjct:   502 AEVPTQ 507

GO:0001786 "phosphatidylserine binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0008150 "biological_process" evidence=ND

MGI|MGI:2142747 Cpne7 "copine VII" [Mus musculus (taxid:10090)]

 Score = 263 (97.6 bits), Expect = 6.0e-21, P = 6.0e-21
 Identities = 89/263 (33%), Positives = 132/263 (50%)

Query:   103 LGIDFTKSNEWTGKVSFNNRSLHAIGD-TPNPYEKAITIIGKTLAPFDEDNLIPCFGFGD 161
             + IDFT SN   G    N+ SLH I    PN Y +A+  +G+    +D D      GFG 
Sbjct:   309 VAIDFTASN---GDPR-NSCSLHHINPYQPNEYLRALVAVGEVCQDYDSDKRFSALGFGA 364

Query:   162 ATTHDQEV-----FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVE--AAMDI 214
                   EV      +F+ +   C G + V+  Y+N +P ++L GPT+ AP++   A M  
Sbjct:   365 RIPPKYEVSHDFAINFNPEDDECEGIQGVVEAYQNCLPKVQLYGPTNVAPIISKVARMAA 424

Query:   215 VEKSGG---QYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVG 271
              E+S G   QY++L+I+ DG VT        ++S     T ++IV AS  P+S+++VGVG
Sbjct:   425 AEESTGEASQYYILLILTDGVVT--------DMSD----TREAIVRASHLPMSVIIVGVG 472

Query:   272 DGPWEDMQKFD--DKI---PARE---FDNFQFVNFTAIMSKNATPSEKETAFALAALMEI 323
             +  + DMQ  D  D +   P  E    D  QFV F  +  KNA+P+    A A   L E+
Sbjct:   473 NADFTDMQILDGDDGVLRSPRGEPALRDIVQFVPFREL--KNASPA----ALAKCVLAEV 526

Query:   324 P---IQYKAAVELG--IMGRTTG 341
             P   ++Y +  EL    +G  TG
Sbjct:   527 PKQVVEYYSHKELPPRSLGAQTG 549

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.X.1323.1 hypothetical protein (362 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	422
cd01459	254	cd01459, vWA_copine_like, VWA Copine: Copines are	3e-99
pfam07002	146	pfam07002, Copine, Copine	4e-69
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	4e-10
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	4e-09
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	7e-08
smart00327	175	smart00327, VWA, von Willebrand factor (vWF) type	1e-06
smart00184	40	smart00184, RING, Ring finger	9e-06
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	8e-05
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-04
pfam14447	55	pfam14447, Prok-RING_4, Prokaryotic RING finger fa	0.001

>gnl|CDD|238736 cd01459, vWA_copine_like, VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium

 Score =  296 bits (759), Expect = 3e-99
 Identities = 122/274 (44%), Positives = 153/274 (55%), Gaps = 43/274 (15%)

Query: 77  IPDTFSSLEQVTA----------ALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHA 126
           I   + S  +VT             R +GLES NLI+ IDFTKSN W G+     RSLH 
Sbjct: 1   IKKVYKSSGEVTLTDCRVQPTFLDYRSAGLES-NLIVAIDFTKSNGWPGE----KRSLHY 55

Query: 127 I-GDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSF---HDDHTPCHGF 182
           I     NPY+KAI I+G+ L P+D D LIP FGFG   T DQ VFSF   + +   C GF
Sbjct: 56  ISPGRLNPYQKAIRIVGEVLQPYDSDKLIPAFGFGAIVTKDQSVFSFFPGYSESPECQGF 115

Query: 183 EEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GGQYHVLVIIADGQVTRSVNTG 240
           E VL  YR  +PN+ L+GPT++APV+ AA +I + S    +YH+L+II DG++T      
Sbjct: 116 EGVLRAYREALPNVSLSGPTNFAPVIRAAANIAKASNSQSKYHILLIITDGEITDMN--- 172

Query: 241 DGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDK-------IPAREFDNF 293
                    +TIK+IV AS YPLSIV+VGVGDGP++ M++ DD              D  
Sbjct: 173 ---------ETIKAIVEASKYPLSIVIVGVGDGPFDAMERLDDDDGLESSDGRIATRDIV 223

Query: 294 QFVNFTAIMSKNATPSEKETAFALAALMEIPIQY 327
           QFV FT  MS        E A A AAL EIP Q 
Sbjct: 224 QFVPFTEFMSN---AGNPEAALATAALAEIPSQL 254

They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding. Length = 254

>gnl|CDD|219263 pfam07002, Copine, Copine

 Score =  215 bits (549), Expect = 4e-69
 Identities = 73/158 (46%), Positives = 96/158 (60%), Gaps = 21/158 (13%)

Query: 123 SLHAIGDT-PNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEV-----FSFHDDH 176
           SLH I    PNPYE+AI I+G+ L P+D D   P FGFG     D EV      +F+ ++
Sbjct: 1   SLHYISPHQPNPYEQAIRIVGEILQPYDSDKRFPAFGFGARLPPDYEVSHDFPLNFNPEN 60

Query: 177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE---KSGGQYHVLVIIADGQV 233
             C+G E VL  YR  +PNL+L+GPT++AP+++AA  I E   +  GQYHVL+II DGQV
Sbjct: 61  PECNGIEGVLNAYREALPNLQLSGPTNFAPIIDAAARIAEASTQKSGQYHVLLIITDGQV 120

Query: 234 TRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVG 271
           T              + TI +IV AS  PLSI++VGVG
Sbjct: 121 T------------DMKATIDAIVRASHLPLSIIIVGVG 146

This family represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth. Length = 146

>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)

 Score = 54.7 bits (132), Expect = 4e-10
 Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 5/45 (11%)

Query: 378 CPICLTNAKDLAF-GCGHM-TCRECGSRV---SNCPICRQRITNR 417
           C ICL   +++ F  CGH+  C EC  R+     CPICRQ I + 
Sbjct: 5   CVICLERPRNVVFLPCGHLCLCEECAKRLRSKKKCPICRQPIESV 49

Length = 49

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 51.7 bits (124), Expect = 4e-09
 Identities = 20/41 (48%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 378 CPICLTNAKD--LAFGCGHMTCRECGSRV----SNCPICRQ 412
           CPICL   +D  +   CGH+ CREC  R     S CPICR 
Sbjct: 5   CPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

 Score = 48.2 bits (115), Expect = 7e-08
 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 7/44 (15%)

Query: 378 CPICLTNAKDLAF--GCGHMTCREC-----GSRVSNCPICRQRI 414
           CPICL   ++      CGH+ CR C      S  + CP+CR  I
Sbjct: 2   CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

>gnl|CDD|214621 smart00327, VWA, von Willebrand factor (vWF) type A domain

 Score = 48.2 bits (115), Expect = 1e-06
 Identities = 31/211 (14%), Positives = 67/211 (31%), Gaps = 49/211 (23%)

Query: 100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFG- 158
           +++  +D + S                     N +E A   + K +   D        G 
Sbjct: 1   DVVFLLDGSGSM------------------GGNRFELAKEFVLKLVEQLDIGPDGDRVGL 42

Query: 159 --FGDATTHDQEVFSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE 216
             F D       +F  +D  +     + +L    ++    +L G T+    ++ A++ + 
Sbjct: 43  VTFSDDAR---VLFPLNDSRSK----DALLEALASLSY--KLGGGTNLGAALQYALENLF 93

Query: 217 KS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVG 271
                   G   V+++I DG+                +  +K+        + + +VGVG
Sbjct: 94  SKSAGSRRGAPKVVILITDGESNDG-----------PKDLLKAAKELKRSGVKVFVVGVG 142

Query: 272 -DGPWEDMQKFDDKIPAREFDNFQFVNFTAI 301
            D   E+++K            F       +
Sbjct: 143 NDVDEEELKKLASA--PGGVYVFLPELLDLL 171

VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods. Length = 175

>gnl|CDD|214546 smart00184, RING, Ring finger

 Score = 42.1 bits (99), Expect = 9e-06
 Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 7/40 (17%)

Query: 378 CPICLTNAKDLAF--GCGHMTCREC-----GSRVSNCPIC 410
           CPICL           CGH  CR C      S  + CPIC
Sbjct: 1   CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s). Length = 40

>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 39.7 bits (93), Expect = 8e-05
 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 8/44 (18%)

Query: 378 CPICL----TNAKDLAFGCGHMTCRECGSRV----SNCPICRQR 413
           CPICL       + +   CGH+  +EC  +     + CP+CR  
Sbjct: 3   CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 7/40 (17%)

Query: 378 CPICLTNAKD--LAFGCGHMTCREC-----GSRVSNCPIC 410
           CPICL   KD      CGH+ C +C      S    CP+C
Sbjct: 1   CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Length = 40

>gnl|CDD|206613 pfam14447, Prok-RING_4, Prokaryotic RING finger family 4

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 12/42 (28%), Positives = 14/42 (33%), Gaps = 3/42 (7%)

Query: 376 QACPICLTNAKDLAF-GCGHMTCREC--GSRVSNCPICRQRI 414
           Q C  C T         CGH+       G R + CP C    
Sbjct: 8   QPCLFCGTVGTKGVLLPCGHLIPDGTFDGERYNGCPFCGTPF 49

RING finger family domain found sporadically in bacteria. The finger is fused to an N-terminal alpha-helical domain, ROT/Trove-like repeats and a C-terminal TerD domain. The architecture suggests a possible role in an RNA-processing complex. Length = 55

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	422
KOG1327	529	consensus Copine [Signal transduction mechanisms]	100.0
cd01459	254	vWA_copine_like VWA Copine: Copines are phospholip	100.0
PF07002	146	Copine: Copine; InterPro: IPR010734 This represent	100.0
PF10138	200	vWA-TerF-like: vWA found in TerF C terminus ; Inte	99.96
cd01457	199	vWA_ORF176_type VWA ORF176 type: Von Willebrand fa	99.81
smart00327	177	VWA von Willebrand factor (vWF) type A domain. VWA	98.72
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.59
cd01461	171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	98.58
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.53
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.5
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.46
cd01463	190	vWA_VGCC_like VWA Voltage gated Calcium channel li	98.42
cd01471	186	vWA_micronemal_protein Micronemal proteins: The To	98.42
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.42
cd00198	161	vWFA Von Willebrand factor type A (vWA) domain was	98.4
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.38
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.37
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	98.34
cd01464	176	vWA_subfamily VWA subfamily: Von Willebrand factor	98.3
cd01450	161	vWFA_subfamily_ECM Von Willebrand factor type A (v	98.26
PHA02929	238	N1R/p28-like protein; Provisional	98.25
cd01465	170	vWA_subgroup VWA subgroup: Von Willebrand factor t	98.21
cd01466	155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	98.17
PF13519	172	VWA_2: von Willebrand factor type A domain; PDB: 3	98.16
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.15
cd01454	174	vWA_norD_type norD type: Denitrifying bacteria con	98.15
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.13
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
cd01456	206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	98.09
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.06
PHA02926	242	zinc finger-like protein; Provisional	98.02
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	97.98
cd01482	164	vWA_collagen_alphaI-XII-like Collagen: The extrace	97.95
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
PF14634	44	zf-RING_5: zinc-RING finger domain	97.91
TIGR03788	596	marine_srt_targ marine proteobacterial sortase tar	97.88
cd01472	164	vWA_collagen von Willebrand factor (vWF) type A do	97.85
cd01467	180	vWA_BatA_type VWA BatA type: Von Willebrand factor	97.84
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.8
cd01470	198	vWA_complement_factors Complement factors B and C2	97.77
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	97.75
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	97.75
cd01476	163	VWA_integrin_invertebrates VWA_integrin (invertebr	97.75
cd01473	192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	97.73
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	97.72
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	97.66
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.62
cd01480	186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	97.62
cd01474	185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	97.57
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.56
cd01462	152	VWA_YIEM_type VWA YIEM type: Von Willebrand factor	97.56
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	97.55
PF13768	155	VWA_3: von Willebrand factor type A domain	97.54
PTZ00441	576	sporozoite surface protein 2 (SSP2); Provisional	97.54
PF00092	178	VWA: von Willebrand factor type A domain; InterPro	97.5
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	97.45
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
cd01475	224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	97.4
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.36
cd01453	183	vWA_transcription_factor_IIH_type Transcription fa	97.33
cd01451	178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	97.29
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.28
PRK13685	326	hypothetical protein; Provisional	97.25
cd01460	266	vWA_midasin VWA_Midasin: Midasin is a member of th	97.25
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.24
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	97.18
PF09967	126	DUF2201: VWA-like domain (DUF2201); InterPro: IPR0	97.12
cd01477	193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	97.08
cd01469	177	vWA_integrins_alpha_subunit Integrins are a class	97.04
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	97.03
cd01455	191	vWA_F11C1-5a_type Von Willebrand factor type A (vW	96.91
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	96.9
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	96.88
cd01481	165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	96.86
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.71
cd01458	218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	96.71
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	96.69
cd01452	187	VWA_26S_proteasome_subunit 26S proteasome plays a	96.53
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	96.51
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	96.49
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.47
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	96.44
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.37
TIGR03436	296	acidobact_VWFA VWFA-related Acidobacterial domain.	96.31
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.3
KOG3002	299	consensus Zn finger protein [General function pred	96.3
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	96.15
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	95.76
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	95.76
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.52
KOG2660	331	consensus Locus-specific chromosome binding protei	95.31
COG5152	259	Uncharacterized conserved protein, contains RING a	95.3
KOG0297	391	consensus TNF receptor-associated factor [Signal t	95.01
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	94.99
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.73
PF05762	222	VWA_CoxE: VWA domain containing CoxE-like protein;	94.69
PRK10997	487	yieM hypothetical protein; Provisional	94.43
PF04641	260	Rtf2: Rtf2 RING-finger	94.31
KOG0825	1134	consensus PHD Zn-finger protein [General function	94.23
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	94.23
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	94.06
TIGR00868	863	hCaCC calcium-activated chloride channel protein 1	94.03
KOG1002	791	consensus Nucleotide excision repair protein RAD16	93.77
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.41
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	93.38
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	92.86
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.06
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	91.84
COG5219	1525	Uncharacterized conserved protein, contains RING Z	90.3
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	90.02
KOG1001	674	consensus Helicase-like transcription factor HLTF/	89.28
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	89.18
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	88.87
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	88.86
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	88.64
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	85.78
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	83.92
KOG4445	368	consensus Uncharacterized conserved protein, conta	83.03
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	81.86
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	81.05
COG4245	207	TerY Uncharacterized protein encoded in toxicity p	80.29

>KOG1327 consensus Copine [Signal transduction mechanisms]

Probab=100.00  E-value=2.2e-84  Score=672.16  Aligned_cols=280  Identities=42%  Similarity=0.671  Sum_probs=250.3

Q ss_pred             cccccccCcchhhhcc--Cc-hhhccChhhhhhhcCCcc----cCCccccHHHHHHHHHhcCCccccceeeeeccCCCCC
Q 042398           41 ASSVSTSGTSSAAASA--TP-KENIISSARDKMKKKYSF----IPDTFSSLEQVTAALRDSGLESSNLILGIDFTKSNEW  113 (422)
Q Consensus        41 ~~~~~~~~~~~~~~~~--~~-~~~~i~~~~~~~k~~y~~----i~~~~~~ld~i~~~l~~~G~~~~nl~vaIDfT~SN~~  113 (422)
                      .++..+-.|+.+.+..  .+ ...++|+|+|.|||+|+.    +.+.|+.+++++-++..+|++++||+||||||+||||
T Consensus       221 ~~~ig~~~tt~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~g~~~l~~~~~~~~~sfld~i~gg~~lnf~vgIDfTaSNg~  300 (529)
T KOG1327|consen  221 HDLIGKFQTTLSELQEPGSPNQIMLINPKKKAKKKSYKNSGQLILDRFTSLDQYSFLDYIAGGEQLNFTVGIDFTASNGD  300 (529)
T ss_pred             cCceeEecccHHHhcccCCcccccccChhhhhhhhcccccceEEehheeehhhhhHHHHHccCceeeeEEEEEEeccCCC
Confidence            4555566677777743  33 358999999888886764    5577777777777777789999999999999999999


Q ss_pred             CCCCCCCCCCcccCCCC-CCHHHHHHHHHhccccccCCCCCcceeeecCCCCCC---CCC--cccCCCCCCCCCHHHHHH
Q 042398          114 TGKVSFNNRSLHAIGDT-PNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHD---QEV--FSFHDDHTPCHGFEEVLA  187 (422)
Q Consensus       114 ~g~~~~~~~SLH~~~~~-~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~---~~v--f~~~~~~~~~~G~~gvl~  187 (422)
                      ||    ++.|||||+|. +|+||+||++||+||++||+||+||||||||+.|++   +|+  |+|+|.||+|+|++|||+
T Consensus       301 p~----~~sSLHyi~p~~~N~Y~~Ai~~vG~~lq~ydsdk~fpa~GFGakip~~~~vs~~f~ln~~~~~~~c~Gi~gVl~  376 (529)
T KOG1327|consen  301 PR----NPSSLHYIDPHQPNPYEQAIRSVGETLQDYDSDKLFPAFGFGAKIPPDGQVSHEFVLNFNPEDPECRGIEGVLE  376 (529)
T ss_pred             CC----CCCcceecCCCCCCHHHHHHHHHhhhhcccCCCCccccccccccCCCCcccccceeecCCCCCCccccHHHHHH
Confidence            77    45599999985 999999999999999999999999999999998774   454  567789999999999999


Q ss_pred             HHHhhCCcccccCCCChHHHHHHHHHHHHHcC---CceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHhcCCCee
Q 042398          188 CYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG---GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLS  264 (422)
Q Consensus       188 ~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~---~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~AS~~PlS  264 (422)
                      ||++++|+|+|+|||+|||||++|+++|+++.   ++||||||||||+|||            |++|++|||.||+||||
T Consensus       377 aY~~~lp~v~l~GPTnFaPII~~va~~a~~~~~~~~qY~VLlIitDG~vTd------------m~~T~~AIV~AS~lPlS  444 (529)
T KOG1327|consen  377 AYRKALPNVQLYGPTNFSPIINHVARIAQQSGNTAGQYHVLLIITDGVVTD------------MKETRDAIVSASDLPLS  444 (529)
T ss_pred             HHHhhcccccccCCCccHHHHHHHHHHHHHhccCCcceEEEEEEeCCcccc------------HHHHHHHHHhhccCCeE
Confidence            99999999999999999999999999999886   8999999999999999            89999999999999999


Q ss_pred             EEEEecCCCCccccccccCCCCC-------cccccceecchhhhhccCCCCChHHHHHHHHHHhcccHHHHHHHHhhcc
Q 042398          265 IVLVGVGDGPWEDMQKFDDKIPA-------REFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIM  336 (422)
Q Consensus       265 IiiVGVG~~~f~~m~~LD~~~~~-------r~rDnvqFV~f~~~~~~~~~~~~~~~~la~~vL~EIP~Q~~~~~~~giL  336 (422)
                      ||||||||+||++|++||++.+.       |.|||||||+|++++.++.+...++++||+++|+|||+||+.||+++-+
T Consensus       445 IIiVGVGd~df~~M~~lD~d~~~l~~~gr~~~rD~vQFV~f~~~~~~~~~~~~~~~~lA~~vL~EIP~Q~~~y~~~~~~  523 (529)
T KOG1327|consen  445 IIIVGVGDADFDMMRELDGDDPKLRSPGRIAERDNVQFVPFRDIMNGAENPSDKEAALALAVLAEIPQQYVQYMRLRGI  523 (529)
T ss_pred             EEEEEeCCCCHHHHHHhhcCCcccccccccccccceEeecHHHHhhcCCcccchhHHHHHHHHHHhhHHHHHHHHhcCC
Confidence            99999999999999999987765       7899999999999999887778899999999999999999999998543

>cd01459 vWA_copine_like VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium

Probab=100.00  E-value=1.1e-74  Score=561.60  Aligned_cols=223  Identities=52%  Similarity=0.861  Sum_probs=202.2

Q ss_pred             ccccHHHHHHHHHhcCCccccceeeeeccCCCCCCCCCCCCCCCcccCCCC-CCHHHHHHHHHhccccccCCCCCcceee
Q 042398           80 TFSSLEQVTAALRDSGLESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDT-PNPYEKAITIIGKTLAPFDEDNLIPCFG  158 (422)
Q Consensus        80 ~~~~ld~i~~~l~~~G~~~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~-~N~Y~~AI~~ig~il~~yD~D~~ip~~G  158 (422)
                      .|+||||+.     +|++ +||+||||||+||||++    +++||||+++. +|+||+||++||+||++||+|++||+||
T Consensus        19 ~~tFldy~~-----~G~~-~nl~vaIDfT~SNg~p~----~~~SLHy~~~~~~N~Yq~aI~~vg~il~~yD~D~~ip~~G   88 (254)
T cd01459          19 QPTFLDYRS-----AGLE-SNLIVAIDFTKSNGWPG----EKRSLHYISPGRLNPYQKAIRIVGEVLQPYDSDKLIPAFG   88 (254)
T ss_pred             CCCHHHHHh-----CCCe-eeEEEEEEeCCCCCCCC----CCCCcccCCCCCccHHHHHHHHHHHHHHhcCCCCceeeEe
Confidence            899999998     5555 89999999999999976    56899999885 8999999999999999999999999999


Q ss_pred             ecCCCCCCCCC---cccCCCCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCC--ceEEEEEEeCCcc
Q 042398          159 FGDATTHDQEV---FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGG--QYHVLVIIADGQV  233 (422)
Q Consensus       159 FGa~~~~~~~v---f~~~~~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~--~Y~VLlIiTDG~i  233 (422)
                      ||++.+++..+   |++++++|+|.|++||+++|++++++|+|+|||+|+|||++|++++++...  +|+||||||||+|
T Consensus        89 FGa~~~~~~~v~~~f~~~~~~p~~~Gi~gvl~aY~~~l~~v~lsGpT~fapvI~~a~~~a~~~~~~~~Y~VLLIiTDG~i  168 (254)
T cd01459          89 FGAIVTKDQSVFSFFPGYSESPECQGFEGVLRAYREALPNVSLSGPTNFAPVIRAAANIAKASNSQSKYHILLIITDGEI  168 (254)
T ss_pred             ecccCCCCCccccccCCCCCCCcccCHHHHHHHHHHHhceeeecCcchHHHHHHHHHHHHHHhcCCCceEEEEEECCCCc
Confidence            99998776555   444688999999999999999999999999999999999999999987643  4999999999999


Q ss_pred             cccCCCCCCCCchhHHHHHHHHHHhcCCCeeEEEEecCCCCccccccccC-------CCCCcccccceecchhhhhccCC
Q 042398          234 TRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD-------KIPAREFDNFQFVNFTAIMSKNA  306 (422)
Q Consensus       234 ~d~~~~~~~~~~~~~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~-------~~~~r~rDnvqFV~f~~~~~~~~  306 (422)
                      +|            +++|++||++||++||||||||||++||+.|++||+       ..+.|.|||||||+|++++... 
T Consensus       169 ~D------------~~~t~~aIv~AS~~PlSIiiVGVGd~~F~~M~~LD~d~~l~~~~~~~~~rDnvqFV~f~~~~~~~-  235 (254)
T cd01459         169 TD------------MNETIKAIVEASKYPLSIVIVGVGDGPFDAMERLDDDDGLESSDGRIATRDIVQFVPFTEFMSNA-  235 (254)
T ss_pred             cc------------HHHHHHHHHHHhcCCeEEEEEEeCCCChHHHHHhcCccccccccCCcceecceeeecchhhcccc-
Confidence            99            899999999999999999999999999999999997       3567789999999999997542 


Q ss_pred             CCChHHHHHHHHHHhcccHHH
Q 042398          307 TPSEKETAFALAALMEIPIQY  327 (422)
Q Consensus       307 ~~~~~~~~la~~vL~EIP~Q~  327 (422)
                        ..++++||+++|+|||+|+
T Consensus       236 --~~~~~~La~~~L~EiP~Q~  254 (254)
T cd01459         236 --GNPEAALATAALAEIPSQL  254 (254)
T ss_pred             --cccHHHHHHHHHHhccccC
Confidence              1356899999999999995

They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding.

>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines

Probab=100.00  E-value=5.1e-51  Score=366.53  Aligned_cols=137  Identities=43%  Similarity=0.875  Sum_probs=129.7

Q ss_pred             CcccCCCC-CCHHHHHHHHHhccccccCCCCCcceeeecCCCCCC---CCCcccC--CCCCCCCCHHHHHHHHHhhCCcc
Q 042398          123 SLHAIGDT-PNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHD---QEVFSFH--DDHTPCHGFEEVLACYRNIVPNL  196 (422)
Q Consensus       123 SLH~~~~~-~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~---~~vf~~~--~~~~~~~G~~gvl~~Y~~~l~~v  196 (422)
                      ||||+++. +|+||+||++||+||++||+||+||+|||||+.+++   +++|+|+  +++|+|.|++||+++|++++++|
T Consensus         1 SLH~~~~~~~N~Y~~ai~~vg~il~~Yd~dk~~p~~GFGa~~~~~~~vsh~F~ln~~~~~p~~~Gi~gvl~~Y~~~~~~v   80 (146)
T PF07002_consen    1 SLHYISPNQPNPYQQAIRAVGEILQDYDSDKMIPAYGFGAKIPPDYSVSHCFPLNGNPQNPECQGIDGVLEAYRKALPKV   80 (146)
T ss_pred             CcccCCCCCCCHHHHHHHHHHHHHHhhccCCccceeccCCcCCCCcccccceeeecCCCCCcccCHHHHHHHHHHHhhhe
Confidence            89999996 999999999999999999999999999999998876   4568776  67899999999999999999999


Q ss_pred             cccCCCChHHHHHHHHHHHHH---cCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHhcCCCeeEEEEecC
Q 042398          197 RLAGPTSYAPVVEAAMDIVEK---SGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAASSYPLSIVLVGVG  271 (422)
Q Consensus       197 ~l~GPT~fapiI~~a~~~~~~---~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~AS~~PlSIiiVGVG  271 (422)
                      +|+|||+|+|||++|++++++   .+++||||||||||+|+|            |++|++||++||++||||||||||
T Consensus        81 ~l~GPT~fapiI~~a~~~a~~~~~~~~~Y~iLlIlTDG~i~D------------~~~T~~aIv~AS~~PlSIIiVGVG  146 (146)
T PF07002_consen   81 QLSGPTNFAPIINHAAKIAKQSNQNGQQYFILLILTDGQITD------------MEETIDAIVEASKLPLSIIIVGVG  146 (146)
T ss_pred             EECCCccHHHHHHHHHHHHhhhccCCceEEEEEEeccccccc------------HHHHHHHHHHHccCCeEEEEEEeC
Confidence            999999999999999999984   567999999999999999            899999999999999999999999

Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].

>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts

Probab=99.96  E-value=8.6e-29  Score=231.91  Aligned_cols=197  Identities=25%  Similarity=0.308  Sum_probs=166.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      ..+.+.||-|+|+..           .|-   ....|.+++++..+...||+|+.+++|.||....+..++        .
T Consensus         2 ArV~LVLD~SGSM~~-----------~yk---~G~vQ~~~Er~lalA~~~DdDG~i~v~~Fs~~~~~~~~v--------t   59 (200)
T PF10138_consen    2 ARVYLVLDISGSMRP-----------LYK---DGTVQRVVERILALAAQFDDDGEIDVWFFSTEFDRLPDV--------T   59 (200)
T ss_pred             cEEEEEEeCCCCCch-----------hhh---CccHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCcCCCc--------C
Confidence            357889999999941           122   257899999999999999999999999999987666655        3


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-CC-ceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHH
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-GG-QYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIV  256 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-~~-~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv  256 (422)
                      ...++++++.....++.+...|-|+++|||+.|++...++ .. .....|+||||.++|            .+++.++|+
T Consensus        60 ~~~~~~~v~~~~~~~~~~~~~G~t~y~~vm~~v~~~y~~~~~~~~P~~VlFiTDG~~~~------------~~~~~~~i~  127 (200)
T PF10138_consen   60 LDNYEGYVDELHAGLPDWGRMGGTNYAPVMEDVLDHYFKREPSDAPALVLFITDGGPDD------------RRAIEKLIR  127 (200)
T ss_pred             HHHHHHHHHHHhccccccCCCCCcchHHHHHHHHHHHhhcCCCCCCeEEEEEecCCccc------------hHHHHHHHH
Confidence            3567787766655555556567799999999999987744 22 356668889999998            789999999


Q ss_pred             HhcCCCeeEEEEecCCCCccccccccCCCCCcccccceecchhhhhccCCCCChHHHHHHHHHHhcccHHHHHHHHhhcc
Q 042398          257 AASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNFTAIMSKNATPSEKETAFALAALMEIPIQYKAAVELGIM  336 (422)
Q Consensus       257 ~AS~~PlSIiiVGVG~~~f~~m~~LD~~~~~r~rDnvqFV~f~~~~~~~~~~~~~~~~la~~vL~EIP~Q~~~~~~~giL  336 (422)
                      +||++||+|+|||||+.+|+.+++||+ +.+|.+||+.|+...++.      ..++++|+..+|.|+|.|+.++..+|+|
T Consensus       128 ~as~~pifwqFVgiG~~~f~fL~kLD~-l~gR~vDNa~Ff~~~d~~------~lsD~eLy~~LL~Efp~Wl~~ar~~gi~  200 (200)
T PF10138_consen  128 EASDEPIFWQFVGIGDSNFGFLEKLDD-LAGRVVDNAGFFAIDDID------ELSDEELYDRLLAEFPDWLKAARAKGIL  200 (200)
T ss_pred             hccCCCeeEEEEEecCCcchHHHHhhc-cCCcccCCcCeEecCCcc------cCCHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            999999999999999999999999999 589999999999998874      3567899999999999999999999875

>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=99.81  E-value=1e-19  Score=170.06  Aligned_cols=169  Identities=17%  Similarity=0.224  Sum_probs=128.3

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      ++++.||.|+|+++..    .+.++|    ..+.+++++..++.++..||.|+...+|+||....    .++.       
T Consensus         4 dvv~~ID~SgSM~~~~----~~~~~~----k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~~~~----~~~~-------   64 (199)
T cd01457           4 DYTLLIDKSGSMAEAD----EAKERS----RWEEAQESTRALARKCEEYDSDGITVYLFSGDFRR----YDNV-------   64 (199)
T ss_pred             CEEEEEECCCcCCCCC----CCCCch----HHHHHHHHHHHHHHHHHhcCCCCeEEEEecCCccc----cCCc-------
Confidence            6899999999998532    122333    35899999999999999999999777777766421    1211       


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHH-HHHc-C----CceEEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDI-VEKS-G----GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~-~~~~-~----~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                      . .+++.++|.+    +...|+|++.+.|+.+++. .+.. .    ..|.+++|||||+.+|            .+++.+
T Consensus        65 ~-~~~v~~~~~~----~~p~G~T~l~~~l~~a~~~~~~~~~~~~~~p~~~~vIiiTDG~~~d------------~~~~~~  127 (199)
T cd01457          65 N-SSKVDQLFAE----NSPDGGTNLAAVLQDALNNYFQRKENGATCPEGETFLVITDGAPDD------------KDAVER  127 (199)
T ss_pred             C-HHHHHHHHhc----CCCCCcCcHHHHHHHHHHHHHHHHhhccCCCCceEEEEEcCCCCCc------------HHHHHH
Confidence            1 5667676654    4456999999999999753 3221 1    1388999999999987            678899


Q ss_pred             HHHHhcCC-----CeeEEEEecCCC--CccccccccCCC--CCcccccceecchhhhhcc
Q 042398          254 SIVAASSY-----PLSIVLVGVGDG--PWEDMQKFDDKI--PAREFDNFQFVNFTAIMSK  304 (422)
Q Consensus       254 aIv~AS~~-----PlSIiiVGVG~~--~f~~m~~LD~~~--~~r~rDnvqFV~f~~~~~~  304 (422)
                      +|++|++.     +|.|.|||||++  .|..|++||+.+  .++.||||+||+|.++...
T Consensus       128 ~i~~a~~~l~~~~~i~i~~v~vG~~~~~~~~L~~ld~~~~~~~~~~d~vd~~~~~~~~~~  187 (199)
T cd01457         128 VIIKASDELDADNELAISFLQIGRDPAATAFLKALDDQLQEVGAKFDIVDTVTWDDMERL  187 (199)
T ss_pred             HHHHHHHhhccccCceEEEEEeCCcHHHHHHHHHHhHHHHhcCCcccceeeeeHHhhhcC
Confidence            99999873     888999999885  799999999753  3467899999999998653

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most

>smart00327 VWA von Willebrand factor (vWF) type A domain

Probab=98.72  E-value=8.9e-08  Score=85.03  Aligned_cols=149  Identities=21%  Similarity=0.354  Sum_probs=108.6

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      .++++.||-|.|+.                  ......+...+..++..+..   +..|-+++|++...   ..+++.  
T Consensus         2 ~~v~l~vD~S~SM~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~---~~~~~~--   58 (177)
T smart00327        2 LDVVFLLDGSGSMG------------------PNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDAT---VLFPLN--   58 (177)
T ss_pred             ccEEEEEeCCCccc------------------hHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCce---EEEccc--
Confidence            47899999999983                  13445555555555555554   88999999998532   222221  


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--C---CceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--G---GQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~---~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                        ...+.+.+.+......+.  ..|.|++...|+++++..+..  .   +...+++|||||...+.            +.
T Consensus        59 --~~~~~~~~~~~i~~~~~~--~~~~~~~~~al~~~~~~~~~~~~~~~~~~~~~iviitDg~~~~~------------~~  122 (177)
T smart00327       59 --DSRSKDALLEALASLSYK--LGGGTNLGAALQYALENLFSKSAGSRRGAPKVLILITDGESNDG------------GD  122 (177)
T ss_pred             --ccCCHHHHHHHHHhcCCC--CCCCchHHHHHHHHHHHhcCcCCCCCCCCCeEEEEEcCCCCCCC------------cc
Confidence              346778887777665543  578899999999999886521  1   12579999999999872            35


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC-CccccccccCCCC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG-PWEDMQKFDDKIP  286 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~-~f~~m~~LD~~~~  286 (422)
                      +.+++..+....+.|++||+|+. +.+.|+.|.....
T Consensus       123 ~~~~~~~~~~~~i~i~~i~~~~~~~~~~l~~~~~~~~  159 (177)
T smart00327      123 LLKAAKELKRSGVKVFVVGVGNDVDEEELKKLASAPG  159 (177)
T ss_pred             HHHHHHHHHHCCCEEEEEEccCccCHHHHHHHhCCCc
Confidence            77778888888899999999998 8999999987543

VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=98.59  E-value=1.1e-08  Score=75.75  Aligned_cols=43  Identities=49%  Similarity=1.239  Sum_probs=35.5

Q ss_pred             cCCcccccccccccc-cccCCCc-cchhhhhcC----CCCCCccccccC
Q 042398          374 ETQACPICLTNAKDL-AFGCGHM-TCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       374 e~~~CpIC~~~~~~v-~l~CGH~-fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      |+..|.||++...++ .++|||. ||..|+.++    ..||+||++|+.
T Consensus         1 ~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    1 EDEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             -HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             CcCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            357899999999994 5599999 999999977    789999999875

...

>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin)

Probab=98.58  E-value=6.2e-07  Score=80.22  Aligned_cols=147  Identities=20%  Similarity=0.278  Sum_probs=103.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .++++.+|.|.|+..                  ...+.|-.++..++..++.+..|-+++|+......   +..    +.
T Consensus         3 ~~v~~vlD~S~SM~~------------------~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~---~~~----~~   57 (171)
T cd01461           3 KEVVFVIDTSGSMSG------------------TKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEF---SPS----SV   57 (171)
T ss_pred             ceEEEEEECCCCCCC------------------hhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceee---cCc----ce
Confidence            478999999999941                  13667777777788888877789999999874321   111    01


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                      ..+.+.+ +...+.+..+...|-|++...|+.+.+..+...+.--++++||||..++            .+++.+++.++
T Consensus        58 ~~~~~~~-~~~~~~l~~~~~~g~T~l~~al~~a~~~l~~~~~~~~~iillTDG~~~~------------~~~~~~~~~~~  124 (171)
T cd01461          58 SATAENV-AAAIEYVNRLQALGGTNMNDALEAALELLNSSPGSVPQIILLTDGEVTN------------ESQILKNVREA  124 (171)
T ss_pred             eCCHHHH-HHHHHHHHhcCCCCCcCHHHHHHHHHHhhccCCCCccEEEEEeCCCCCC------------HHHHHHHHHHh
Confidence            1222222 2333445556668999999999999888765333457889999999765            45777888888


Q ss_pred             cCCCeeEEEEecCC-CCccccccccC
Q 042398          259 SSYPLSIVLVGVGD-GPWEDMQKFDD  283 (422)
Q Consensus       259 S~~PlSIiiVGVG~-~~f~~m~~LD~  283 (422)
                      .+.++.|..||+|. .+...|+.+-+
T Consensus       125 ~~~~i~i~~i~~g~~~~~~~l~~ia~  150 (171)
T cd01461         125 LSGRIRLFTFGIGSDVNTYLLERLAR  150 (171)
T ss_pred             cCCCceEEEEEeCCccCHHHHHHHHH
Confidence            77788999999996 46667776654

Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.53  E-value=4e-08  Score=90.47  Aligned_cols=49  Identities=37%  Similarity=0.997  Sum_probs=39.9

Q ss_pred             CcCCccccccccccc---ccccCCCccchhhhhcC----CCCCCccccccCc--cccC
Q 042398          373 AETQACPICLTNAKD---LAFGCGHMTCRECGSRV----SNCPICRQRITNR--LRLF  421 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~---v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~--i~vy  421 (422)
                      +....||||++-...   +...|||+||..|++..    ..||+||+.|+.+  ++||
T Consensus       129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~  186 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFHRIY  186 (187)
T ss_pred             ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhheecc
Confidence            445899999998887   34699999999999954    6899999988753  5655

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.50  E-value=1.1e-08  Score=76.94  Aligned_cols=47  Identities=38%  Similarity=1.041  Sum_probs=41.4

Q ss_pred             Cccccccccccc-ccccCCCcc-chhhhhcC-----CCCCCccccccCccccCC
Q 042398          376 QACPICLTNAKD-LAFGCGHMT-CRECGSRV-----SNCPICRQRITNRLRLFA  422 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l~CGH~f-C~~Ci~~~-----~~CP~CR~~i~~~i~vy~  422 (422)
                      .+|.||++.+.+ +..-|||++ |.+|..++     ..||+||++|..+|+.|+
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~   61 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR   61 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence            689999999999 555999996 99998865     479999999999999885

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.46  E-value=4.5e-08  Score=93.55  Aligned_cols=49  Identities=33%  Similarity=0.790  Sum_probs=41.5

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhcC-------CCCCCcccccc--CccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSRV-------SNCPICRQRIT--NRLRLF  421 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-------~~CP~CR~~i~--~~i~vy  421 (422)
                      .....|.||+|..++ ++..|||.||+-|+-+|       +.||+|+..++  +.+.||
T Consensus        45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlY  103 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLY  103 (230)
T ss_pred             CCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeee
Confidence            456899999999999 66699999999999987       57999999985  456665

>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta

Probab=98.42  E-value=1.9e-06  Score=79.89  Aligned_cols=148  Identities=14%  Similarity=0.241  Sum_probs=98.5

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCC-
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDH-  176 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~-  176 (422)
                      ..++++.||-|+|+..                  +..+.|-..+..++..+..+..|-++.|+.....   ++++..+. 
T Consensus        13 p~~vv~llD~SgSM~~------------------~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~---~~~~~~~~~   71 (190)
T cd01463          13 PKDIVILLDVSGSMTG------------------QRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNP---VVPCFNDTL   71 (190)
T ss_pred             CceEEEEEECCCCCCc------------------HHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeE---Eeeecccce
Confidence            4789999999999951                  2455666666666777777778999999987432   22221110 


Q ss_pred             --CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHH---c------CCceEEEEEEeCCcccccCCCCCCCCc
Q 042398          177 --TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEK---S------GGQYHVLVIIADGQVTRSVNTGDGELS  245 (422)
Q Consensus       177 --~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~---~------~~~Y~VLlIiTDG~i~d~~~~~~~~~~  245 (422)
                        ......+.+    .+.+..++..|.|++...|+.+.+...+   .      ...-.++++||||..++          
T Consensus        72 ~~~~~~~~~~~----~~~l~~l~~~G~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~----------  137 (190)
T cd01463          72 VQATTSNKKVL----KEALDMLEAKGIANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAIMLITDGVPEN----------  137 (190)
T ss_pred             EecCHHHHHHH----HHHHhhCCCCCcchHHHHHHHHHHHHHHhhhcccccccCCceeEEEEEeCCCCCc----------
Confidence              001123333    3445677788999999999999877654   1      12236789999998876          


Q ss_pred             hhHHHHHHHHHHh--cCCCeeEEEEecCCC--Ccccccccc
Q 042398          246 SQEQKTIKSIVAA--SSYPLSIVLVGVGDG--PWEDMQKFD  282 (422)
Q Consensus       246 ~~~~~T~~aIv~A--S~~PlSIiiVGVG~~--~f~~m~~LD  282 (422)
                        ..+..+++...  ...|+-|..||||.+  +...|+.|=
T Consensus       138 --~~~~~~~~~~~~~~~~~v~i~tigiG~~~~d~~~L~~lA  176 (190)
T cd01463         138 --YKEIFDKYNWDKNSEIPVRVFTYLIGREVTDRREIQWMA  176 (190)
T ss_pred             --HhHHHHHhcccccCCCcEEEEEEecCCccccchHHHHHH
Confidence              34445554322  235899999999975  577777764

The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.

>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell

Probab=98.42  E-value=2.5e-06  Score=78.38  Aligned_cols=170  Identities=12%  Similarity=0.153  Sum_probs=108.4

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++.+.||-|+|.+.                 .|-+.++...+..+++.+.   ++-.+-++.|+....   .++++...
T Consensus         1 ~Dv~~vlD~SgSm~~-----------------~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~---~~~~l~~~   60 (186)
T cd01471           1 LDLYLLVDGSGSIGY-----------------SNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAK---ELIRLSSP   60 (186)
T ss_pred             CcEEEEEeCCCCccc-----------------hhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCce---EEEECCCc
Confidence            368899999999852                 1225566666777777664   445799999997532   23444321


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc----CCceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                      .  -...+.+.+.-..........|-|++++.++.+.+...+.    ...-.+++|||||..++.            .++
T Consensus        61 ~--~~~~~~~~~~i~~l~~~~~~~G~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~~~------------~~~  126 (186)
T cd01471          61 N--STNKDLALNAIRALLSLYYPNGSTNTTSALLVVEKHLFDTRGNRENAPQLVIIMTDGIPDSK------------FRT  126 (186)
T ss_pred             c--ccchHHHHHHHHHHHhCcCCCCCccHHHHHHHHHHHhhccCCCcccCceEEEEEccCCCCCC------------cch
Confidence            1  1123332222233333445689999999999999877542    122357789999997662            344


Q ss_pred             HHHHHHhcCCCeeEEEEecCC-CCccccccccCCC-CCcccccceecchhhhh
Q 042398          252 IKSIVAASSYPLSIVLVGVGD-GPWEDMQKFDDKI-PAREFDNFQFVNFTAIM  302 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~-~~f~~m~~LD~~~-~~r~rDnvqFV~f~~~~  302 (422)
                      .++..++.+.++-|.+||||. .+.+.|+.|-+.. .....+++-+.+|+++.
T Consensus       127 ~~~a~~l~~~gv~v~~igiG~~~d~~~l~~ia~~~~~~~~~~~~~~~~~~~~~  179 (186)
T cd01471         127 LKEARKLRERGVIIAVLGVGQGVNHEENRSLVGCDPDDSPCPLYLQSSWSEVQ  179 (186)
T ss_pred             hHHHHHHHHCCCEEEEEEeehhhCHHHHHHhcCCCCCCCCCCeeecCCHHHHH
Confidence            555555556789999999997 5777788776532 12224777777777764

In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.42  E-value=9.6e-08  Score=89.59  Aligned_cols=45  Identities=29%  Similarity=0.840  Sum_probs=38.2

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC--------------------CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV--------------------SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~--------------------~~CP~CR~~i~~  416 (422)
                      ..++..|+||++..++ ++++|||.||+.|+.+|                    ..||+||..++.
T Consensus        15 ~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         15 SGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            4567899999999999 56699999999999753                    369999999864

>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.40  E-value=4.1e-06  Score=71.98  Aligned_cols=147  Identities=14%  Similarity=0.307  Sum_probs=98.9

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      ++++.||.|+|.+                  ...++++...+..++..+..   ...+-+++|+....   ..+.++.  
T Consensus         2 ~v~~viD~S~Sm~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~---~~~~~~~--   58 (161)
T cd00198           2 DIVFLLDVSGSMG------------------GEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNAR---VVLPLTT--   58 (161)
T ss_pred             cEEEEEeCCCCcC------------------cchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccc---eeecccc--
Confidence            6889999998872                  23455666666666666665   77899999997421   1222221  


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKS  254 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~a  254 (422)
                        ....+.+.+.-.. +.. ...|.|++...++.+.+...+.  .....++++||||..++.           .....+.
T Consensus        59 --~~~~~~~~~~~~~-~~~-~~~~~t~~~~al~~~~~~~~~~~~~~~~~~lvvitDg~~~~~-----------~~~~~~~  123 (161)
T cd00198          59 --DTDKADLLEAIDA-LKK-GLGGGTNIGAALRLALELLKSAKRPNARRVIILLTDGEPNDG-----------PELLAEA  123 (161)
T ss_pred             --cCCHHHHHHHHHh-ccc-CCCCCccHHHHHHHHHHHhcccCCCCCceEEEEEeCCCCCCC-----------cchhHHH
Confidence              1233344333222 222 4789999999999999887663  456889999999988762           1245556


Q ss_pred             HHHhcCCCeeEEEEecCC-CCccccccccCC
Q 042398          255 IVAASSYPLSIVLVGVGD-GPWEDMQKFDDK  284 (422)
Q Consensus       255 Iv~AS~~PlSIiiVGVG~-~~f~~m~~LD~~  284 (422)
                      +..+....+.|.+||+|+ .+-..++.|+..
T Consensus       124 ~~~~~~~~v~v~~v~~g~~~~~~~l~~l~~~  154 (161)
T cd00198         124 ARELRKLGITVYTIGIGDDANEDELKEIADK  154 (161)
T ss_pred             HHHHHHcCCEEEEEEcCCCCCHHHHHHHhcc
Confidence            666777799999999999 666677777653

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=98.38  E-value=9.5e-08  Score=68.62  Aligned_cols=33  Identities=52%  Similarity=1.222  Sum_probs=25.5

Q ss_pred             cccccccccc-ccccCCCccchhhhhcC--------CCCCCc
Q 042398          378 CPICLTNAKD-LAFGCGHMTCRECGSRV--------SNCPIC  410 (422)
Q Consensus       378 CpIC~~~~~~-v~l~CGH~fC~~Ci~~~--------~~CP~C  410 (422)
                      |+||++.+.+ ++++|||+||..|+.++        ..||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999999 77899999999999953        368887

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]

Probab=98.37  E-value=1.2e-07  Score=93.02  Aligned_cols=44  Identities=34%  Similarity=0.890  Sum_probs=38.5

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +....|.+|++...+ ..+||||.||+.|+..|    ..||+||..++.
T Consensus       237 ~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p  285 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQP  285 (293)
T ss_pred             CCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence            445799999999999 56799999999999977    579999999865

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.34  E-value=6.1e-08  Score=95.14  Aligned_cols=49  Identities=43%  Similarity=1.112  Sum_probs=44.9

Q ss_pred             cCCccccccccccc-ccccCCCcc-chhhhhcCCCCCCccccccCccccCC
Q 042398          374 ETQACPICLTNAKD-LAFGCGHMT-CRECGSRVSNCPICRQRITNRLRLFA  422 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v~l~CGH~f-C~~Ci~~~~~CP~CR~~i~~~i~vy~  422 (422)
                      ....|.||++.+.+ +.|+|||+. |.+|.+++..||+||+.|.+..|+|+
T Consensus       299 ~~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm~eCPICRqyi~rvvrif~  349 (350)
T KOG4275|consen  299 TRRLCAICMDAPRDCVFLECGHMVTCTKCGKRMNECPICRQYIVRVVRIFR  349 (350)
T ss_pred             HHHHHHHHhcCCcceEEeecCcEEeehhhccccccCchHHHHHHHHHhhhc
Confidence            36799999999999 556999996 99999999999999999999999985

>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.30  E-value=2.8e-06  Score=77.60  Aligned_cols=145  Identities=19%  Similarity=0.232  Sum_probs=95.9

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||.|+|...        ..       ...-.+|+..+...|...+   .+-.+-++.|+....   .++++..
T Consensus         3 ~~~v~~llD~SgSM~~--------~~-------~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~---~~~~l~~   64 (176)
T cd01464           3 RLPIYLLLDTSGSMAG--------EP-------IEALNQGLQMLQSELRQDPYALESVEISVITFDSAAR---VIVPLTP   64 (176)
T ss_pred             CCCEEEEEECCCCCCC--------hH-------HHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCce---EecCCcc
Confidence            3688999999999952        11       1233455665555554432   345799999998532   2344432


Q ss_pred             CCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCc---------eEEEEEEeCCcccccCCCCCCCCc
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQ---------YHVLVIIADGQVTRSVNTGDGELS  245 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~---------Y~VLlIiTDG~i~d~~~~~~~~~~  245 (422)
                      .       .      ......+...|-|++...++++.+......+.         -.++++||||+.+|.         
T Consensus        65 ~-------~------~~~~~~l~~~GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~---------  122 (176)
T cd01464          65 L-------E------SFQPPRLTASGGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDD---------  122 (176)
T ss_pred             H-------H------hcCCCcccCCCCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCch---------
Confidence            1       1      11245567789999999999999876442111         247899999998762         


Q ss_pred             hhHHHHHHHHHHhcCCCeeEEEEecCC-CCccccccccCC
Q 042398          246 SQEQKTIKSIVAASSYPLSIVLVGVGD-GPWEDMQKFDDK  284 (422)
Q Consensus       246 ~~~~~T~~aIv~AS~~PlSIiiVGVG~-~~f~~m~~LD~~  284 (422)
                        .....+++.++-..++-|..||||. .+.+.|++|-+.
T Consensus       123 --~~~~~~~~~~~~~~~~~i~~igiG~~~~~~~L~~ia~~  160 (176)
T cd01464         123 --LTAAIERIKEARDSKGRIVACAVGPKADLDTLKQITEG  160 (176)
T ss_pred             --HHHHHHHHHhhcccCCcEEEEEeccccCHHHHHHHHCC
Confidence              2334477877777789999999995 677778877654

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if

>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.26  E-value=4.7e-06  Score=73.05  Aligned_cols=145  Identities=16%  Similarity=0.246  Sum_probs=95.8

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccc---cccCCCCCcceeeecCCCCCCCCCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTL---APFDEDNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il---~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      ++++.+|.|+|...                  ..++.+...+..++   ...+.+-.+-++.|++...   .++++....
T Consensus         2 di~~llD~S~Sm~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~---~~~~~~~~~   60 (161)
T cd01450           2 DIVFLLDGSESVGP------------------ENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVR---VEFSLNDYK   60 (161)
T ss_pred             cEEEEEeCCCCcCH------------------HHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCce---EEEECCCCC
Confidence            67899999999851                  13344444444444   4444578899999998642   233332221


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC----CceEEEEEEeCCcccccCCCCCCCCchhHHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG----GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTI  252 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~----~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~  252 (422)
                          ..+.+.+.........  .|-|++...++.+.+...+..    ....++++||||..++.            .+..
T Consensus        61 ----~~~~~~~~i~~~~~~~--~~~t~~~~al~~a~~~~~~~~~~~~~~~~~iiliTDG~~~~~------------~~~~  122 (161)
T cd01450          61 ----SKDDLLKAVKNLKYLG--GGGTNTGKALQYALEQLFSESNARENVPKVIIVLTDGRSDDG------------GDPK  122 (161)
T ss_pred             ----CHHHHHHHHHhcccCC--CCCccHHHHHHHHHHHhcccccccCCCCeEEEEECCCCCCCC------------cchH
Confidence                3455555444322111  147999999999998876553    56788999999988762            1344


Q ss_pred             HHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          253 KSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       253 ~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      +++....+..+-|++||+|..+.+.|++|-+
T Consensus       123 ~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~  153 (161)
T cd01450         123 EAAAKLKDEGIKVFVVGVGPADEEELREIAS  153 (161)
T ss_pred             HHHHHHHHCCCEEEEEeccccCHHHHHHHhC
Confidence            5555555668999999999988888887754

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.25  E-value=4.1e-07  Score=88.34  Aligned_cols=45  Identities=29%  Similarity=0.806  Sum_probs=36.5

Q ss_pred             cCCccccccccccc---------ccccCCCccchhhhhcC----CCCCCccccccCcc
Q 042398          374 ETQACPICLTNAKD---------LAFGCGHMTCRECGSRV----SNCPICRQRITNRL  418 (422)
Q Consensus       374 e~~~CpIC~~~~~~---------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i  418 (422)
                      ++..|+||++.+.+         ++.+|+|.||..|+..|    ..||+||.++...+
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~v~  230 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVI  230 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeEEe
Confidence            35799999997654         23489999999999866    68999999987654

>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.21  E-value=2e-05  Score=70.48  Aligned_cols=147  Identities=14%  Similarity=0.189  Sum_probs=96.4

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      +|+++.+|.|.|...                  ..++.|..++..++..+..+..+-++.|+....   .++.+.+.   
T Consensus         1 ~~~~~vlD~S~SM~~------------------~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~---~~~~~~~~---   56 (170)
T cd01465           1 LNLVFVIDRSGSMDG------------------PKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAE---TVLPATPV---   56 (170)
T ss_pred             CcEEEEEECCCCCCC------------------hhHHHHHHHHHHHHHhCCCCCEEEEEEecCCcc---EEecCccc---
Confidence            478999999999841                  125677777777888887777899999998632   22332221   


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC--CceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHH
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG--GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIV  256 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~--~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv  256 (422)
                       ...+.+.    +.+.+++..|.|++..-++.+.+..++..  ..--.+++||||..++..        ...++..+++.
T Consensus        57 -~~~~~l~----~~l~~~~~~g~T~~~~al~~a~~~~~~~~~~~~~~~ivl~TDG~~~~~~--------~~~~~~~~~~~  123 (170)
T cd01465          57 -RDKAAIL----AAIDRLTAGGSTAGGAGIQLGYQEAQKHFVPGGVNRILLATDGDFNVGE--------TDPDELARLVA  123 (170)
T ss_pred             -chHHHHH----HHHHcCCCCCCCCHHHHHHHHHHHHHhhcCCCCeeEEEEEeCCCCCCCC--------CCHHHHHHHHH
Confidence             1223333    33445566899999999999998876532  223557899999876511        11345556666


Q ss_pred             HhcCCCeeEEEEecCCC-Ccccccccc
Q 042398          257 AASSYPLSIVLVGVGDG-PWEDMQKFD  282 (422)
Q Consensus       257 ~AS~~PlSIiiVGVG~~-~f~~m~~LD  282 (422)
                      .+.+..+-|..||+|.. +...|+++=
T Consensus       124 ~~~~~~v~i~~i~~g~~~~~~~l~~ia  150 (170)
T cd01465         124 QKRESGITLSTLGFGDNYNEDLMEAIA  150 (170)
T ss_pred             HhhcCCeEEEEEEeCCCcCHHHHHHHH
Confidence            66667888999999943 444555543

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n

>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.17  E-value=1.1e-05  Score=72.42  Aligned_cols=141  Identities=13%  Similarity=0.232  Sum_probs=91.7

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      ++++.||.|+|...                  +..+.|-.++..+++.+.++..+-+++|+.....   ++++.+..+  
T Consensus         2 ~v~~vlD~S~SM~~------------------~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~---~~~~~~~~~--   58 (155)
T cd01466           2 DLVAVLDVSGSMAG------------------DKLQLVKHALRFVISSLGDADRLSIVTFSTSAKR---LSPLRRMTA--   58 (155)
T ss_pred             cEEEEEECCCCCCc------------------HHHHHHHHHHHHHHHhCCCcceEEEEEecCCccc---cCCCcccCH--
Confidence            68899999999851                  1344455555555555555556999999986422   233332211  


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC--CceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHH
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG--GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVA  257 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~--~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~  257 (422)
                      .+-+    ...+.+..+...|-|+...-++.+.+..++..  +.-.++++||||..++            .    .++..
T Consensus        59 ~~~~----~~~~~i~~~~~~g~T~~~~al~~a~~~~~~~~~~~~~~~iillTDG~~~~------------~----~~~~~  118 (155)
T cd01466          59 KGKR----SAKRVVDGLQAGGGTNVVGGLKKALKVLGDRRQKNPVASIMLLSDGQDNH------------G----AVVLR  118 (155)
T ss_pred             HHHH----HHHHHHHhccCCCCccHHHHHHHHHHHHhhcccCCCceEEEEEcCCCCCc------------c----hhhhc
Confidence            1122    22334445677888999999999998876532  2346889999998765            1    22344


Q ss_pred             hcCCCeeEEEEecC-CCCccccccccC
Q 042398          258 ASSYPLSIVLVGVG-DGPWEDMQKFDD  283 (422)
Q Consensus       258 AS~~PlSIiiVGVG-~~~f~~m~~LD~  283 (422)
                      +.+.++-|..||+| +.+...|++|=+
T Consensus       119 ~~~~~v~v~~igig~~~~~~~l~~iA~  145 (155)
T cd01466         119 ADNAPIPIHTFGLGASHDPALLAFIAE  145 (155)
T ss_pred             ccCCCceEEEEecCCCCCHHHHHHHHh
Confidence            55679999999999 456667776643

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,

>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A

Probab=98.16  E-value=1.7e-05  Score=69.93  Aligned_cols=146  Identities=17%  Similarity=0.264  Sum_probs=99.7

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      ++++.+|-|+|+.+.             +...+..++|...+..++..+..| .|-+++|+...   ...+++      .
T Consensus         1 dvv~v~D~SgSM~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~-~v~l~~f~~~~---~~~~~~------t   57 (172)
T PF13519_consen    1 DVVFVLDNSGSMNGY-------------DGNRTRIDQAKDALNELLANLPGD-RVGLVSFSDSS---RTLSPL------T   57 (172)
T ss_dssp             EEEEEEE-SGGGGTT-------------TSSS-HHHHHHHHHHHHHHHHTTS-EEEEEEESTSC---EEEEEE------E
T ss_pred             CEEEEEECCcccCCC-------------CCCCcHHHHHHHHHHHHHHHCCCC-EEEEEEecccc---cccccc------c
Confidence            578999999999642             113578899999999999988755 99999999853   112333      2


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHhc
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAAS  259 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~AS  259 (422)
                      .+.+.+.++..+..+.....|.|++...|+.+.+........=-++++||||.-+.              ...+++..+.
T Consensus        58 ~~~~~~~~~l~~~~~~~~~~~~t~~~~al~~a~~~~~~~~~~~~~iv~iTDG~~~~--------------~~~~~~~~~~  123 (172)
T PF13519_consen   58 SDKDELKNALNKLSPQGMPGGGTNLYDALQEAAKMLASSDNRRRAIVLITDGEDNS--------------SDIEAAKALK  123 (172)
T ss_dssp             SSHHHHHHHHHTHHHHG--SSS--HHHHHHHHHHHHHC-SSEEEEEEEEES-TTHC--------------HHHHHHHHHH
T ss_pred             ccHHHHHHHhhcccccccCccCCcHHHHHHHHHHHHHhCCCCceEEEEecCCCCCc--------------chhHHHHHHH
Confidence            46777777777666666678999999999999998876643445668889997654              3334666777


Q ss_pred             CCCeeEEEEecCCCCcc--cccccc
Q 042398          260 SYPLSIVLVGVGDGPWE--DMQKFD  282 (422)
Q Consensus       260 ~~PlSIiiVGVG~~~f~--~m~~LD  282 (422)
                      ...+.|.+||+|...-.  .|+.+-
T Consensus       124 ~~~i~i~~v~~~~~~~~~~~l~~la  148 (172)
T PF13519_consen  124 QQGITIYTVGIGSDSDANEFLQRLA  148 (172)
T ss_dssp             CTTEEEEEEEES-TT-EHHHHHHHH
T ss_pred             HcCCeEEEEEECCCccHHHHHHHHH
Confidence            88999999999986543  444443

>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

Probab=98.15  E-value=3.8e-07  Score=65.53  Aligned_cols=35  Identities=43%  Similarity=1.113  Sum_probs=29.4

Q ss_pred             ccccccccccc----ccccCCCccchhhhhcC----CCCCCcc
Q 042398          377 ACPICLTNAKD----LAFGCGHMTCRECGSRV----SNCPICR  411 (422)
Q Consensus       377 ~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~----~~CP~CR  411 (422)
                      .|+||++.+..    +.++|||.||.+|+..|    ..||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            69999999854    45699999999999976    6899997

...

>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases

Probab=98.15  E-value=3.6e-05  Score=70.12  Aligned_cols=151  Identities=12%  Similarity=0.149  Sum_probs=93.2

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC-CCCCcceeeecCCCCCCC--CCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD-EDNLIPCFGFGDATTHDQ--EVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD-~D~~ip~~GFGa~~~~~~--~vf~~~~~~  176 (422)
                      .+.+.||.|+|...       .          +..+.|-.++..++.... .+-.+-+|+|+...+...  .++...+-+
T Consensus         2 ~v~~llD~SgSM~~-------~----------~kl~~ak~a~~~l~~~l~~~~d~~~l~~F~~~~~~~~~~~~~~~~~~~   64 (174)
T cd01454           2 AVTLLLDLSGSMRS-------D----------RRIDVAKKAAVLLAEALEACGVPHAILGFTTDAGGRERVRWIKIKDFD   64 (174)
T ss_pred             EEEEEEECCCCCCC-------C----------cHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCCCCccceEEEEecCcc
Confidence            47889999999952       0          334444444444443333 245799999987632111  122110101


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIV  256 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv  256 (422)
                         ..   +..+.++.+..+...|-|++.+.|+.+.+...+....--++++||||..++.. ...+++. ..++.++++.
T Consensus        65 ---~~---~~~~~~~~l~~~~~~g~T~~~~al~~a~~~l~~~~~~~~~iiliTDG~~~~~~-~~~~~~~-~~~~~~~~~~  136 (174)
T cd01454          65 ---ES---LHERARKRLAALSPGGNTRDGAAIRHAAERLLARPEKRKILLVISDGEPNDLD-YYEGNVF-ATEDALRAVI  136 (174)
T ss_pred             ---cc---cchhHHHHHHccCCCCCCcHHHHHHHHHHHHhcCCCcCcEEEEEeCCCcCccc-ccCcchh-HHHHHHHHHH
Confidence               00   11222344455666788999999999998877554445688999999988642 1122221 2345566688


Q ss_pred             HhcCCCeeEEEEecCCCCc
Q 042398          257 AASSYPLSIVLVGVGDGPW  275 (422)
Q Consensus       257 ~AS~~PlSIiiVGVG~~~f  275 (422)
                      +|-+..+.+..||||+...
T Consensus       137 ~~~~~gi~v~~igig~~~~  155 (174)
T cd01454         137 EARKLGIEVFGITIDRDAT  155 (174)
T ss_pred             HHHhCCcEEEEEEecCccc
Confidence            8888899999999998753

Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.13  E-value=1.1e-06  Score=90.91  Aligned_cols=49  Identities=27%  Similarity=0.621  Sum_probs=41.3

Q ss_pred             CCCCCCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          368 GSTPVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       368 s~~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      .-..+++.+.|+||++.+.+ ++++|||.||..|+..+    ..||+||..+..
T Consensus        19 ~l~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        19 SLYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             cccccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            34557888999999999999 56699999999999853    579999998754

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.11  E-value=7.6e-07  Score=89.86  Aligned_cols=49  Identities=37%  Similarity=0.997  Sum_probs=42.0

Q ss_pred             CcCCccccccccccc-ccccCCCcc-chhhhhcC----CCCCCccccccCccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMT-CRECGSRV----SNCPICRQRITNRLRLF  421 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~f-C~~Ci~~~----~~CP~CR~~i~~~i~vy  421 (422)
                      +.-..|.||+...+| +++||.|.+ |..|.+.+    ..||+||++|...+.+|
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~  342 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIY  342 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhheec
Confidence            345789999999999 677999997 99999955    57999999999877765

>cd01456 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.09  E-value=1.9e-05  Score=74.13  Aligned_cols=160  Identities=16%  Similarity=0.248  Sum_probs=95.7

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCC--CC-CcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHD--QE-VFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~--~~-vf~~~~~  175 (422)
                      .++++.||.|+|+...            -....+..+.|...+-.++..+..+..|-++.|+......  .. +++..+-
T Consensus        21 ~~vv~vlD~SgSM~~~------------~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~~~~~~~~~p~~~~   88 (206)
T cd01456          21 PNVAIVLDNSGSMREV------------DGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDNPLDVRVLVPKGCL   88 (206)
T ss_pred             CcEEEEEeCCCCCcCC------------CCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCCCcccccccccccc
Confidence            6899999999999631            0112456666777777777778777899999999854221  11 1211110


Q ss_pred             CCCCCCHH-HHHHHHHhhCCccc-ccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          176 HTPCHGFE-EVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       176 ~~~~~G~~-gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                      -....+.. .-.+...+.+..++ ..|-|+...-|+.+.+...  .+.-..+++||||.-++..         +..+..+
T Consensus        89 ~~~~~~~~~~~~~~l~~~i~~i~~~~G~T~l~~aL~~a~~~l~--~~~~~~iillTDG~~~~~~---------~~~~~~~  157 (206)
T cd01456          89 TAPVNGFPSAQRSALDAALNSLQTPTGWTPLAAALAEAAAYVD--PGRVNVVVLITDGEDTCGP---------DPCEVAR  157 (206)
T ss_pred             ccccCCCCcccHHHHHHHHHhhcCCCCcChHHHHHHHHHHHhC--CCCcceEEEEcCCCccCCC---------CHHHHHH
Confidence            00111211 11233344556666 7889999999999987765  2333678899999876511         0123333


Q ss_pred             HHHHh--cCCCeeEEEEecCCC-Cccccccc
Q 042398          254 SIVAA--SSYPLSIVLVGVGDG-PWEDMQKF  281 (422)
Q Consensus       254 aIv~A--S~~PlSIiiVGVG~~-~f~~m~~L  281 (422)
                      .+.+.  ..-++.|-+||+|.+ +-..|+++
T Consensus       158 ~~~~~~~~~~~i~i~~igiG~~~~~~~l~~i  188 (206)
T cd01456         158 ELAKRRTPAPPIKVNVIDFGGDADRAELEAI  188 (206)
T ss_pred             HHHHhcCCCCCceEEEEEecCcccHHHHHHH
Confidence            44333  124788999999975 34445444

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if

>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

Probab=98.06  E-value=9.7e-07  Score=61.97  Aligned_cols=33  Identities=45%  Similarity=1.228  Sum_probs=26.8

Q ss_pred             ccccccccccc--cccCCCccchhhhhcC----CCCCCc
Q 042398          378 CPICLTNAKDL--AFGCGHMTCRECGSRV----SNCPIC  410 (422)
Q Consensus       378 CpIC~~~~~~v--~l~CGH~fC~~Ci~~~----~~CP~C  410 (422)
                      |+||++.+.+.  .++|||.||.+|+.++    ..||+|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999999994  4599999999999964    678887

>PHA02926 zinc finger-like protein; Provisional

Probab=98.02  E-value=1.7e-06  Score=82.63  Aligned_cols=45  Identities=38%  Similarity=0.800  Sum_probs=35.1

Q ss_pred             CcCCcccccccccc------c----ccccCCCccchhhhhcCC----------CCCCccccccCc
Q 042398          373 AETQACPICLTNAK------D----LAFGCGHMTCRECGSRVS----------NCPICRQRITNR  417 (422)
Q Consensus       373 ~e~~~CpIC~~~~~------~----v~l~CGH~fC~~Ci~~~~----------~CP~CR~~i~~~  417 (422)
                      .++..|+||++...      +    ++.+|+|.||..|+..|.          .||+||..+...
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I  232 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI  232 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence            45689999998742      1    334999999999999762          399999998754

>smart00504 Ubox Modified RING finger domain

Probab=97.98  E-value=3.6e-06  Score=64.32  Aligned_cols=41  Identities=27%  Similarity=0.397  Sum_probs=36.0

Q ss_pred             Cccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          376 QACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +.|+||.+.+.+ ++++|||.||..|+..+    ..||+|+.+++.
T Consensus         2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            679999999999 66699999999999965    579999998854

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions

Probab=97.95  E-value=7.1e-05  Score=67.61  Aligned_cols=143  Identities=16%  Similarity=0.268  Sum_probs=91.0

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCCCCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      ++++.+|-|.|.+.                  ..++++...+-.++..+   .++-.|-++.|+....   .+|+++.  
T Consensus         2 Dv~~vlD~S~Sm~~------------------~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~---~~~~l~~--   58 (164)
T cd01482           2 DIVFLVDGSWSIGR------------------SNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPR---TEFDLNA--   58 (164)
T ss_pred             CEEEEEeCCCCcCh------------------hhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCee---EEEecCC--
Confidence            57899999988851                  12344444444444444   3567899999998742   2344431  


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                        ....+.++++..+. +  ...|.|+...-|+.+.+...+.     ...-.+++|||||.-+|.           .++.
T Consensus        59 --~~~~~~l~~~l~~~-~--~~~g~T~~~~aL~~a~~~~~~~~~~~r~~~~k~iillTDG~~~~~-----------~~~~  122 (164)
T cd01482          59 --YTSKEDVLAAIKNL-P--YKGGNTRTGKALTHVREKNFTPDAGARPGVPKVVILITDGKSQDD-----------VELP  122 (164)
T ss_pred             --CCCHHHHHHHHHhC-c--CCCCCChHHHHHHHHHHHhcccccCCCCCCCEEEEEEcCCCCCch-----------HHHH
Confidence              23455666654432 1  1478899999999888654221     234678899999987651           2233


Q ss_pred             HHHHHHhcCCCeeEEEEecCCCCccccccccCC
Q 042398          252 IKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDK  284 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~~  284 (422)
                      .+.   +-...+-|..||+|+.+...|+++-+.
T Consensus       123 a~~---lk~~gi~i~~ig~g~~~~~~L~~ia~~  152 (164)
T cd01482         123 ARV---LRNLGVNVFAVGVKDADESELKMIASK  152 (164)
T ss_pred             HHH---HHHCCCEEEEEecCcCCHHHHHHHhCC
Confidence            333   334688999999999887777777653

The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.92  E-value=3.3e-06  Score=88.64  Aligned_cols=42  Identities=40%  Similarity=0.921  Sum_probs=35.7

Q ss_pred             CCccccccccccc-ccccCCCccchhhhhc---------CCCCCCccccccC
Q 042398          375 TQACPICLTNAKD-LAFGCGHMTCRECGSR---------VSNCPICRQRITN  416 (422)
Q Consensus       375 ~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~---------~~~CP~CR~~i~~  416 (422)
                      ...||||++...- +.+.|||.||..|+.+         +..||+||..|.-
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            5799999999887 4558999999999884         3689999998865

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=97.91  E-value=4.6e-06  Score=60.17  Aligned_cols=36  Identities=36%  Similarity=1.057  Sum_probs=30.3

Q ss_pred             ccccccccccc----ccccCCCccchhhhhcCC----CCCCccc
Q 042398          377 ACPICLTNAKD----LAFGCGHMTCRECGSRVS----NCPICRQ  412 (422)
Q Consensus       377 ~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~~----~CP~CR~  412 (422)
                      .|++|++.+..    .+++|||.||..|+..+.    .||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            48999999832    456999999999999775    8999985

>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein

Probab=97.88  E-value=9.3e-05  Score=80.62  Aligned_cols=146  Identities=23%  Similarity=0.228  Sum_probs=96.8

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .++++.||.|+|+.  |                +..++|-.++..+|....++-.|-++.|+......   +...    .
T Consensus       272 ~~vvfvlD~SgSM~--g----------------~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~---~~~~----~  326 (596)
T TIGR03788       272 RELVFVIDTSGSMA--G----------------ESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLL---FPVP----V  326 (596)
T ss_pred             ceEEEEEECCCCCC--C----------------ccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEe---cccc----c
Confidence            57999999999984  1                23566777777777888777799999999874321   1110    0


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHH
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVA  257 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~  257 (422)
                      ..+ ++-++...+.+..++..|-|++.+.|+.+.+..... .+.--.+++||||++++            +.+.++++..
T Consensus       327 ~~~-~~~~~~a~~~i~~l~a~GgT~l~~aL~~a~~~~~~~~~~~~~~iillTDG~~~~------------~~~~~~~~~~  393 (596)
T TIGR03788       327 PAT-AHNLARARQFVAGLQADGGTEMAGALSAALRDDGPESSGALRQVVFLTDGAVGN------------EDALFQLIRT  393 (596)
T ss_pred             cCC-HHHHHHHHHHHhhCCCCCCccHHHHHHHHHHhhcccCCCceeEEEEEeCCCCCC------------HHHHHHHHHH
Confidence            011 222333344566677789999999999988763222 22234567899999876            5667777765


Q ss_pred             hcCCCeeEEEEecCCC-CccccccccC
Q 042398          258 ASSYPLSIVLVGVGDG-PWEDMQKFDD  283 (422)
Q Consensus       258 AS~~PlSIiiVGVG~~-~f~~m~~LD~  283 (422)
                      +. -..-|-.||||++ +...|+.|-.
T Consensus       394 ~~-~~~ri~tvGiG~~~n~~lL~~lA~  419 (596)
T TIGR03788       394 KL-GDSRLFTVGIGSAPNSYFMRKAAQ  419 (596)
T ss_pred             hc-CCceEEEEEeCCCcCHHHHHHHHH
Confidence            43 2456778999986 6666766643

Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).

>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins

Probab=97.85  E-value=0.00013  Score=65.71  Aligned_cols=141  Identities=18%  Similarity=0.301  Sum_probs=89.3

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      ++++.||-|+|...                  ..++.+...+..++..|+   .+-.+-++-|+....   .+++++.  
T Consensus         2 Dvv~vlD~SgSm~~------------------~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~---~~~~~~~--   58 (164)
T cd01472           2 DIVFLVDGSESIGL------------------SNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPR---TEFYLNT--   58 (164)
T ss_pred             CEEEEEeCCCCCCH------------------HHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCcee---EEEecCC--
Confidence            68899999999851                  123444444444555554   344788999987642   2344431  


Q ss_pred             CCCCCHHHHHHHHHhhCCcccc-cCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRL-AGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l-~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                        ....+.+.++    +.+++. .|.|+....+..|.+.....     .+.-.++++||||.-++              .
T Consensus        59 --~~~~~~~~~~----l~~l~~~~g~T~~~~al~~a~~~l~~~~~~~~~~~~~~iiliTDG~~~~--------------~  118 (164)
T cd01472          59 --YRSKDDVLEA----VKNLRYIGGGTNTGKALKYVRENLFTEASGSREGVPKVLVVITDGKSQD--------------D  118 (164)
T ss_pred             --CCCHHHHHHH----HHhCcCCCCCchHHHHHHHHHHHhCCcccCCCCCCCEEEEEEcCCCCCc--------------h
Confidence              1234444443    333443 78899999999999876541     23356788899997654              1


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      ...+..+.....+.|..||+|+.+.+.|+.+=+
T Consensus       119 ~~~~~~~l~~~gv~i~~ig~g~~~~~~L~~ia~  151 (164)
T cd01472         119 VEEPAVELKQAGIEVFAVGVKNADEEELKQIAS  151 (164)
T ss_pred             HHHHHHHHHHCCCEEEEEECCcCCHHHHHHHHC
Confidence            222333344467899999999988888877654

This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.

>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=97.84  E-value=0.00018  Score=65.32  Aligned_cols=140  Identities=17%  Similarity=0.228  Sum_probs=84.1

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .++++.||.|.|....   .+        . .++..+.|...+...+...+ +..+-++.|++...   .++.+.     
T Consensus         3 ~~vv~vlD~S~SM~~~---~~--------~-~~~r~~~a~~~~~~~~~~~~-~~~v~lv~f~~~~~---~~~~~~-----   61 (180)
T cd01467           3 RDIMIALDVSGSMLAQ---DF--------V-KPSRLEAAKEVLSDFIDRRE-NDRIGLVVFAGAAF---TQAPLT-----   61 (180)
T ss_pred             ceEEEEEECCcccccc---cC--------C-CCCHHHHHHHHHHHHHHhCC-CCeEEEEEEcCCee---eccCCC-----
Confidence            5799999999999632   11        1 23444555555656666554 44799999987642   122222     


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                       .+.+.+.+ .-+.+......|.|+...-|..+.+...+....-.++++||||.-++      +...+  .+..   ..+
T Consensus        62 -~~~~~~~~-~l~~l~~~~~~g~T~l~~al~~a~~~l~~~~~~~~~iiliTDG~~~~------g~~~~--~~~~---~~~  128 (180)
T cd01467          62 -LDRESLKE-LLEDIKIGLAGQGTAIGDAIGLAIKRLKNSEAKERVIVLLTDGENNA------GEIDP--ATAA---ELA  128 (180)
T ss_pred             -ccHHHHHH-HHHHhhhcccCCCCcHHHHHHHHHHHHHhcCCCCCEEEEEeCCCCCC------CCCCH--HHHH---HHH
Confidence             12222222 22222233457889998888888887765544558889999997653      22222  2222   233


Q ss_pred             cCCCeeEEEEecCC
Q 042398          259 SSYPLSIVLVGVGD  272 (422)
Q Consensus       259 S~~PlSIiiVGVG~  272 (422)
                      ....+-|..||+|.
T Consensus       129 ~~~gi~i~~i~ig~  142 (180)
T cd01467         129 KNKGVRIYTIGVGK  142 (180)
T ss_pred             HHCCCEEEEEEecC
Confidence            45677888888887

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.83  E-value=4.9e-06  Score=84.20  Aligned_cols=48  Identities=33%  Similarity=0.865  Sum_probs=42.1

Q ss_pred             CCcccccccccccc-cccCCCcc-chhhhhcCCCCCCccccccCccccCC
Q 042398          375 TQACPICLTNAKDL-AFGCGHMT-CRECGSRVSNCPICRQRITNRLRLFA  422 (422)
Q Consensus       375 ~~~CpIC~~~~~~v-~l~CGH~f-C~~Ci~~~~~CP~CR~~i~~~i~vy~  422 (422)
                      ...|.||.+.+++. .+||||++ |..|...+..||+||+.|...+++|+
T Consensus       305 p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~l~~CPvCR~rI~~~~k~y~  354 (355)
T KOG1571|consen  305 PDLCVVCLDEPKSAVFVPCGHVCCCTLCSKHLPQCPVCRQRIRLVRKRYR  354 (355)
T ss_pred             CCceEEecCCccceeeecCCcEEEchHHHhhCCCCchhHHHHHHHHHHhc
Confidence            35899999999995 45999996 77888889999999999999999885

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=97.80  E-value=5.8e-06  Score=90.32  Aligned_cols=50  Identities=32%  Similarity=0.704  Sum_probs=41.0

Q ss_pred             CCcCCcccccccccccccc-cCCCccchhhhhc-----CCCCCCccccccC--ccccC
Q 042398          372 VAETQACPICLTNAKDLAF-GCGHMTCRECGSR-----VSNCPICRQRITN--RLRLF  421 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v~l-~CGH~fC~~Ci~~-----~~~CP~CR~~i~~--~i~vy  421 (422)
                      .++.+.|++|.+.++++++ .|||.||..|+..     .+.||.|...|..  +.+||
T Consensus       640 yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~  697 (698)
T KOG0978|consen  640 YKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIH  697 (698)
T ss_pred             HHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence            3566899999999999555 9999999999994     4899999999864  34444

>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation

Probab=97.77  E-value=0.00021  Score=66.45  Aligned_cols=156  Identities=15%  Similarity=0.227  Sum_probs=90.7

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      +|+.+.||-|.|.+.        .       ..+.-.+++..+...|..|..+-.+-++.|+....   .+|++....  
T Consensus         1 ~di~~vlD~SgSM~~--------~-------~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~---~~~~~~~~~--   60 (198)
T cd01470           1 LNIYIALDASDSIGE--------E-------DFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPK---EIVSIRDFN--   60 (198)
T ss_pred             CcEEEEEECCCCccH--------H-------HHHHHHHHHHHHHHHccccCCCceEEEEEecCCce---EEEecccCC--
Confidence            478999999999851        0       11223344444444444444455799999987632   234443211  


Q ss_pred             CCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHHHHc--------CCceEEEEEEeCCcccccCCCCCCCCchhHH
Q 042398          179 CHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIVEKS--------GGQYHVLVIIADGQVTRSVNTGDGELSSQEQ  249 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~~~~--------~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~  249 (422)
                      -...+.++++-...-.... ..|-|++...|+++.+.....        ...-.++++||||+-++-       .+|  .
T Consensus        61 ~~~~~~~~~~l~~~~~~~~~~~ggT~~~~Al~~~~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g-------~~~--~  131 (198)
T cd01470          61 SNDADDVIKRLEDFNYDDHGDKTGTNTAAALKKVYERMALEKVRNKEAFNETRHVIILFTDGKSNMG-------GSP--L  131 (198)
T ss_pred             CCCHHHHHHHHHhCCcccccCccchhHHHHHHHHHHHHHHHHhcCccchhhcceEEEEEcCCCcCCC-------CCh--h
Confidence            1234455443333222221 246799999998887654211        112478999999988751       122  3


Q ss_pred             HHHHHHHHh----------cCCCeeEEEEecCCC-CccccccccC
Q 042398          250 KTIKSIVAA----------SSYPLSIVLVGVGDG-PWEDMQKFDD  283 (422)
Q Consensus       250 ~T~~aIv~A----------S~~PlSIiiVGVG~~-~f~~m~~LD~  283 (422)
                      +..+.|.++          ....+.|..||||+. +.+.|+++=.
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~v~i~~iGvG~~~~~~~L~~iA~  176 (198)
T cd01470         132 PTVDKIKNLVYKNNKSDNPREDYLDVYVFGVGDDVNKEELNDLAS  176 (198)
T ss_pred             HHHHHHHHHHhcccccccchhcceeEEEEecCcccCHHHHHHHhc
Confidence            344444443          334689999999974 7888887754

They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.75  E-value=7.6e-06  Score=57.58  Aligned_cols=33  Identities=45%  Similarity=1.229  Sum_probs=28.5

Q ss_pred             cccccccccc-c-cccCCCccchhhhhcC------CCCCCc
Q 042398          378 CPICLTNAKD-L-AFGCGHMTCRECGSRV------SNCPIC  410 (422)
Q Consensus       378 CpIC~~~~~~-v-~l~CGH~fC~~Ci~~~------~~CP~C  410 (422)
                      |+||++.+.+ . +++|||.||..|+.++      ..||+|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999999999 4 5699999999999854      569887

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Probab=97.75  E-value=1.2e-05  Score=55.95  Aligned_cols=38  Identities=42%  Similarity=1.182  Sum_probs=30.5

Q ss_pred             ccccccccccc-ccc-cCCCccchhhhhcC-----CCCCCccccc
Q 042398          377 ACPICLTNAKD-LAF-GCGHMTCRECGSRV-----SNCPICRQRI  414 (422)
Q Consensus       377 ~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~-----~~CP~CR~~i  414 (422)
                      .|+||++.+.+ +.+ +|||.||..|+..+     ..||.||..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            49999999855 444 69999999999843     5799998753

>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions

Probab=97.75  E-value=0.00043  Score=61.89  Aligned_cols=142  Identities=21%  Similarity=0.327  Sum_probs=88.6

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.+|-|.|...                   .|+++...+..++..+..   .-.+-+++|+.... ..-.|++...
T Consensus         1 ldv~~llD~S~Sm~~-------------------~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~~~~-~~~~~~l~~~   60 (163)
T cd01476           1 LDLLFVLDSSGSVRG-------------------KFEKYKKYIERIVEGLEIGPTATRVALITYSGRGR-QRVRFNLPKH   60 (163)
T ss_pred             CCEEEEEeCCcchhh-------------------hHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcCCCc-eEEEecCCCC
Confidence            468899999988741                   144555555555666654   57799999988521 1123444321


Q ss_pred             CCCCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHHHHc----CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIVEKS----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~~~~----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                          ...+.++++-.    .++ ..|.|+....|+.+.+...+.    .+...+++++|||..++.           ..+
T Consensus        61 ----~~~~~l~~~i~----~l~~~gg~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~~~-----------~~~  121 (163)
T cd01476          61 ----NDGEELLEKVD----NLRFIGGTTATGAAIEVALQQLDPSEGRREGIPKVVVVLTDGRSHDD-----------PEK  121 (163)
T ss_pred             ----CCHHHHHHHHH----hCccCCCCccHHHHHHHHHHHhccccCCCCCCCeEEEEECCCCCCCc-----------hHH
Confidence                23344444333    233 467899999999999887521    123488999999987651           233


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC---Cccccccc
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG---PWEDMQKF  281 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~---~f~~m~~L  281 (422)
                      ..+.+.+  ..-+.|+.||+|+.   +...|+.+
T Consensus       122 ~~~~l~~--~~~v~v~~vg~g~~~~~~~~~L~~i  153 (163)
T cd01476         122 QARILRA--VPNIETFAVGTGDPGTVDTEELHSI  153 (163)
T ss_pred             HHHHHhh--cCCCEEEEEECCCccccCHHHHHHH
Confidence            4555554  46688999999986   34444444

Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.

>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology

Probab=97.73  E-value=0.00077  Score=63.16  Aligned_cols=170  Identities=15%  Similarity=0.216  Sum_probs=106.0

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHH-HHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYE-KAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~-~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      .+++.+|=|.|-+.                  ..++ .++..+-.+++.|+-   +-.+-+.=|+....   ..++|+.+
T Consensus         2 Di~fllD~S~Si~~------------------~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~---~~~~~~~~   60 (192)
T cd01473           2 DLTLILDESASIGY------------------SNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNR---DVVPFSDE   60 (192)
T ss_pred             cEEEEEeCCCcccH------------------HHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCce---eEEecCcc
Confidence            47888998888751                  1233 244455556666653   45788888887541   23555432


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCC----ceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGG----QYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~----~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                      .  -..-++++++=++.-+.....|-|+....|+.+.+......+    .--|+++||||.-++..          ....
T Consensus        61 ~--~~~~~~l~~~i~~l~~~~~~~g~T~~~~AL~~a~~~~~~~~~~r~~~~kv~IllTDG~s~~~~----------~~~~  128 (192)
T cd01473          61 E--RYDKNELLKKINDLKNSYRSGGETYIVEALKYGLKNYTKHGNRRKDAPKVTMLFTDGNDTSAS----------KKEL  128 (192)
T ss_pred             c--ccCHHHHHHHHHHHHhccCCCCcCcHHHHHHHHHHHhccCCCCcccCCeEEEEEecCCCCCcc----------hhhH
Confidence            1  123456666555444334446889999999998877643221    36899999999988621          2345


Q ss_pred             HHHHHHhcCCCeeEEEEecCCCCccccccccCCC-CCcccccceecchhhhh
Q 042398          252 IKSIVAASSYPLSIVLVGVGDGPWEDMQKFDDKI-PAREFDNFQFVNFTAIM  302 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~~~-~~r~rDnvqFV~f~~~~  302 (422)
                      .++...+-+..+-|..||||..+-..++.+=+.- ......+|=..+|+++.
T Consensus       129 ~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia~~~~~~~~~~~~~~~~f~~l~  180 (192)
T cd01473         129 QDISLLYKEENVKLLVVGVGAASENKLKLLAGCDINNDNCPNVIKTEWNNLN  180 (192)
T ss_pred             HHHHHHHHHCCCEEEEEEeccccHHHHHHhcCCCCCCCCCCeEEecchhhHH
Confidence            6777777888999999999998766666665431 11112344445566553

CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]

Probab=97.72  E-value=5.6e-06  Score=83.01  Aligned_cols=45  Identities=24%  Similarity=0.640  Sum_probs=38.9

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +.+-+.|.||++++.. +.+||+|.||.-||...    ..||.|+.+++.
T Consensus        20 lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   20 LDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             hHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccch
Confidence            5667899999999999 55699999999999964    689999998864

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.68  E-value=1.3e-05  Score=75.99  Aligned_cols=42  Identities=40%  Similarity=1.020  Sum_probs=36.6

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccc
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQ  412 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~  412 (422)
                      ...+...|+||++.+.+ .+++|||.||..|+..+    ..||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            36778999999999999 56799999999999964    58999993

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.66  E-value=1.6e-05  Score=77.56  Aligned_cols=43  Identities=28%  Similarity=0.696  Sum_probs=36.8

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhc-C-----CCCCCcccccc
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSR-V-----SNCPICRQRIT  415 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~-~-----~~CP~CR~~i~  415 (422)
                      ..+..|.||++.... ..++|||.||..|+.. |     ..||+||+...
T Consensus       213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~  262 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY  262 (271)
T ss_pred             ccccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence            457899999999998 5679999999999986 4     45999999764

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=97.62  E-value=1.7e-05  Score=61.95  Aligned_cols=44  Identities=32%  Similarity=0.843  Sum_probs=25.8

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC--CCCCCcccccc
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV--SNCPICRQRIT  415 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~--~~CP~CR~~i~  415 (422)
                      +++.+.|++|.+.++. +.+ .|.|.||+.|+...  ..||+|+.+-.
T Consensus         4 le~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw   51 (65)
T PF14835_consen    4 LEELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAW   51 (65)
T ss_dssp             HHHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S
T ss_pred             HHHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHH
Confidence            3456899999999999 444 99999999999965  67999999864

>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions

Probab=97.62  E-value=0.00044  Score=63.98  Aligned_cols=148  Identities=16%  Similarity=0.233  Sum_probs=93.3

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---------CCCCCcceeeecCCCCCCCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---------DEDNLIPCFGFGDATTHDQE  168 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---------D~D~~ip~~GFGa~~~~~~~  168 (422)
                      .+++++.||-|.|.+.                  ..++.+...+-.++..+         ..+-.+-++.|+....   .
T Consensus         2 ~~dvv~vlD~S~Sm~~------------------~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~---~   60 (186)
T cd01480           2 PVDITFVLDSSESVGL------------------QNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQE---V   60 (186)
T ss_pred             CeeEEEEEeCCCccch------------------hhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCce---e
Confidence            3789999999999851                  12344444444444444         2235788999987632   2


Q ss_pred             CcccCCCCCCCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHHHH--cCCceEEEEEEeCCcccccCCCCCCCCc
Q 042398          169 VFSFHDDHTPCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIVEK--SGGQYHVLVIIADGQVTRSVNTGDGELS  245 (422)
Q Consensus       169 vf~~~~~~~~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~~~--~~~~Y~VLlIiTDG~i~d~~~~~~~~~~  245 (422)
                      +|++..+   -...+.+.+    .+..++ ..|.|+...-|+++.+....  ..+.-.++++||||.-++..        
T Consensus        61 ~~~l~~~---~~~~~~l~~----~i~~l~~~gg~T~~~~AL~~a~~~l~~~~~~~~~~~iillTDG~~~~~~--------  125 (186)
T cd01480          61 EAGFLRD---IRNYTSLKE----AVDNLEYIGGGTFTDCALKYATEQLLEGSHQKENKFLLVITDGHSDGSP--------  125 (186)
T ss_pred             eEecccc---cCCHHHHHH----HHHhCccCCCCccHHHHHHHHHHHHhccCCCCCceEEEEEeCCCcCCCc--------
Confidence            3555421   123444433    344444 47899999999999987764  12345788999999864311        


Q ss_pred             hhHHHHHHHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          246 SQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       246 ~~~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                        .....+++.++.+..+.|..||||..+-..|+++=+
T Consensus       126 --~~~~~~~~~~~~~~gi~i~~vgig~~~~~~L~~IA~  161 (186)
T cd01480         126 --DGGIEKAVNEADHLGIKIFFVAVGSQNEEPLSRIAC  161 (186)
T ss_pred             --chhHHHHHHHHHHCCCEEEEEecCccchHHHHHHHc
Confidence              123345556666889999999999966555555543

The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.

>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax

Probab=97.57  E-value=0.00038  Score=64.16  Aligned_cols=146  Identities=15%  Similarity=0.216  Sum_probs=88.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC-CCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD-EDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD-~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +++++.||-|+|.+..                   +.+++..+-+++..|+ .+-.+-++.|+...   ..+|+|+... 
T Consensus         5 ~Dvv~llD~SgSm~~~-------------------~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~---~~~~~l~~~~-   61 (185)
T cd01474           5 FDLYFVLDKSGSVAAN-------------------WIEIYDFVEQLVDRFNSPGLRFSFITFSTRA---TKILPLTDDS-   61 (185)
T ss_pred             eeEEEEEeCcCchhhh-------------------HHHHHHHHHHHHHHcCCCCcEEEEEEecCCc---eEEEeccccH-
Confidence            6899999999998520                   1111222222333332 34689999998753   2356664322 


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHH--cCCce--EEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEK--SGGQY--HVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~--~~~~Y--~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                           +.+.++.. .++.+...|-|+...-|+.|.+....  .++..  .++++||||.-++..          ...+.+
T Consensus        62 -----~~~~~~l~-~l~~~~~~g~T~~~~aL~~a~~~l~~~~~~~r~~~~~villTDG~~~~~~----------~~~~~~  125 (185)
T cd01474          62 -----SAIIKGLE-VLKKVTPSGQTYIHEGLENANEQIFNRNGGGRETVSVIIALTDGQLLLNG----------HKYPEH  125 (185)
T ss_pred             -----HHHHHHHH-HHhccCCCCCCcHHHHHHHHHHHHHhhccCCCCCCeEEEEEcCCCcCCCC----------CcchHH
Confidence                 12222221 24455567899999999999876532  22222  788999999985410          112333


Q ss_pred             HHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          254 SIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       254 aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      +...+-+..+-|..||||+.+...|+.+=+
T Consensus       126 ~a~~l~~~gv~i~~vgv~~~~~~~L~~iA~  155 (185)
T cd01474         126 EAKLSRKLGAIVYCVGVTDFLKSQLINIAD  155 (185)
T ss_pred             HHHHHHHcCCEEEEEeechhhHHHHHHHhC
Confidence            344444567889999998888777877754

ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=97.56  E-value=2.1e-05  Score=77.64  Aligned_cols=45  Identities=29%  Similarity=0.635  Sum_probs=38.2

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +...+.|.||-+.++. +..+|||.||.-||.+.    ..||+||.....
T Consensus        22 LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          22 LDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             chhHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            4556899999999998 56699999999999964    689999998643

>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=97.56  E-value=0.0016  Score=57.74  Aligned_cols=133  Identities=16%  Similarity=0.175  Sum_probs=78.8

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      .+.+.||.|+|...+               ..-....++..++..+..  .+..+-++.|+...    ....+.    .-
T Consensus         2 ~v~illD~SgSM~~~---------------k~~~a~~~~~~l~~~~~~--~~~~v~li~F~~~~----~~~~~~----~~   56 (152)
T cd01462           2 PVILLVDQSGSMYGA---------------PEEVAKAVALALLRIALA--ENRDTYLILFDSEF----QTKIVD----KT   56 (152)
T ss_pred             CEEEEEECCCCCCCC---------------HHHHHHHHHHHHHHHHHH--cCCcEEEEEeCCCc----eEEecC----Cc
Confidence            478999999999520               011234444555555544  23468999998871    111111    11


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCc-ccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQ-VTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~-i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                      ..+..+++.    +..+...|.|++++.+..+.+..++....=.+++|||||. -.+            ..+..++...+
T Consensus        57 ~~~~~~~~~----l~~~~~~ggT~l~~al~~a~~~l~~~~~~~~~ivliTDG~~~~~------------~~~~~~~~~~~  120 (152)
T cd01462          57 DDLEEPVEF----LSGVQLGGGTDINKALRYALELIERRDPRKADIVLITDGYEGGV------------SDELLREVELK  120 (152)
T ss_pred             ccHHHHHHH----HhcCCCCCCcCHHHHHHHHHHHHHhcCCCCceEEEECCCCCCCC------------CHHHHHHHHHH
Confidence            345555543    3345678999999999999988776433336789999995 222            12332223333


Q ss_pred             cCCCeeEEEEecCCC
Q 042398          259 SSYPLSIVLVGVGDG  273 (422)
Q Consensus       259 S~~PlSIiiVGVG~~  273 (422)
                      .....=|-.||||+.
T Consensus       121 ~~~~~~v~~~~~g~~  135 (152)
T cd01462         121 RSRVARFVALALGDH  135 (152)
T ss_pred             HhcCcEEEEEEecCC
Confidence            344566777777763

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=97.55  E-value=1.9e-05  Score=57.09  Aligned_cols=26  Identities=35%  Similarity=1.097  Sum_probs=16.5

Q ss_pred             cccccccccc-----ccccCCCccchhhhhcC
Q 042398          378 CPICLTNAKD-----LAFGCGHMTCRECGSRV  404 (422)
Q Consensus       378 CpIC~~~~~~-----v~l~CGH~fC~~Ci~~~  404 (422)
                      ||||.+ +.+     ++|+|||+||.+|+.++
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l   31 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKL   31 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHH
Confidence            899999 544     56799999999999965

>PF13768 VWA_3: von Willebrand factor type A domain

Probab=97.54  E-value=0.00039  Score=61.81  Aligned_cols=143  Identities=15%  Similarity=0.253  Sum_probs=88.4

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      ++++-||.+.|+..           +    . ..-..|++.+.+-|.   +...|-++.||.........  +-+-  .-
T Consensus         2 ~vvilvD~S~Sm~g-----------~----~-~~~k~al~~~l~~L~---~~d~fnii~f~~~~~~~~~~--~~~~--~~   58 (155)
T PF13768_consen    2 DVVILVDTSGSMSG-----------E----K-ELVKDALRAILRSLP---PGDRFNIIAFGSSVRPLFPG--LVPA--TE   58 (155)
T ss_pred             eEEEEEeCCCCCCC-----------c----H-HHHHHHHHHHHHhCC---CCCEEEEEEeCCEeeEcchh--HHHH--hH
Confidence            58999999999952           1    1 334455555555544   45589999999863211110  0000  01


Q ss_pred             CCHHHHHHHHHhhCCcccc-cCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          180 HGFEEVLACYRNIVPNLRL-AGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l-~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                      .+.+.+    .+-+..+.. .|.|+..+.++.|.+.... .+.-..+++||||..++.           .+++.+.+..+
T Consensus        59 ~~~~~a----~~~I~~~~~~~G~t~l~~aL~~a~~~~~~-~~~~~~IilltDG~~~~~-----------~~~i~~~v~~~  122 (155)
T PF13768_consen   59 ENRQEA----LQWIKSLEANSGGTDLLAALRAALALLQR-PGCVRAIILLTDGQPVSG-----------EEEILDLVRRA  122 (155)
T ss_pred             HHHHHH----HHHHHHhcccCCCccHHHHHHHHHHhccc-CCCccEEEEEEeccCCCC-----------HHHHHHHHHhc
Confidence            223333    333444666 8999999999988865422 234566688899997431           46777766654


Q ss_pred             cCCCeeEEEEecCC-CCcccccccc
Q 042398          259 SSYPLSIVLVGVGD-GPWEDMQKFD  282 (422)
Q Consensus       259 S~~PlSIiiVGVG~-~~f~~m~~LD  282 (422)
                      . -.+-|..+|+|. .+...|++|=
T Consensus       123 ~-~~~~i~~~~~g~~~~~~~L~~LA  146 (155)
T PF13768_consen  123 R-GHIRIFTFGIGSDADADFLRELA  146 (155)
T ss_pred             C-CCceEEEEEECChhHHHHHHHHH
Confidence            3 557788899998 5666666553

>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional

Probab=97.54  E-value=0.00092  Score=72.24  Aligned_cols=142  Identities=13%  Similarity=0.213  Sum_probs=96.3

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCC-CCcc--eeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDED-NLIP--CFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D-~~ip--~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||-|+|.+.                 .|-.++|...+..++..++.. ..+-  +..|+...   ..+|++..
T Consensus        42 ~lDIvFLLD~SgSMg~-----------------~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~---r~vfpL~s  101 (576)
T PTZ00441         42 EVDLYLLVDGSGSIGY-----------------HNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNT---TELIRLGS  101 (576)
T ss_pred             CceEEEEEeCCCccCC-----------------ccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCc---eEEEecCC
Confidence            4789999999999862                 144567777777777777532 1233  35776653   23455533


Q ss_pred             CCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC---CceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG---GQYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~---~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                      ..  -...+.++.+-.+....+..+|-|++...+..+.+...+.+   ..--++++||||.-++            ..++
T Consensus       102 ~~--s~Dk~~aL~~I~sL~~~~~pgGgTnig~AL~~Aae~L~sr~~R~nvpKVVILLTDG~sns------------~~dv  167 (576)
T PTZ00441        102 GA--SKDKEQALIIVKSLRKTYLPYGKTNMTDALLEVRKHLNDRVNRENAIQLVILMTDGIPNS------------KYRA  167 (576)
T ss_pred             Cc--cccHHHHHHHHHHHHhhccCCCCccHHHHHHHHHHHHhhcccccCCceEEEEEecCCCCC------------cccH
Confidence            21  13445677766666666777899999999999887765431   2236889999998654            2345


Q ss_pred             HHHHHHhcCCCeeEEEEecCCC
Q 042398          252 IKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      ++++.......+-|..||||.+
T Consensus       168 leaAq~LR~~GVeI~vIGVG~g  189 (576)
T PTZ00441        168 LEESRKLKDRNVKLAVIGIGQG  189 (576)
T ss_pred             HHHHHHHHHCCCEEEEEEeCCC
Confidence            5666666677899999999974

>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma

Probab=97.50  E-value=0.00042  Score=61.76  Aligned_cols=148  Identities=14%  Similarity=0.212  Sum_probs=88.9

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      ++++.||-|.|.+..               ..+...+++..+..-+...+..-.+-+.-||....   .+|+|+-.    
T Consensus         1 DivflvD~S~sm~~~---------------~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~---~~~~~~~~----   58 (178)
T PF00092_consen    1 DIVFLVDTSGSMSGD---------------NFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSAR---VLFSLTDY----   58 (178)
T ss_dssp             EEEEEEE-STTSCHH---------------HHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEE---EEEETTSH----
T ss_pred             CEEEEEeCCCCCchH---------------HHHHHHHHHHHHHHhhhccccccccceeeeecccc---cccccccc----
Confidence            478999999998520               12334444444444444667777889999998753   34555321    


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHH
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKS  254 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~a  254 (422)
                      ...+.+++.-  ........|.|+++..|++|.+.....     .....++++||||..++..         ........
T Consensus        59 ~~~~~~~~~i--~~~~~~~~g~t~~~~aL~~a~~~l~~~~~~~r~~~~~~iiliTDG~~~~~~---------~~~~~~~~  127 (178)
T PF00092_consen   59 QSKNDLLNAI--NDSIPSSGGGTNLGAALKFAREQLFSSNNGGRPNSPKVIILITDGNSNDSD---------SPSEEAAN  127 (178)
T ss_dssp             SSHHHHHHHH--HTTGGCCBSSB-HHHHHHHHHHHTTSGGGTTGTTSEEEEEEEESSSSSSHS---------GHHHHHHH
T ss_pred             cccccccccc--cccccccchhhhHHHHHhhhhhcccccccccccccccceEEEEeecccCCc---------chHHHHHH
Confidence            2344554432  234455779999999999999886543     4578999999999998831         12222333


Q ss_pred             HHHhcCCCeeEEEEecCCCCcccccccc
Q 042398          255 IVAASSYPLSIVLVGVGDGPWEDMQKFD  282 (422)
Q Consensus       255 Iv~AS~~PlSIiiVGVG~~~f~~m~~LD  282 (422)
                      +...  .-+.++.||+++.+-..|+.|-
T Consensus       128 ~~~~--~~i~~~~ig~~~~~~~~l~~la  153 (178)
T PF00092_consen  128 LKKS--NGIKVIAIGIDNADNEELRELA  153 (178)
T ss_dssp             HHHH--CTEEEEEEEESCCHHHHHHHHS
T ss_pred             HHHh--cCcEEEEEecCcCCHHHHHHHh
Confidence            3322  4555555555445566666554

Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....

>smart00184 RING Ring finger

Probab=97.45  E-value=6.9e-05  Score=50.26  Aligned_cols=33  Identities=52%  Similarity=1.301  Sum_probs=27.5

Q ss_pred             cccccccccc-ccccCCCccchhhhhcC-----CCCCCc
Q 042398          378 CPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPIC  410 (422)
Q Consensus       378 CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~C  410 (422)
                      |+||++...+ +.++|||.||..|+..+     ..||+|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            8899999777 56699999999999854     568887

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.43  E-value=1.2e-05  Score=81.06  Aligned_cols=47  Identities=30%  Similarity=0.754  Sum_probs=39.5

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC-----CCCCCccccccCcc
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV-----SNCPICRQRITNRL  418 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~i  418 (422)
                      +..+..|+||+++++. ++. .|+|.||.+|+...     ..||.||+.+..+.
T Consensus        40 ~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr   93 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR   93 (381)
T ss_pred             hhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence            5567899999999999 544 99999999999953     68999999886543

>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity

Probab=97.40  E-value=0.001  Score=63.32  Aligned_cols=142  Identities=16%  Similarity=0.268  Sum_probs=90.8

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|.|.+                  ...++++...+..++..++.   .-.+-++.|+....   .+|+|+..
T Consensus         3 ~DlvfllD~S~Sm~------------------~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~---~~~~l~~~   61 (224)
T cd01475           3 TDLVFLIDSSRSVR------------------PENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVK---QEFPLGRF   61 (224)
T ss_pred             ccEEEEEeCCCCCC------------------HHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCcee---EEeccccc
Confidence            57899999998874                  13477888888888888764   34799999998742   34666431


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHH-H-c---CCc---eEEEEEEeCCcccccCCCCCCCCchh
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE-K-S---GGQ---YHVLVIIADGQVTRSVNTGDGELSSQ  247 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~-~-~---~~~---Y~VLlIiTDG~i~d~~~~~~~~~~~~  247 (422)
                          ...+++.++-.. ++.  +.|.|+-.-.|+.+.+.+- + .   .+.   -.|+++||||.-.|.           
T Consensus        62 ----~~~~~l~~~i~~-i~~--~~~~t~tg~AL~~a~~~~~~~~~g~r~~~~~~~kvvillTDG~s~~~-----------  123 (224)
T cd01475          62 ----KSKADLKRAVRR-MEY--LETGTMTGLAIQYAMNNAFSEAEGARPGSERVPRVGIVVTDGRPQDD-----------  123 (224)
T ss_pred             ----CCHHHHHHHHHh-CcC--CCCCChHHHHHHHHHHHhCChhcCCCCCCCCCCeEEEEEcCCCCccc-----------
Confidence                223455554332 222  3566777767777765421 1 1   111   478999999987651           


Q ss_pred             HHHHHHHHHHhcCCCeeEEEEecCCCCcccccccc
Q 042398          248 EQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFD  282 (422)
Q Consensus       248 ~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD  282 (422)
                      ..+   ++.++-..-+.|..||||+.+...|+++=
T Consensus       124 ~~~---~a~~lk~~gv~i~~VgvG~~~~~~L~~ia  155 (224)
T cd01475         124 VSE---VAAKARALGIEMFAVGVGRADEEELREIA  155 (224)
T ss_pred             HHH---HHHHHHHCCcEEEEEeCCcCCHHHHHHHh
Confidence            223   33344456789999999997766666554

Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.36  E-value=6.3e-05  Score=74.70  Aligned_cols=40  Identities=30%  Similarity=0.752  Sum_probs=35.3

Q ss_pred             Cccccccccccc----ccccCCCccchhhhhcC-----CCCCCcccccc
Q 042398          376 QACPICLTNAKD----LAFGCGHMTCRECGSRV-----SNCPICRQRIT  415 (422)
Q Consensus       376 ~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~  415 (422)
                      -.|.||+..+..    +++||.|.|+..|+.+|     ..||+||.++.
T Consensus       324 veCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP  372 (374)
T COG5540         324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP  372 (374)
T ss_pred             ceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence            689999998865    57899999999999987     57999999875

>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme

Probab=97.33  E-value=0.0019  Score=60.03  Aligned_cols=139  Identities=12%  Similarity=0.189  Sum_probs=89.4

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      -+++++||-|.|+...             +-.||-.+.|-..+...+..+.+   ...+-++.|++...+.  +.+++.|
T Consensus         4 r~ivi~lD~S~SM~a~-------------D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~--~~PlT~D   68 (183)
T cd01453           4 RHLIIVIDCSRSMEEQ-------------DLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEK--LTDLTGN   68 (183)
T ss_pred             eEEEEEEECcHHHhcC-------------CCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEE--EECCCCC
Confidence            4799999999998531             11479999999999999987733   3578888896443221  2333322


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCC--ceEEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGG--QYHVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~--~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                            .+.++..-+..   +...|-|++...|+.|.+..++...  .=.|+|++|||.-.|            ..+..+
T Consensus        69 ------~~~~~~~L~~~---~~~~G~t~l~~aL~~A~~~l~~~~~~~~~~iiil~sd~~~~~------------~~~~~~  127 (183)
T cd01453          69 ------PRKHIQALKTA---RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCD------------PGNIYE  127 (183)
T ss_pred             ------HHHHHHHhhcc---cCCCCchhHHHHHHHHHHHHhcCCccCceEEEEEEcCCCcCC------------hhhHHH
Confidence                  23333333222   2446779999999999888765322  234788899987654            112223


Q ss_pred             HHHHhcCCCeeEEEEecCCC
Q 042398          254 SIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       254 aIv~AS~~PlSIiiVGVG~~  273 (422)
                      ++..+.+..+-|-+||||.+
T Consensus       128 ~~~~l~~~~I~v~~IgiG~~  147 (183)
T cd01453         128 TIDKLKKENIRVSVIGLSAE  147 (183)
T ss_pred             HHHHHHHcCcEEEEEEechH
Confidence            44455556788888999853

Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.

>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto)

Probab=97.29  E-value=0.0041  Score=57.02  Aligned_cols=146  Identities=14%  Similarity=0.207  Sum_probs=90.3

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccc-ccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLA-PFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~-~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      +++.||.|+|+..                 .+..+.|...+..++. .+..+..+-++.|++...  ..++++.      
T Consensus         3 v~lvlD~SgSM~~-----------------~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~--~~~~~~t------   57 (178)
T cd01451           3 VIFVVDASGSMAA-----------------RHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEA--EVLLPPT------   57 (178)
T ss_pred             EEEEEECCccCCC-----------------ccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCc--eEEeCCC------
Confidence            5788999999951                 1345666666666664 344556899999976421  1122221      


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHH-Hc--CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHH
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE-KS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIV  256 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~-~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv  256 (422)
                      .+.+.+.    +.+..+...|-|++..-+..+.+..+ +.  .+.-.++++||||.-+...+       +......++..
T Consensus        58 ~~~~~~~----~~l~~l~~~G~T~l~~aL~~a~~~l~~~~~~~~~~~~ivliTDG~~~~g~~-------~~~~~~~~~~~  126 (178)
T cd01451          58 RSVELAK----RRLARLPTGGGTPLAAGLLAAYELAAEQARDPGQRPLIVVITDGRANVGPD-------PTADRALAAAR  126 (178)
T ss_pred             CCHHHHH----HHHHhCCCCCCCcHHHHHHHHHHHHHHHhcCCCCceEEEEECCCCCCCCCC-------chhHHHHHHHH
Confidence            2344443    34455677899999999999998872 21  12247889999998764211       11112255555


Q ss_pred             HhcCCCeeEEEEecCCCCc--ccccccc
Q 042398          257 AASSYPLSIVLVGVGDGPW--EDMQKFD  282 (422)
Q Consensus       257 ~AS~~PlSIiiVGVG~~~f--~~m~~LD  282 (422)
                      ++...++.|+.||+|..+.  +.|++|=
T Consensus       127 ~l~~~gi~v~~I~~~~~~~~~~~l~~iA  154 (178)
T cd01451         127 KLRARGISALVIDTEGRPVRRGLAKDLA  154 (178)
T ss_pred             HHHhcCCcEEEEeCCCCccCccHHHHHH
Confidence            5667788889999987543  3455553

In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.28  E-value=9.1e-05  Score=75.47  Aligned_cols=41  Identities=27%  Similarity=0.716  Sum_probs=35.1

Q ss_pred             Cccccccccccc----ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          376 QACPICLTNAKD----LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       376 ~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      ..|.||+|.++.    ..|||.|.|+..|+..|     ..||+|+..+.+
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            499999999887    36799999999999987     459999997743

>PRK13685 hypothetical protein; Provisional

Probab=97.25  E-value=0.0021  Score=64.96  Aligned_cols=143  Identities=18%  Similarity=0.193  Sum_probs=92.6

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .+++++||-|+|+..+             +..+|..+.|-..+..++..+..+..+-++.|++...   .+.++.     
T Consensus        89 ~~vvlvlD~S~SM~~~-------------D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~---~~~p~t-----  147 (326)
T PRK13685         89 AVVMLVIDVSQSMRAT-------------DVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTAT---VLVSPT-----  147 (326)
T ss_pred             ceEEEEEECCccccCC-------------CCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCcee---ecCCCC-----
Confidence            4689999999999632             1236888999999999999987677899999998642   122222     


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHH--------cCCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEK--------SGGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~--------~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                       ...+.+    ...+..++..|-|+...-|..+.+..++        .+...-++++||||+-+...+.    ..  ...
T Consensus       148 -~d~~~l----~~~l~~l~~~~~T~~g~al~~A~~~l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~----~~--~~~  216 (326)
T PRK13685        148 -TNREAT----KNAIDKLQLADRTATGEAIFTALQAIATVGAVIGGGDTPPPARIVLMSDGKETVPTNP----DN--PRG  216 (326)
T ss_pred             -CCHHHH----HHHHHhCCCCCCcchHHHHHHHHHHHHhhhcccccccCCCCCEEEEEcCCCCCCCCCC----CC--ccc
Confidence             233333    2334455566778888888888877652        1112345689999976541100    00  111


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      ..++...|.+..+.|-+||||..
T Consensus       217 ~~~aa~~a~~~gi~i~~Ig~G~~  239 (326)
T PRK13685        217 AYTAARTAKDQGVPISTISFGTP  239 (326)
T ss_pred             HHHHHHHHHHcCCeEEEEEECCC
Confidence            23455566677888888999873

>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family

Probab=97.25  E-value=0.0043  Score=61.55  Aligned_cols=139  Identities=18%  Similarity=0.297  Sum_probs=91.8

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      ..++++|||-|+|+...             +-.++..| |+..|.+.+..-.. +.+-+.+||....   .+.+|+.  +
T Consensus        60 ~~qIvlaID~S~SM~~~-------------~~~~~ale-ak~lIs~al~~Le~-g~vgVv~Fg~~~~---~v~Plt~--d  119 (266)
T cd01460          60 DYQILIAIDDSKSMSEN-------------NSKKLALE-SLCLVSKALTLLEV-GQLGVCSFGEDVQ---ILHPFDE--Q  119 (266)
T ss_pred             CceEEEEEecchhcccc-------------cccccHHH-HHHHHHHHHHhCcC-CcEEEEEeCCCce---EeCCCCC--C
Confidence            35799999999999632             11356666 88888888887775 5799999998631   2233321  1


Q ss_pred             CCCCHHHHHHHHHhhCCccccc-CCCChHHHHHHHHHHHHHcC----C--ceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLA-GPTSYAPVVEAAMDIVEKSG----G--QYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~-GPT~fapiI~~a~~~~~~~~----~--~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                          +..  ++.-+++....+. +-|+.+..|..+++..++..    +  .-.++||||||.-.+.           +..
T Consensus       120 ----~~~--~a~~~~l~~~~f~~~~Tni~~aL~~a~~~f~~~~~~~~s~~~~qlilLISDG~~~~~-----------e~~  182 (266)
T cd01460         120 ----FSS--QSGPRILNQFTFQQDKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFS-----------EGA  182 (266)
T ss_pred             ----chh--hHHHHHhCcccCCCCCCcHHHHHHHHHHHHHhhhccccccccccEEEEEECCCcccC-----------ccH
Confidence                111  2223334433332 44899999999998765431    1  1279999999994331           223


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      ...++.+|....+.+++|||=+.
T Consensus       183 ~~~~~r~a~e~~i~l~~I~ld~~  205 (266)
T cd01460         183 QKVRLREAREQNVFVVFIIIDNP  205 (266)
T ss_pred             HHHHHHHHHHcCCeEEEEEEcCC
Confidence            34557888888999999999775

The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]

Probab=97.24  E-value=8.4e-05  Score=76.12  Aligned_cols=42  Identities=38%  Similarity=0.945  Sum_probs=37.8

Q ss_pred             Ccccccccccccccc-cCCCccchhhhhcC------CCCCCccccccCc
Q 042398          376 QACPICLTNAKDLAF-GCGHMTCRECGSRV------SNCPICRQRITNR  417 (422)
Q Consensus       376 ~~CpIC~~~~~~v~l-~CGH~fC~~Ci~~~------~~CP~CR~~i~~~  417 (422)
                      ..|.||-++-+++.+ ||||..|..|+..|      ..||.||..|...
T Consensus       370 eLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt  418 (563)
T KOG1785|consen  370 ELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT  418 (563)
T ss_pred             HHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence            589999999999877 99999999999977      5799999999754

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis

Probab=97.18  E-value=0.00012  Score=58.44  Aligned_cols=44  Identities=25%  Similarity=0.378  Sum_probs=33.5

Q ss_pred             cCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccCc
Q 042398          374 ETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITNR  417 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~  417 (422)
                      +.+.||||.+.+.+ ++++|||.|+..|+.++     ..||.|+.+++..
T Consensus         3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            56899999999999 66799999999999965     5699999998753

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function

Probab=97.12  E-value=0.0016  Score=57.32  Aligned_cols=121  Identities=19%  Similarity=0.323  Sum_probs=79.7

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCCC
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPCH  180 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~~  180 (422)
                      +.||||-|+|-.                  .....+++..|..+++.+  ...+-++=|-++......+          .
T Consensus         1 i~vaiDtSGSis------------------~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~~~~~~----------~   50 (126)
T PF09967_consen    1 IVVAIDTSGSIS------------------DEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQDVQVF----------R   50 (126)
T ss_pred             CEEEEECCCCCC------------------HHHHHHHHHHHHHHHHhC--CCCEEEEEECCEeeeeeEE----------e
Confidence            579999999973                  146778899999999999  3447777777765432221          1


Q ss_pred             CHHHHHHHHHhhCCcccc--cCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          181 GFEEVLACYRNIVPNLRL--AGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       181 G~~gvl~~Y~~~l~~v~l--~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                      .       +...+..+++  .|-|+|.|+++++.+.    .....++++||||......                   .+
T Consensus        51 ~-------~~~~~~~~~~~GgGGTdf~pvf~~~~~~----~~~~~~vi~fTDg~~~~~~-------------------~~  100 (126)
T PF09967_consen   51 S-------LEDELRDIKLKGGGGTDFRPVFEYLEEN----RPRPSVVIYFTDGEGWPPE-------------------EA  100 (126)
T ss_pred             c-------ccccccccccCCCCCCcchHHHHHHHhc----CCCCCEEEEEeCCCCCCCC-------------------CC
Confidence            1       1112222333  4789999999998754    3356788899999885411                   12


Q ss_pred             cCCCeeEEEEe--cCCCCccccccc
Q 042398          259 SSYPLSIVLVG--VGDGPWEDMQKF  281 (422)
Q Consensus       259 S~~PlSIiiVG--VG~~~f~~m~~L  281 (422)
                      =.+|.=|++.|  -...||...-+|
T Consensus       101 P~~~vlWvl~~~~~~~~P~G~vv~l  125 (126)
T PF09967_consen  101 PPYPVLWVLPGNRNPKAPFGRVVRL  125 (126)
T ss_pred             CCCcEEEEEeCCCCCCCCCEEEEEe
Confidence            27899999999  333466655444

>cd01477 vWA_F09G8-8_type VWA F09G8

Probab=97.08  E-value=0.0057  Score=57.62  Aligned_cols=139  Identities=9%  Similarity=0.138  Sum_probs=95.1

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---------CCCcceeeecCCCCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---------DNLIPCFGFGDATTHDQEV  169 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---------D~~ip~~GFGa~~~~~~~v  169 (422)
                      +.+++.||-+.|.+.                  +.++++..-|..++..++.         .-.+-+.-|+....   -.
T Consensus        20 ~DivfvlD~S~Sm~~------------------~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~---~~   78 (193)
T cd01477          20 LDIVFVVDNSKGMTQ------------------GGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNAT---VV   78 (193)
T ss_pred             eeEEEEEeCCCCcch------------------hhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceE---EE
Confidence            679999999999851                  2477887777777776664         24677777776532   23


Q ss_pred             cccCCCCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCC
Q 042398          170 FSFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGEL  244 (422)
Q Consensus       170 f~~~~~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~  244 (422)
                      |+|+    .....++++++....++.+...|-|+...-|..|.+.....     .+.--|+++||||.-.+..       
T Consensus        79 ~~L~----d~~~~~~~~~ai~~~~~~~~~~ggT~ig~aL~~A~~~l~~~~~~~R~~v~kvvIllTDg~~~~~~-------  147 (193)
T cd01477          79 ADLN----DLQSFDDLYSQIQGSLTDVSSTNASYLDTGLQAAEQMLAAGKRTSRENYKKVVIVFASDYNDEGS-------  147 (193)
T ss_pred             Eecc----cccCHHHHHHHHHHHhhccccCCcchHHHHHHHHHHHHHhhhccccCCCCeEEEEEecCccCCCC-------
Confidence            5553    22457788888777666666667899999999998876542     2246789999998544310       


Q ss_pred             chhHHHHHHHHHHhcCCCeeEEEEecCCC
Q 042398          245 SSQEQKTIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       245 ~~~~~~T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                          ....++..++.+..+-|.-||||++
T Consensus       148 ----~~~~~~a~~l~~~GI~i~tVGiG~~  172 (193)
T cd01477         148 ----NDPRPIAARLKSTGIAIITVAFTQD  172 (193)
T ss_pred             ----CCHHHHHHHHHHCCCEEEEEEeCCC
Confidence                1123344445577999999999984

8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo

>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration

Probab=97.04  E-value=0.0049  Score=56.59  Aligned_cols=135  Identities=19%  Similarity=0.285  Sum_probs=90.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +.+++.||=+.|-+                  +..++++...+..++..++.   .-.+-+..|+....   ..|+|.. 
T Consensus         1 ~Di~fvlD~S~S~~------------------~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~---~~~~l~~-   58 (177)
T cd01469           1 MDIVFVLDGSGSIY------------------PDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFR---TEFTLNE-   58 (177)
T ss_pred             CcEEEEEeCCCCCC------------------HHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCcee---EEEecCc-
Confidence            35788899887763                  24577888888888888876   45788888988632   2355531 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHH--HHc---CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIV--EKS---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~--~~~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                         -...+.++++=.. ++  .+.|.|+....|+.|.+..  ...   .+.-.|+++||||.-+|..            .
T Consensus        59 ---~~~~~~~~~~i~~-~~--~~~g~T~~~~AL~~a~~~l~~~~~g~R~~~~kv~illTDG~~~~~~------------~  120 (177)
T cd01469          59 ---YRTKEEPLSLVKH-IS--QLLGLTNTATAIQYVVTELFSESNGARKDATKVLVVITDGESHDDP------------L  120 (177)
T ss_pred             ---cCCHHHHHHHHHh-Cc--cCCCCccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEeCCCCCCcc------------c
Confidence               1234455544332 22  2578899999999998765  221   1246788999999998721            2


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      +.+++..|-..-+-|.-||||+.
T Consensus       121 ~~~~~~~~k~~gv~v~~Vgvg~~  143 (177)
T cd01469         121 LKDVIPQAEREGIIRYAIGVGGH  143 (177)
T ss_pred             cHHHHHHHHHCCcEEEEEEeccc
Confidence            24455556667889999999985

Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.

>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

Probab=97.03  E-value=0.00021  Score=57.20  Aligned_cols=36  Identities=36%  Similarity=0.946  Sum_probs=27.8

Q ss_pred             Cccccccccccc-------------ccc-cCCCccchhhhhcC----CCCCCcc
Q 042398          376 QACPICLTNAKD-------------LAF-GCGHMTCRECGSRV----SNCPICR  411 (422)
Q Consensus       376 ~~CpIC~~~~~~-------------v~l-~CGH~fC~~Ci~~~----~~CP~CR  411 (422)
                      ..|.||++.+.+             +.+ +|||.|+..|+.++    ..||+||
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            459999998821             233 89999999999965    6899998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=96.91  E-value=0.0083  Score=56.76  Aligned_cols=156  Identities=17%  Similarity=0.174  Sum_probs=90.3

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      .++++||.|+|+..     ++    . .+..+-.-..|...|.+.+..|.+.....-.||++......-+   ..+.|.-
T Consensus         2 ~l~lavDlSgSM~~-----~~----~-~dg~~~~RL~a~k~v~~~f~~f~~~r~~DriG~~g~~~~~~~l---t~d~p~t   68 (191)
T cd01455           2 RLKLVVDVSGSMYR-----FN----G-YDGRLDRSLEAVVMVMEAFDGFEDKIQYDIIGHSGDGPCVPFV---KTNHPPK   68 (191)
T ss_pred             ceEEEEECcHhHHH-----Hh----c-cCCccccHHHHHHHHHHHHHHHHHhCccceeeecCcccccCcc---ccccCcc
Confidence            47999999999952     21    1 2223334455666666666666677777778887654321111   2233333


Q ss_pred             CCHH--HHHHHHHhhCCcccccCCCChHHHHHHHHHHHH-HcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHH-HH
Q 042398          180 HGFE--EVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE-KSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIK-SI  255 (422)
Q Consensus       180 ~G~~--gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~-~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~-aI  255 (422)
                      ..-+  .++...-.- -++-+.|+.- +.-|..+++..+ ++..+=.|+++||||.-+.      +.++|     .+ |-
T Consensus        69 ~d~~~~~~l~~~l~~-~q~g~ag~~T-adAi~~av~rl~~~~~a~~kvvILLTDG~n~~------~~i~P-----~~aAa  135 (191)
T cd01455          69 NNKERLETLKMMHAH-SQFCWSGDHT-VEATEFAIKELAAKEDFDEAIVIVLSDANLER------YGIQP-----KKLAD  135 (191)
T ss_pred             cchhHHHHHHHHHHh-cccCccCccH-HHHHHHHHHHHHhcCcCCCcEEEEEeCCCcCC------CCCCh-----HHHHH
Confidence            3333  344333322 2445677643 377787877776 5544456889999998765      33444     22 22


Q ss_pred             HHhcCCCeeEEEEecCCCCccccccc
Q 042398          256 VAASSYPLSIVLVGVGDGPWEDMQKF  281 (422)
Q Consensus       256 v~AS~~PlSIiiVGVG~~~f~~m~~L  281 (422)
                      .-|.+.-+=|-.||||..+.+.++.+
T Consensus       136 ~lA~~~gV~iytIgiG~~d~~~l~~i  161 (191)
T cd01455         136 ALAREPNVNAFVIFIGSLSDEADQLQ  161 (191)
T ss_pred             HHHHhCCCEEEEEEecCCCHHHHHHH
Confidence            33556677788888888654444443

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=96.90  E-value=0.00039  Score=70.87  Aligned_cols=42  Identities=29%  Similarity=0.775  Sum_probs=34.6

Q ss_pred             CcCCccccccccccc--------------ccccCCCccchhhhhcC----CCCCCccccc
Q 042398          373 AETQACPICLTNAKD--------------LAFGCGHMTCRECGSRV----SNCPICRQRI  414 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~--------------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i  414 (422)
                      .++..|.||+|....              -.+||||.++-.|++.|    ..||+||.++
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence            456899999997322              24699999999999976    7899999994

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=96.88  E-value=0.00054  Score=71.29  Aligned_cols=44  Identities=30%  Similarity=0.706  Sum_probs=36.9

Q ss_pred             CCcCCccccccccccc-c----cccCCCccchhhhhcC--CCCCCcccccc
Q 042398          372 VAETQACPICLTNAKD-L----AFGCGHMTCRECGSRV--SNCPICRQRIT  415 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v----~l~CGH~fC~~Ci~~~--~~CP~CR~~i~  415 (422)
                      +.|..+||||++.+-. +    .+.|.|.|...|+.+|  ..||+||...+
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhcC
Confidence            5677899999998877 2    3499999999999988  68999997654

>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions

Probab=96.86  E-value=0.012  Score=53.89  Aligned_cols=141  Identities=15%  Similarity=0.265  Sum_probs=89.1

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      .+.+.||=|.|-+                  ...++++..-+..++..|+   +.-.+.+.-|+....   ..|+|+-- 
T Consensus         2 DivfllD~S~Si~------------------~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~---~~~~l~~~-   59 (165)
T cd01481           2 DIVFLIDGSDNVG------------------SGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPR---PEFYLNTH-   59 (165)
T ss_pred             CEEEEEeCCCCcC------------------HHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCee---EEEecccc-
Confidence            4678888877764                  2456777777777777776   456788888887642   23665421 


Q ss_pred             CCCCCHHHHHHHHHhhCCcccc-cC-CCChHHHHHHHHHHHHH--c-----CCceEEEEEEeCCcccccCCCCCCCCchh
Q 042398          177 TPCHGFEEVLACYRNIVPNLRL-AG-PTSYAPVVEAAMDIVEK--S-----GGQYHVLVIIADGQVTRSVNTGDGELSSQ  247 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l-~G-PT~fapiI~~a~~~~~~--~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~  247 (422)
                         ...++++++-.+    ++. .| .|+-...|+.+.+..-.  .     .+--.||++||||.-+|.           
T Consensus        60 ---~~~~~l~~~i~~----i~~~~g~~t~t~~AL~~~~~~~f~~~~g~R~~~~~~kv~vviTdG~s~d~-----------  121 (165)
T cd01481          60 ---STKADVLGAVRR----LRLRGGSQLNTGSALDYVVKNLFTKSAGSRIEEGVPQFLVLITGGKSQDD-----------  121 (165)
T ss_pred             ---CCHHHHHHHHHh----cccCCCCcccHHHHHHHHHHhhcCccccCCccCCCCeEEEEEeCCCCcch-----------
Confidence               245667665443    333 45 47888888888765321  1     123579999999997761           


Q ss_pred             HHHHHHHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          248 EQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       248 ~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      ..+..+.+.   +.-+-|+.||+|..+...|+.+-+
T Consensus       122 ~~~~a~~lr---~~gv~i~~vG~~~~~~~eL~~ias  154 (165)
T cd01481         122 VERPAVALK---RAGIVPFAIGARNADLAELQQIAF  154 (165)
T ss_pred             HHHHHHHHH---HCCcEEEEEeCCcCCHHHHHHHhC
Confidence            223333443   456777888888766666665554

The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.71  E-value=0.0011  Score=65.13  Aligned_cols=44  Identities=25%  Similarity=0.711  Sum_probs=35.8

Q ss_pred             CCcCCcccccccccccc-cc-cCCCccchhhhhcC------CCCCCcccccc
Q 042398          372 VAETQACPICLTNAKDL-AF-GCGHMTCRECGSRV------SNCPICRQRIT  415 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v-~l-~CGH~fC~~Ci~~~------~~CP~CR~~i~  415 (422)
                      .....+|++|-+.+..+ +. +|||.+|..|+...      ..||.|.....
T Consensus       236 ~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            34567999999999983 33 79999999999953      58999988765

>cd01458 vWA_ku Ku70/Ku80 N-terminal domain

Probab=96.71  E-value=0.045  Score=51.90  Aligned_cols=155  Identities=12%  Similarity=0.200  Sum_probs=96.6

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc---cCCCCCcceeeecCCCCC----CCCCccc
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP---FDEDNLIPCFGFGDATTH----DQEVFSF  172 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~---yD~D~~ip~~GFGa~~~~----~~~vf~~  172 (422)
                      .++++||.+.|+...          + -+..++..+.|+..+..+++.   ....-.+-++.||...+.    ..+++.+
T Consensus         3 ~ivf~iDvS~SM~~~----------~-~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~~~~~~~i~v~   71 (218)
T cd01458           3 SVVFLVDVSPSMFES----------K-DGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNPVGYENIYVL   71 (218)
T ss_pred             EEEEEEeCCHHHcCC----------C-CCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCCcCCCCceEEe
Confidence            478999999999621          0 011368999999999999997   566668999999987533    2345444


Q ss_pred             CCCCCCCCCHHHHHHHHHhhCCccc--------ccCCCChHHHHHHHHHHHHHcC-C-ceEEEEEEeCCcccccCCCCCC
Q 042398          173 HDDHTPCHGFEEVLACYRNIVPNLR--------LAGPTSYAPVVEAAMDIVEKSG-G-QYHVLVIIADGQVTRSVNTGDG  242 (422)
Q Consensus       173 ~~~~~~~~G~~gvl~~Y~~~l~~v~--------l~GPT~fapiI~~a~~~~~~~~-~-~Y~VLlIiTDG~i~d~~~~~~~  242 (422)
                      .|=+  .... +.++.+.+.+....        -.+.|.+...|..+.+...+.. . .=-.+++||||.=.-      +
T Consensus        72 ~~l~--~~~~-~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~a~~~~~~~~~~~~~k~IvL~TDg~~p~------~  142 (218)
T cd01458          72 LDLD--TPGA-ERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALWVCLDLFSKGKKKKSHKRIFLFTNNDDPH------G  142 (218)
T ss_pred             ecCC--CCCH-HHHHHHHHHhhcchhhhcccCCCCCCccHHHHHHHHHHHHHhccccccccEEEEECCCCCCC------C
Confidence            3311  1122 33344444332221        2457899999999988776521 1 124678889996320      0


Q ss_pred             CCchhHHHHHHHHHHhcCCCeeEEEEecCCCC
Q 042398          243 ELSSQEQKTIKSIVAASSYPLSIVLVGVGDGP  274 (422)
Q Consensus       243 ~~~~~~~~T~~aIv~AS~~PlSIiiVGVG~~~  274 (422)
                      .=.-..++..+.+.+..+.-+.|..||+|..+
T Consensus       143 ~~~~~~~~~~~~a~~l~~~gI~i~~i~i~~~~  174 (218)
T cd01458         143 GDSIKDSQAAVKAEDLKDKGIELELFPLSSPG  174 (218)
T ss_pred             CCHHHHHHHHHHHHHHHhCCcEEEEEecCCCC
Confidence            00001244455666677778999999998754

The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.69  E-value=0.00068  Score=64.83  Aligned_cols=45  Identities=27%  Similarity=0.705  Sum_probs=39.5

Q ss_pred             ccccccccccccc-ccCCCcc-chhhhhcCCCCCCccccccCccccC
Q 042398          377 ACPICLTNAKDLA-FGCGHMT-CRECGSRVSNCPICRQRITNRLRLF  421 (422)
Q Consensus       377 ~CpIC~~~~~~v~-l~CGH~f-C~~Ci~~~~~CP~CR~~i~~~i~vy  421 (422)
                      .|..|.+....++ +||.|.+ |..|......||+|+.+....+.+|
T Consensus       160 ~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~~~CPiC~~~~~s~~~v~  206 (207)
T KOG1100|consen  160 SCRKCGEREATVLLLPCRHLCLCGICDESLRICPICRSPKTSSVEVN  206 (207)
T ss_pred             cceecCcCCceEEeecccceEecccccccCccCCCCcChhhceeecc
Confidence            3999999998854 4999995 9999988889999999999888876

>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins

Probab=96.53  E-value=0.022  Score=53.63  Aligned_cols=160  Identities=10%  Similarity=0.167  Sum_probs=99.1

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCCCCC
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      .+|+||.+.|+...             +-.||.++.+...+..++..|-+   ...+-+..|+++....  +.+++.   
T Consensus         6 ~vi~lD~S~sM~a~-------------D~~PnRL~aak~~i~~~~~~f~~~np~~~vGlv~fag~~a~v--~~plT~---   67 (187)
T cd01452           6 TMICIDNSEYMRNG-------------DYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPEV--LVTLTN---   67 (187)
T ss_pred             EEEEEECCHHHHcC-------------CCCCCHHHHHHHHHHHHHHHHHhcCCCccEEEEEecCCceEE--EECCCC---
Confidence            68999999987531             11479999999999988755432   3467778888743211  122222   


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC---CceEEEEEEeCCcccccCCCCCCCCchhHHHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG---GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKS  254 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~---~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~a  254 (422)
                         ..+.++.    .+..+.+.|.|++...|+.|....+...   ..=-|++|++++.-.|            ++...++
T Consensus        68 ---D~~~~~~----~L~~i~~~g~~~l~~AL~~A~~~L~~~~~~~~~~rivi~v~S~~~~d------------~~~i~~~  128 (187)
T cd01452          68 ---DQGKILS----KLHDVQPKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEED------------EKDLVKL  128 (187)
T ss_pred             ---CHHHHHH----HHHhCCCCCcchHHHHHHHHHHHHhcCCCcCCcceEEEEEecCCcCC------------HHHHHHH
Confidence               2344433    3345667799999999998887665332   2225566666664344            3455677


Q ss_pred             HHHhcCCCeeEEEEecCCCC--ccccccccCCCCCcccccceecchh
Q 042398          255 IVAASSYPLSIVLVGVGDGP--WEDMQKFDDKIPAREFDNFQFVNFT  299 (422)
Q Consensus       255 Iv~AS~~PlSIiiVGVG~~~--f~~m~~LD~~~~~r~rDnvqFV~f~  299 (422)
                      +.++.+..+.+-+||+|+..  =+.++.|-+....  -|+-+||...
T Consensus       129 ~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~~~~~~--~~~s~~~~~~  173 (187)
T cd01452         129 AKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNG--KDGSHLVSVP  173 (187)
T ss_pred             HHHHHHcCCeEEEEEeCCCCCCHHHHHHHHHHhcC--CCCceEEEeC
Confidence            77777889999999999762  2333333322221  2666776543

It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.51  E-value=0.00076  Score=72.94  Aligned_cols=42  Identities=29%  Similarity=0.710  Sum_probs=35.5

Q ss_pred             CcCCccccccccccc-----c-cccCCCccchhhhhcC----CCCCCccccc
Q 042398          373 AETQACPICLTNAKD-----L-AFGCGHMTCRECGSRV----SNCPICRQRI  414 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-----v-~l~CGH~fC~~Ci~~~----~~CP~CR~~i  414 (422)
                      .....|+||.+.+..     + .++|||.||..|+..|    ..||+||..+
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence            346799999998877     3 4599999999999977    7899999943

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=96.49  E-value=0.035  Score=60.87  Aligned_cols=156  Identities=14%  Similarity=0.214  Sum_probs=99.9

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccc-ccCCCCCcceeeecCCCCCCCCCcccCCCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLA-PFDEDNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~-~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      ...+++.||.|+|+.                  .|.-..|-.++-.+|. .|-..-.+-++.|+....  ..+++.    
T Consensus       401 ~~~vvfvvD~SGSM~------------------~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a--~~~lpp----  456 (584)
T PRK13406        401 ETTTIFVVDASGSAA------------------LHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGA--ELLLPP----  456 (584)
T ss_pred             CccEEEEEECCCCCc------------------HhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCce--eEEcCC----
Confidence            467899999999983                  1355556666666563 465556899999965411  112221    


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKS  254 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~a  254 (422)
                        -..++.+    ++.+..+.-.|-|.++.-|..+.+..++.  .+.-.++|+||||.-+...+...|. ....++..++
T Consensus       457 --T~~~~~~----~~~L~~l~~gGgTpL~~gL~~A~~~l~~~~~~~~~~~iVLlTDG~~n~~~~~~~~~-~~~~~~~~~~  529 (584)
T PRK13406        457 --TRSLVRA----KRSLAGLPGGGGTPLAAGLDAAAALALQVRRKGMTPTVVLLTDGRANIARDGTAGR-AQAEEDALAA  529 (584)
T ss_pred             --CcCHHHH----HHHHhcCCCCCCChHHHHHHHHHHHHHHhccCCCceEEEEEeCCCCCCCccccccc-cchhhHHHHH
Confidence              1234444    34555777889999999999999876653  2335788999999976421111011 1122445555


Q ss_pred             HHHhcCCCeeEEEEecCCCCccccccccCC
Q 042398          255 IVAASSYPLSIVLVGVGDGPWEDMQKFDDK  284 (422)
Q Consensus       255 Iv~AS~~PlSIiiVGVG~~~f~~m~~LD~~  284 (422)
                      ...+...-+.+++|+.|..+...|++|=+.
T Consensus       530 a~~~~~~gi~~~vId~g~~~~~~~~~LA~~  559 (584)
T PRK13406        530 ARALRAAGLPALVIDTSPRPQPQARALAEA  559 (584)
T ss_pred             HHHHHhcCCeEEEEecCCCCcHHHHHHHHh
Confidence            666666778899999998877777776543

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.47  E-value=0.0014  Score=49.75  Aligned_cols=43  Identities=28%  Similarity=0.726  Sum_probs=35.1

Q ss_pred             cCCccccccccccc-ccccCCCccchhhhh--cCCCCCCccccccC
Q 042398          374 ETQACPICLTNAKD-LAFGCGHMTCRECGS--RVSNCPICRQRITN  416 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~--~~~~CP~CR~~i~~  416 (422)
                      ....|..|...-.. ++++|||..|..|..  +...||.|..++..
T Consensus         6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~rYngCPfC~~~~~~   51 (55)
T PF14447_consen    6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPGERYNGCPFCGTPFEF   51 (55)
T ss_pred             cceeEEEccccccccccccccceeeccccChhhccCCCCCCCcccC
Confidence            44678888877655 788999999999988  56889999998864

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=96.44  E-value=0.036  Score=60.77  Aligned_cols=154  Identities=14%  Similarity=0.159  Sum_probs=92.7

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc-cCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP-FDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~-yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      ..+++.||-|+|+..                  +..+.|-..+..++.. |-..-.+-++.|+....  ..++++     
T Consensus       408 ~~v~fvvD~SGSM~~------------------~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a--~~~lp~-----  462 (589)
T TIGR02031       408 RLLIFVVDASGSAAV------------------ARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAA--EVLLPP-----  462 (589)
T ss_pred             ceEEEEEECCCCCCh------------------HHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCc--eEECCC-----
Confidence            458899999999841                  3466666666666653 43333699999975421  112222     


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC--CceEEEEEEeCCcccccCCCC-CC---CCchhHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG--GQYHVLVIIADGQVTRSVNTG-DG---ELSSQEQKT  251 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~--~~Y~VLlIiTDG~i~d~~~~~-~~---~~~~~~~~T  251 (422)
                       -.+.+.+    ++.+..+...|.|.++.-|..+.+..++..  ..-.++++||||.-+-..+.. ++   ..-+-.++.
T Consensus       463 -t~~~~~~----~~~L~~l~~gGgTpL~~gL~~A~~~~~~~~~~~~~~~ivllTDG~~nv~~~~~~~~~~~~~~~~~~~~  537 (589)
T TIGR02031       463 -SRSVEQA----KRRLDVLPGGGGTPLAAGLAAAFQTALQARSSGGTPTIVLITDGRGNIPLDGDPESIKADREQAAEEA  537 (589)
T ss_pred             -CCCHHHH----HHHHhcCCCCCCCcHHHHHHHHHHHHHHhcccCCceEEEEECCCCCCCCCCcccccccccchhHHHHH
Confidence             2344444    345778888999999999999998876532  223678999999865311100 00   000101222


Q ss_pred             HHHHHHhcCCCeeEEEEecCCCCc--ccccccc
Q 042398          252 IKSIVAASSYPLSIVLVGVGDGPW--EDMQKFD  282 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~~f--~~m~~LD  282 (422)
                      ..+........+.+++||+|.+..  +.|++|=
T Consensus       538 ~~~a~~~~~~gi~~~vid~~~~~~~~~~~~~lA  570 (589)
T TIGR02031       538 LALARKIREAGMPALVIDTAMRFVSTGFAQKLA  570 (589)
T ss_pred             HHHHHHHHhcCCeEEEEeCCCCCccchHHHHHH
Confidence            222333345678999999998644  3366654

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.37  E-value=0.0013  Score=68.44  Aligned_cols=45  Identities=29%  Similarity=0.775  Sum_probs=38.2

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      ...++.|.||+..+-. ++++|||.||..|+.+.    ..||.||..+..
T Consensus        81 ~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   81 IRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             ccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            3567999999999988 67799999999997753    689999998764

>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain

Probab=96.31  E-value=0.038  Score=54.68  Aligned_cols=134  Identities=19%  Similarity=0.199  Sum_probs=78.0

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc-cCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP-FDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~-yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +++++.||.|+|..                   +..+.|..++...+.. +..+..+-++.|+.....   ++.|.    
T Consensus        54 ~~vvlvlD~SgSM~-------------------~~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~---~~~~t----  107 (296)
T TIGR03436        54 LTVGLVIDTSGSMR-------------------NDLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRL---LQDFT----  107 (296)
T ss_pred             ceEEEEEECCCCch-------------------HHHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeE---eecCC----
Confidence            78999999999984                   1234555666666655 556778999999986432   22332    


Q ss_pred             CCCCHHHHHHHHHhhCC-----------cccccCCCChHHHHHHHHH-HHHHcC----CceEEEEEEeCCcccccCCCCC
Q 042398          178 PCHGFEEVLACYRNIVP-----------NLRLAGPTSYAPVVEAAMD-IVEKSG----GQYHVLVIIADGQVTRSVNTGD  241 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~-----------~v~l~GPT~fapiI~~a~~-~~~~~~----~~Y~VLlIiTDG~i~d~~~~~~  241 (422)
                        ...+.+.++-...-+           .+...|.|++..-|..++. ...+..    +. -++++||||.-+..     
T Consensus       108 --~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~g~T~l~~al~~aa~~~~~~~~~~~p~r-k~iIllTDG~~~~~-----  179 (296)
T TIGR03436       108 --SDPRLLEAALNRLKPPLRTDYNSSGAFVRDGGGTALYDAITLAALEQLANALAGIPGR-KALIVISDGGDNRS-----  179 (296)
T ss_pred             --CCHHHHHHHHHhccCCCccccccccccccCCCcchhHHHHHHHHHHHHHHhhcCCCCC-eEEEEEecCCCcch-----
Confidence              224444444433322           1233688887777765543 322221    22 57899999965431     


Q ss_pred             CCCchhHHHHHHHHHHhcCCCeeEEEEecCC
Q 042398          242 GELSSQEQKTIKSIVAASSYPLSIVLVGVGD  272 (422)
Q Consensus       242 ~~~~~~~~~T~~aIv~AS~~PlSIiiVGVG~  272 (422)
                            .....+++..+...-+.|-.||+|+
T Consensus       180 ------~~~~~~~~~~~~~~~v~vy~I~~~~  204 (296)
T TIGR03436       180 ------RDTLERAIDAAQRADVAIYSIDARG  204 (296)
T ss_pred             ------HHHHHHHHHHHHHcCCEEEEeccCc
Confidence                  1122233333344567888888875

Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.30  E-value=0.0017  Score=65.85  Aligned_cols=49  Identities=27%  Similarity=0.746  Sum_probs=39.6

Q ss_pred             CCCCCCcCCcccccccccccccc-cCCCccchhhhhcC----CCCCCccccccC
Q 042398          368 GSTPVAETQACPICLTNAKDLAF-GCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       368 s~~~~~e~~~CpIC~~~~~~v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      .+.|..|+..||||+....+.++ ||+|.-|+.|+.+.    +.|=.|+..+..
T Consensus       415 ~~lp~sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  415 KDLPDSEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CCCCCcccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            34445678899999999999655 99999999999953    678888887654

>KOG3002 consensus Zn finger protein [General function prediction only]

Probab=96.30  E-value=0.0018  Score=65.21  Aligned_cols=45  Identities=33%  Similarity=0.891  Sum_probs=39.3

Q ss_pred             CCcCCcccccccccccccccC--CCccchhhhh-cCCCCCCccccccC
Q 042398          372 VAETQACPICLTNAKDLAFGC--GHMTCRECGS-RVSNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v~l~C--GH~fC~~Ci~-~~~~CP~CR~~i~~  416 (422)
                      ..+-+.||||.+.+....+.|  ||..|..|-. ....||.||.++..
T Consensus        45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGN   92 (299)
T ss_pred             chhhccCchhhccCcccceecCCCcEehhhhhhhhcccCCcccccccc
Confidence            456789999999999989988  8999999995 45789999999983

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=96.15  E-value=0.0025  Score=52.69  Aligned_cols=25  Identities=32%  Similarity=0.717  Sum_probs=21.9

Q ss_pred             cCCCccchhhhhcC-------CCCCCcccccc
Q 042398          391 GCGHMTCRECGSRV-------SNCPICRQRIT  415 (422)
Q Consensus       391 ~CGH~fC~~Ci~~~-------~~CP~CR~~i~  415 (422)
                      .|+|.|+..|+.++       ..||+||++..
T Consensus        51 ~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   51 KCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             cCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            89999999999965       57999999864

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=95.76  E-value=0.17  Score=56.03  Aligned_cols=141  Identities=14%  Similarity=0.195  Sum_probs=86.8

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccc-ccCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLA-PFDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~-~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      ..+++.||.|+|+..                 .+..+.|...+..++. .|-..-.+-+++|++...  ..++++     
T Consensus       466 ~~vv~vvD~SgSM~~-----------------~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a--~~~~p~-----  521 (633)
T TIGR02442       466 NLVIFVVDASGSMAA-----------------RGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEA--EVLLPP-----  521 (633)
T ss_pred             ceEEEEEECCccCCC-----------------ccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCc--eEEcCC-----
Confidence            468899999999951                 1456666666666653 465666899999975411  112222     


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHH----cCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEK----SGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~----~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                       -.+.+.+.    ..+..+...|-|.++.-|..+.+....    ....-.++++||||.-+.. +.  +  .+..++..+
T Consensus       522 -t~~~~~~~----~~L~~l~~gG~Tpl~~aL~~A~~~l~~~~~~~~~~~~~vvliTDG~~n~~-~~--~--~~~~~~~~~  591 (633)
T TIGR02442       522 -TSSVELAA----RRLEELPTGGRTPLAAGLLKAAEVLSNELLRDDDGRPLLVVITDGRANVA-DG--G--EPPTDDART  591 (633)
T ss_pred             -CCCHHHHH----HHHHhCCCCCCCCHHHHHHHHHHHHHHhhccCCCCceEEEEECCCCCCCC-CC--C--CChHHHHHH
Confidence             13344332    345566778999999999999988763    2233467889999987652 11  0  011233333


Q ss_pred             HHHHhcCCCeeEEEEecCCC
Q 042398          254 SIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       254 aIv~AS~~PlSIiiVGVG~~  273 (422)
                      +-.......+-+++|+.+.+
T Consensus       592 ~a~~l~~~~i~~~vIdt~~~  611 (633)
T TIGR02442       592 IAAKLAARGILFVVIDTESG  611 (633)
T ss_pred             HHHHHHhcCCeEEEEeCCCC
Confidence            33333445677788887664

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.76  E-value=0.0041  Score=63.68  Aligned_cols=45  Identities=27%  Similarity=0.680  Sum_probs=36.9

Q ss_pred             CcCCccccccccccccc---------ccCCCccchhhhhcC-----------CCCCCccccccCc
Q 042398          373 AETQACPICLTNAKDLA---------FGCGHMTCRECGSRV-----------SNCPICRQRITNR  417 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~v~---------l~CGH~fC~~Ci~~~-----------~~CP~CR~~i~~~  417 (422)
                      ..+..|.||++...+..         .+|.|.||..|+..|           +.||.||......
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            35679999999887744         479999999999965           5799999987654

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=95.52  E-value=0.0064  Score=61.70  Aligned_cols=46  Identities=30%  Similarity=0.819  Sum_probs=38.6

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC------CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV------SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~------~~CP~CR~~i~~~  417 (422)
                      -+++..|.||-.-..- .++||+|..|.-|..++      +.||+||.....+
T Consensus        58 DEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V  110 (493)
T COG5236          58 DEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETEAV  110 (493)
T ss_pred             ccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCccccccceE
Confidence            4667899999998887 56799999999999864      7899999876554

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]

Probab=95.31  E-value=0.0041  Score=62.74  Aligned_cols=47  Identities=23%  Similarity=0.528  Sum_probs=38.8

Q ss_pred             CCcCCccccccccccccc--ccCCCccchhhhhcC----CCCCCccccccCcc
Q 042398          372 VAETQACPICLTNAKDLA--FGCGHMTCRECGSRV----SNCPICRQRITNRL  418 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v~--l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i  418 (422)
                      ......|.+|..++.|.+  .-|-|.||..|+.+.    ..||.|...+....
T Consensus        12 ~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~   64 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTH   64 (331)
T ss_pred             cccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCcc
Confidence            345679999999999943  399999999999854    78999999886653

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=95.30  E-value=0.0068  Score=57.31  Aligned_cols=42  Identities=29%  Similarity=0.721  Sum_probs=34.7

Q ss_pred             Cccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccCc
Q 042398          376 QACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      +.|.||..-+.. ++..|||.||..|..+-    ..|-+|.+.....
T Consensus       197 F~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~  243 (259)
T COG5152         197 FLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR  243 (259)
T ss_pred             eeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence            699999998888 77799999999998842    6799998765443

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=95.01  E-value=0.016  Score=60.46  Aligned_cols=46  Identities=37%  Similarity=0.889  Sum_probs=39.0

Q ss_pred             CCcCCccccccccccccc--ccCCCccchhhhhcC----CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKDLA--FGCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v~--l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      +++++.|++|.....+.+  ..|||.||..|+..+    ..||.|+..+...
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQA   69 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchh
Confidence            678899999999999943  499999999999965    5799998877543

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=94.99  E-value=0.011  Score=58.99  Aligned_cols=43  Identities=26%  Similarity=0.639  Sum_probs=36.4

Q ss_pred             Cccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccCcc
Q 042398          376 QACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITNRL  418 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i  418 (422)
                      ..|-||...+.+ ++..|||.||..|....    ..|.+|.+.+...+
T Consensus       242 f~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~  289 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSF  289 (313)
T ss_pred             ccccccccccccchhhcCCceeehhhhccccccCCcceeccccccccc
Confidence            479999999999 77799999999998843    57999998876543

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.73  E-value=0.015  Score=56.67  Aligned_cols=44  Identities=18%  Similarity=0.496  Sum_probs=37.7

Q ss_pred             cCCccccccccccc----ccc-cCCCccchhhhhcC----CCCCCccccccCc
Q 042398          374 ETQACPICLTNAKD----LAF-GCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       374 e~~~CpIC~~~~~~----v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      ....||||.+.+.+    ++| +|||++|.+|..++    ..||+|-.++..+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr  272 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR  272 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence            56899999999998    355 99999999999976    5799999988654

>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown

Probab=94.69  E-value=0.24  Score=47.51  Aligned_cols=105  Identities=19%  Similarity=0.164  Sum_probs=64.7

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      ..++|.+|-|+|+..            |.    --+.+.+.+   +...+.   .+-+|-|+.........+  .     
T Consensus        58 ~~lvvl~DvSGSM~~------------~s----~~~l~~~~~---l~~~~~---~~~~f~F~~~l~~vT~~l--~-----  108 (222)
T PF05762_consen   58 RRLVVLCDVSGSMAG------------YS----EFMLAFLYA---LQRQFR---RVRVFVFSTRLTEVTPLL--R-----  108 (222)
T ss_pred             ccEEEEEeCCCChHH------------HH----HHHHHHHHH---HHHhCC---CEEEEEEeeehhhhhhhh--c-----
Confidence            369999999999952            10    112222222   222222   688999998653322222  1     


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCccc
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVT  234 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~  234 (422)
                      -.+..+.+.........  ++|-|++...++++.+......-.-.++|||+||.=+
T Consensus       109 ~~~~~~~l~~~~~~~~~--~~GgTdi~~aL~~~~~~~~~~~~~~t~vvIiSDg~~~  162 (222)
T PF05762_consen  109 RRDPEEALARLSALVQS--FGGGTDIGQALREFLRQYARPDLRRTTVVIISDGWDT  162 (222)
T ss_pred             cCCHHHHHHHHHhhccC--CCCccHHHHHHHHHHHHhhcccccCcEEEEEeccccc
Confidence            12445555554433333  8999999999999998876433256889999999433

It is found as part of a CO oxidising (Cox) system operon in several bacteria [].

>PRK10997 yieM hypothetical protein; Provisional

Probab=94.43  E-value=0.62  Score=50.10  Aligned_cols=144  Identities=17%  Similarity=0.147  Sum_probs=83.8

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHH-HHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKA-ITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~A-I~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      -.++|.||-|+|..  |.              +-.|.+| .-+++.+...=+  ..+-++.|++.....    .+.    
T Consensus       324 GpiII~VDtSGSM~--G~--------------ke~~AkalAaAL~~iAl~q~--dr~~li~Fs~~i~~~----~l~----  377 (487)
T PRK10997        324 GPFIVCVDTSGSMG--GF--------------NEQCAKAFCLALMRIALAEN--RRCYIMLFSTEVVTY----ELT----  377 (487)
T ss_pred             CcEEEEEECCCCCC--CC--------------HHHHHHHHHHHHHHHHHhcC--CCEEEEEecCCceee----ccC----
Confidence            45999999999994  20              1256555 334444433222  346688898864321    121    


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVA  257 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~  257 (422)
                      .-.|+..+++.-..     .+.|.|++++.++.+++..++..-+=-.+|||||+......        ....+.++.+.+
T Consensus       378 ~~~gl~~ll~fL~~-----~f~GGTDl~~aL~~al~~l~~~~~r~adIVVISDF~~~~~~--------eel~~~L~~Lk~  444 (487)
T PRK10997        378 GPDGLEQAIRFLSQ-----SFRGGTDLAPCLRAIIEKMQGREWFDADAVVISDFIAQRLP--------DELVAKVKELQR  444 (487)
T ss_pred             CccCHHHHHHHHHH-----hcCCCCcHHHHHHHHHHHHcccccCCceEEEECCCCCCCCh--------HHHHHHHHHHHH
Confidence            23578887775533     35899999999999998877543233678999999654310        112334444444


Q ss_pred             hcCCCeeEEEEecCC-CCccccccccC
Q 042398          258 ASSYPLSIVLVGVGD-GPWEDMQKFDD  283 (422)
Q Consensus       258 AS~~PlSIiiVGVG~-~~f~~m~~LD~  283 (422)
                      ....=+--+.|  |+ +.=+-|+.||.
T Consensus       445 ~~~~rf~~l~i--~~~~~p~l~~ifD~  469 (487)
T PRK10997        445 QHQHRFHAVAM--SAHGKPGIMRIFDH  469 (487)
T ss_pred             hcCcEEEEEEe--CCCCCchHHHhcCe
Confidence            44444444444  43 22233666663

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.31  E-value=0.024  Score=55.85  Aligned_cols=45  Identities=18%  Similarity=0.493  Sum_probs=37.4

Q ss_pred             CCcCCccccccccccc----ccc-cCCCccchhhhhcCC---CCCCccccccC
Q 042398          372 VAETQACPICLTNAKD----LAF-GCGHMTCRECGSRVS---NCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~----v~l-~CGH~fC~~Ci~~~~---~CP~CR~~i~~  416 (422)
                      ....+.|||+...+..    +.+ +|||+|+..++..+.   .||+|-.++..
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~  162 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTE  162 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcccc
Confidence            4566899999988754    444 999999999999775   79999999874

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]

Probab=94.23  E-value=0.011  Score=65.19  Aligned_cols=45  Identities=27%  Similarity=0.558  Sum_probs=36.6

Q ss_pred             cCCccccccccccc--c--cccCCCccchhhhhcC----CCCCCccccccCcc
Q 042398          374 ETQACPICLTNAKD--L--AFGCGHMTCRECGSRV----SNCPICRQRITNRL  418 (422)
Q Consensus       374 e~~~CpIC~~~~~~--v--~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i  418 (422)
                      ....|++|+....+  +  -..|+|.||..|+..|    ..||+||..+..++
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            34689999988877  2  2399999999999987    67999999887654

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]

Probab=94.23  E-value=0.03  Score=56.61  Aligned_cols=50  Identities=24%  Similarity=0.640  Sum_probs=37.6

Q ss_pred             CcCCccccccccccc-ccc-cCCCccchhhhhcC----CCCCCccccc--cCccccCC
Q 042398          373 AETQACPICLTNAKD-LAF-GCGHMTCRECGSRV----SNCPICRQRI--TNRLRLFA  422 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i--~~~i~vy~  422 (422)
                      .+...||||+....+ .++ -.|-+||..|+-..    ..||+-..+.  +..+|+|+
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~  355 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFN  355 (357)
T ss_pred             CccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHHHHHhc
Confidence            455799999999888 444 77999999999853    7899866554  45566653

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=94.06  E-value=0.018  Score=60.95  Aligned_cols=44  Identities=30%  Similarity=0.696  Sum_probs=33.6

Q ss_pred             CcCCcccccccccc-----------------c-ccccCCCccchhhhhcC----C-CCCCccccccC
Q 042398          373 AETQACPICLTNAK-----------------D-LAFGCGHMTCRECGSRV----S-NCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~-----------------~-v~l~CGH~fC~~Ci~~~----~-~CP~CR~~i~~  416 (422)
                      +....|+||+....                 + ++.||.|.|...|+.+|    + .||+||.++..
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            44568999996321                 1 34499999999999976    3 79999998753

>TIGR00868 hCaCC calcium-activated chloride channel protein 1

Probab=94.03  E-value=0.35  Score=55.22  Aligned_cols=141  Identities=14%  Similarity=0.171  Sum_probs=83.8

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHH-hccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITII-GKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~i-g~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      +++.||-|+|+...       +       ..+.-.+|+... ..++   ..+-.+-++.|+......   ..+.+-.   
T Consensus       307 VVLVLDvSGSM~g~-------d-------RL~~lkqAA~~fL~~~l---~~~DrVGLVtFsssA~vl---~pLt~It---  363 (863)
T TIGR00868       307 VCLVLDKSGSMTVE-------D-------RLKRMNQAAKLFLLQTV---EKGSWVGMVTFDSAAYIK---NELIQIT---  363 (863)
T ss_pred             EEEEEECCcccccc-------C-------HHHHHHHHHHHHHHHhC---CCCCEEEEEEECCceeEe---eccccCC---
Confidence            77899999999521       0       234445565543 3343   445589999999864321   2222211   


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCC--ceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHH
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGG--QYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVA  257 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~--~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~  257 (422)
                       . ....++-...++ ....|-|++..-|..|.+..++...  .=-.+++||||+-++            ..+..+   +
T Consensus       364 -s-~~dr~aL~~~L~-~~A~GGT~I~~GL~~Alq~L~~~~~~~~~~~IILLTDGedn~------------~~~~l~---~  425 (863)
T TIGR00868       364 -S-SAERDALTANLP-TAASGGTSICSGLKAAFQVIKKSYQSTDGSEIVLLTDGEDNT------------ISSCFE---E  425 (863)
T ss_pred             -c-HHHHHHHHHhhc-cccCCCCcHHHHHHHHHHHHHhcccccCCCEEEEEeCCCCCC------------HHHHHH---H
Confidence             1 122333333444 3467889999999999988776421  123567789998654            223333   3


Q ss_pred             hcCCCeeEEEEecCCCCcccccccc
Q 042398          258 ASSYPLSIVLVGVGDGPWEDMQKFD  282 (422)
Q Consensus       258 AS~~PlSIiiVGVG~~~f~~m~~LD  282 (422)
                      +....+.|-.||+|...=..|++|=
T Consensus       426 lk~~gVtI~TIg~G~dad~~L~~IA  450 (863)
T TIGR00868       426 VKQSGAIIHTIALGPSAAKELEELS  450 (863)
T ss_pred             HHHcCCEEEEEEeCCChHHHHHHHH
Confidence            4445788888999976544455443

distributions. found a row in 1A13.INFO that was not parsed out

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=93.77  E-value=0.018  Score=61.39  Aligned_cols=44  Identities=27%  Similarity=0.702  Sum_probs=37.0

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC---------CCCCCcccccc
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV---------SNCPICRQRIT  415 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~---------~~CP~CR~~i~  415 (422)
                      ..++..|.+|.+...+ +...|.|.||..|+...         ..||.|...++
T Consensus       533 nk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             ccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            4566899999999999 67799999999999742         68999987764

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=93.41  E-value=0.032  Score=55.77  Aligned_cols=37  Identities=32%  Similarity=0.886  Sum_probs=32.0

Q ss_pred             Cccccccccccc-ccc-cCCCccchhhhhcC-----CCCCCccc
Q 042398          376 QACPICLTNAKD-LAF-GCGHMTCRECGSRV-----SNCPICRQ  412 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~-----~~CP~CR~  412 (422)
                      +.|+.|...+.+ +.. .|+|.||.+|+...     ..||.|..
T Consensus       275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            689999999999 555 78999999999942     78999976

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B

Probab=93.38  E-value=0.035  Score=41.18  Aligned_cols=37  Identities=32%  Similarity=0.941  Sum_probs=17.8

Q ss_pred             cccccccccc--cc-c--cCCCccchhhhhcC-----CCCCCccccc
Q 042398          378 CPICLTNAKD--LA-F--GCGHMTCRECGSRV-----SNCPICRQRI  414 (422)
Q Consensus       378 CpIC~~~~~~--v~-l--~CGH~fC~~Ci~~~-----~~CP~CR~~i  414 (422)
                      ||+|.+.+..  .. +  +||+.+|..|..+.     ..||-||++.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7889888733  33 3  67899999997743     5799999874

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.86  E-value=0.05  Score=53.75  Aligned_cols=43  Identities=19%  Similarity=0.600  Sum_probs=34.1

Q ss_pred             CcCCccccccccccc-----------ccccCCCccchhhhhcC------CCCCCcccccc
Q 042398          373 AETQACPICLTNAKD-----------LAFGCGHMTCRECGSRV------SNCPICRQRIT  415 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-----------v~l~CGH~fC~~Ci~~~------~~CP~CR~~i~  415 (422)
                      .++..|.||-..+..           -.+.|+|+|...|+..|      ..||-|++.+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            345689999875543           24699999999999965      68999998875

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.06  E-value=0.063  Score=54.59  Aligned_cols=44  Identities=30%  Similarity=0.828  Sum_probs=32.6

Q ss_pred             CcCCccccccccccc---ccc--cCCCccchhhhhcC-----CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD---LAF--GCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~---v~l--~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      .|+..||.|++....   -.+  +||...|.-|....     ..||.||...+.
T Consensus        12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d   65 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD   65 (480)
T ss_pred             cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence            344569999987654   233  77888899998754     589999998753

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=91.84  E-value=0.047  Score=43.37  Aligned_cols=43  Identities=28%  Similarity=0.556  Sum_probs=21.0

Q ss_pred             CCcccccccccc-c---ccc-----cCCCccchhhhhcC---------------CCCCCccccccCc
Q 042398          375 TQACPICLTNAK-D---LAF-----GCGHMTCRECGSRV---------------SNCPICRQRITNR  417 (422)
Q Consensus       375 ~~~CpIC~~~~~-~---v~l-----~CGH~fC~~Ci~~~---------------~~CP~CR~~i~~~  417 (422)
                      +..|+||+.... +   ..+     .|++.|+..|+..|               ..||.|+.+|+-.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            468999998765 2   112     68888999999865               2499999998643

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=90.30  E-value=0.083  Score=59.80  Aligned_cols=45  Identities=29%  Similarity=0.597  Sum_probs=34.3

Q ss_pred             CCcCCccccccccccc--cc------ccCCCccchhhhhcC------CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD--LA------FGCGHMTCRECGSRV------SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~--v~------l~CGH~fC~~Ci~~~------~~CP~CR~~i~~  416 (422)
                      .....+|+||+....-  -.      -.|.|.|+..|+-+|      ..||+||..|+-
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence            3455799999987652  12      257899999999987      679999987753

>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

Probab=90.02  E-value=0.13  Score=42.91  Aligned_cols=31  Identities=29%  Similarity=0.735  Sum_probs=25.4

Q ss_pred             CcCCccccccccccc---ccccCCCccchhhhhc
Q 042398          373 AETQACPICLTNAKD---LAFGCGHMTCRECGSR  403 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~---v~l~CGH~fC~~Ci~~  403 (422)
                      .+...|++|...+.+   +++||||.++..|+.+
T Consensus        76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r  109 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR  109 (109)
T ss_pred             CCCCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence            445689999999887   4669999999999753

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=89.28  E-value=0.12  Score=57.70  Aligned_cols=40  Identities=33%  Similarity=0.845  Sum_probs=32.5

Q ss_pred             Cccccccccccc-ccccCCCccchhhhhcC------CCCCCccccccC
Q 042398          376 QACPICLTNAKD-LAFGCGHMTCRECGSRV------SNCPICRQRITN  416 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~------~~CP~CR~~i~~  416 (422)
                      ..|.+|.+ ... +...|||.+|..|+...      ..||.||..+..
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence            79999999 444 45599999999999854      469999987754

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=89.18  E-value=0.084  Score=42.85  Aligned_cols=39  Identities=33%  Similarity=0.732  Sum_probs=27.5

Q ss_pred             ccccccccccc--ccc-cCCCccchhhhhcC-------CCCCCcccccc
Q 042398          377 ACPICLTNAKD--LAF-GCGHMTCRECGSRV-------SNCPICRQRIT  415 (422)
Q Consensus       377 ~CpIC~~~~~~--v~l-~CGH~fC~~Ci~~~-------~~CP~CR~~i~  415 (422)
                      .||-|.-.-.+  .++ .|.|.|...|+.++       ..||+||+..+
T Consensus        33 ~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   33 CCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             cCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            44444443344  234 89999999999975       47999998754

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C

Probab=88.87  E-value=0.13  Score=39.40  Aligned_cols=37  Identities=30%  Similarity=0.551  Sum_probs=24.2

Q ss_pred             CcCCcccccccccccc-c-ccCCCccchhhhhcC------CCCCC
Q 042398          373 AETQACPICLTNAKDL-A-FGCGHMTCRECGSRV------SNCPI  409 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~v-~-l~CGH~fC~~Ci~~~------~~CP~  409 (422)
                      .-...|||.+..+.+. . ..|||.|..+.+..+      ..||+
T Consensus         9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            3457999999999994 3 499999999998854      46887

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]

Probab=88.86  E-value=0.16  Score=51.23  Aligned_cols=41  Identities=27%  Similarity=0.651  Sum_probs=30.6

Q ss_pred             Cccccccccccc--ccccCCCccchhhhhcC--CCCCCccccccC
Q 042398          376 QACPICLTNAKD--LAFGCGHMTCRECGSRV--SNCPICRQRITN  416 (422)
Q Consensus       376 ~~CpIC~~~~~~--v~l~CGH~fC~~Ci~~~--~~CP~CR~~i~~  416 (422)
                      ..|.-|---.+.  -.++|.|+||.+|...-  +.||.|-.++.+
T Consensus        91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen   91 HFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQR  135 (389)
T ss_pred             EeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHH
Confidence            456667554444  35699999999999854  699999877654

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=88.64  E-value=0.14  Score=53.34  Aligned_cols=30  Identities=23%  Similarity=0.666  Sum_probs=25.1

Q ss_pred             cCCccccccccccc---c-cccCCCccchhhhhc
Q 042398          374 ETQACPICLTNAKD---L-AFGCGHMTCRECGSR  403 (422)
Q Consensus       374 e~~~CpIC~~~~~~---v-~l~CGH~fC~~Ci~~  403 (422)
                      ....|.||++...-   + .+||+|+||..|+..
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kd  216 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKD  216 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHH
Confidence            44799999998876   3 459999999999984

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

Probab=85.78  E-value=0.24  Score=55.73  Aligned_cols=44  Identities=23%  Similarity=0.576  Sum_probs=35.3

Q ss_pred             CCccccccccccc--ccccCCCccchhhhhc-CCCCCCccccccCcc
Q 042398          375 TQACPICLTNAKD--LAFGCGHMTCRECGSR-VSNCPICRQRITNRL  418 (422)
Q Consensus       375 ~~~CpIC~~~~~~--v~l~CGH~fC~~Ci~~-~~~CP~CR~~i~~~i  418 (422)
                      ...|..|-..+.-  |.+.|||.|+..|+.+ ...||.|+......+
T Consensus       840 ~skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~~~~m  886 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPELRGVM  886 (933)
T ss_pred             eeeecccCCccccceeeeecccHHHHHhhccCcccCCccchhhhhhH
Confidence            3689999988776  5669999999999994 478999998655443

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

Probab=83.92  E-value=0.48  Score=38.85  Aligned_cols=25  Identities=32%  Similarity=0.534  Sum_probs=22.0

Q ss_pred             cCCCccchhhhhcC----CCCCCcccccc
Q 042398          391 GCGHMTCRECGSRV----SNCPICRQRIT  415 (422)
Q Consensus       391 ~CGH~fC~~Ci~~~----~~CP~CR~~i~  415 (422)
                      -|.|.|...|+.++    ..||+||++..
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            89999999999987    57999998753

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]

Probab=83.03  E-value=0.21  Score=50.14  Aligned_cols=40  Identities=35%  Similarity=0.777  Sum_probs=31.8

Q ss_pred             Cccccccccccc----ccccCCCccchhhhhcC---------------------------CCCCCcccccc
Q 042398          376 QACPICLTNAKD----LAFGCGHMTCRECGSRV---------------------------SNCPICRQRIT  415 (422)
Q Consensus       376 ~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~---------------------------~~CP~CR~~i~  415 (422)
                      -.|.||+--+.+    .+++|-|.+.+.|+.+.                           ..||+||..|.
T Consensus       116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~  186 (368)
T KOG4445|consen  116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK  186 (368)
T ss_pred             CceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence            479999987776    35599999999997742                           35999999885

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins

Probab=81.86  E-value=0.64  Score=34.40  Aligned_cols=35  Identities=31%  Similarity=0.777  Sum_probs=25.2

Q ss_pred             ccccccccccc---ccccCC-----CccchhhhhcC------CCCCCcc
Q 042398          377 ACPICLTNAKD---LAFGCG-----HMTCRECGSRV------SNCPICR  411 (422)
Q Consensus       377 ~CpIC~~~~~~---v~l~CG-----H~fC~~Ci~~~------~~CP~CR  411 (422)
                      .|.||++...+   ...||.     |.+...|+.+|      ..||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            48899983222   345884     67899999976      4799994

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=81.05  E-value=1.1  Score=44.92  Aligned_cols=30  Identities=27%  Similarity=0.741  Sum_probs=25.4

Q ss_pred             CcCCcccccccccccccc-cC----CCccchhhhh
Q 042398          373 AETQACPICLTNAKDLAF-GC----GHMTCRECGS  402 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~v~l-~C----GH~fC~~Ci~  402 (422)
                      ...+.|.+|.+.+.|..| .|    .|.||.-|-.
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR  300 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR  300 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCH
Confidence            445899999999999766 88    6889999976

>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]

Probab=80.29  E-value=3  Score=39.68  Aligned_cols=143  Identities=19%  Similarity=0.287  Sum_probs=78.1

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC-CCCCcceeeecCCC---CCCCCCcccCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD-EDNLIPCFGFGDAT---THDQEVFSFHDD  175 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD-~D~~ip~~GFGa~~---~~~~~vf~~~~~  175 (422)
                      -+.+-+|.+.|.-        +.++|.++.   -.|.-|+.+-+  .+|- .--.+-+.-||...   .+..++-||+| 
T Consensus         5 P~~lllDtSgSM~--------Ge~IealN~---Glq~m~~~Lkq--dp~Ale~v~lsIVTF~~~a~~~~pf~~~~nF~~-   70 (207)
T COG4245           5 PCYLLLDTSGSMI--------GEPIEALNA---GLQMMIDTLKQ--DPYALERVELSIVTFGGPARVIQPFTDAANFNP-   70 (207)
T ss_pred             CEEEEEecCcccc--------cccHHHHHH---HHHHHHHHHHh--ChhhhheeEEEEEEecCcceEEechhhHhhcCC-
Confidence            4677899999983        567776542   12222222211  0110 11246667777532   12223334443 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--------CCce-EEEEEEeCCcccccCCCCCCCCch
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--------GGQY-HVLVIIADGQVTRSVNTGDGELSS  246 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--------~~~Y-~VLlIiTDG~i~d~~~~~~~~~~~  246 (422)
                                        |.+...|-|...-.|+.+.+.+++.        .+.| .+..+||||..+|-  .       
T Consensus        71 ------------------p~L~a~GgT~lGaAl~~a~d~Ie~~~~~~~a~~kgdyrP~vfLiTDG~PtD~--w-------  123 (207)
T COG4245          71 ------------------PILTAQGGTPLGAALTLALDMIEERKRKYDANGKGDYRPWVFLITDGEPTDD--W-------  123 (207)
T ss_pred             ------------------CceecCCCCchHHHHHHHHHHHHHHHhhcccCCccccceEEEEecCCCcchH--H-------
Confidence                              4455568898888999888776543        1334 34457799999981  1       


Q ss_pred             hHHHHHHHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          247 QEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       247 ~~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      ++..++..--+++.--+-+..||+-++|-..++++-+
T Consensus       124 ~~~~~~~~~~~~~~k~v~a~~~G~~~ad~~~L~qit~  160 (207)
T COG4245         124 QAGAALVFQGERRAKSVAAFSVGVQGADNKTLNQITE  160 (207)
T ss_pred             HhHHHHhhhcccccceEEEEEecccccccHHHHHHHH
Confidence            2333344444455555555555655567666666553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	422
4auq_B	62	Structure Of Birc7-Ubch5b-Ub Complex. Length = 62		3e-06
3eb5_A	74	Structure Of The Ciap2 Ring Domain Length = 74		5e-04

>pdb|4AUQ|B Chain B, Structure Of Birc7-Ubch5b-Ub Complex. Length = 62

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 374 ETQACPICLTNAKDLAF-GCGHMTCRECGSRVSNCPICRQRITNRLRLF 421
           E + C +CL  A  + F  CGH+ C EC   +  CPICR  + +R+R F
Sbjct: 12  EERTCKVCLDRAVSIVFVPCGHLVCAECAPGLQLCPICRAPVRSRVRTF 60

>pdb|3EB5|A Chain A, Structure Of The Ciap2 Ring Domain Length = 74

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 374 ETQACPICLTNAKDLAF-GCGHMT-CRECGSRVSNCPICRQRITNRLRLF 421
           E + C +C+     + F  CGH+  C++C   +  CPICR  I   +R F
Sbjct: 23  EERTCKVCMDKEVSIVFIPCGHLVVCKDCAPSLRKCPICRSTIKGTVRTF 72

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	422
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	6e-16
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	2e-15
2ea5_A	68	Cell growth regulator with ring finger domain prot	9e-14
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	4e-13
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	1e-11
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	3e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-11
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-07
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-07
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	3e-07
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	5e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	1e-06
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-06
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-06
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	5e-06
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	8e-06
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	1e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	1e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-05
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	4e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	4e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	4e-05
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-05
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	6e-05
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	6e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	7e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	8e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	8e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-04
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-04
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-04
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-04
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	5e-04
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	5e-04
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	7e-04

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A Length = 79

 Score = 71.3 bits (175), Expect = 6e-16
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 374 ETQACPICLTNAKDLAFG-CGHM-TCRECGSRVSNCPICRQRITNRLRLF 421
           E   C +C     +  F  CGH   C  C +++ +CP+CR R+ +   ++
Sbjct: 17  EAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVY 66

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 70.2 bits (172), Expect = 2e-15
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 374 ETQACPICLTNAKDLAFG-CGHM-TCRECGSRVSNCPICRQRITNRLRLF 421
           E + C IC+     + F  CGH+ TC++C   V  CP+C   IT + ++F
Sbjct: 24  EEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDKCPMCYTVITFKQKIF 73

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 68

 Score = 64.8 bits (158), Expect = 9e-14
 Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 2/50 (4%)

Query: 374 ETQACPICLTNAKDLAFG-CGHM-TCRECGSRVSNCPICRQRITNRLRLF 421
            ++ C +C     +     C H   C  C      CP+CRQ +     L 
Sbjct: 14  NSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYFQQCPMCRQFVQESFALS 63

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A Length = 64

 Score = 62.9 bits (153), Expect = 4e-13
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 8/61 (13%)

Query: 369 STPVAETQACPICLTNAKDLAF---GCGHM-TCRECGSRV----SNCPICRQRITNRLRL 420
           S P+   + C IC    K+        GH+  C  C  ++      CP+CRQ I   +  
Sbjct: 2   SLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLT 61

Query: 421 F 421
           +
Sbjct: 62  Y 62

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A Length = 345

 Score = 65.0 bits (156), Expect = 1e-11
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 371 PVAETQACPICLTNAKDLAFG-CGHM-TCRECGSRVSNCPICRQRITNRLRLF 421
            + E + C +C+     + F  CGH+  C+EC   +  CPICR  I   +R F
Sbjct: 291 RLQEERTCKVCMDKEVSVVFIPCGHLVVCQECAPSLRKCPICRGIIKGTVRTF 343

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B* Length = 63

 Score = 57.9 bits (140), Expect = 3e-11
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 378 CPICLTNAKDLAFG---CGHM-TCRECGSRV----SNCPICRQRITNRLRLF 421
           C +C    +D        GH+ TC  C  R+    ++CPIC++ I   +++F
Sbjct: 10  CSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVF 61

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

 Score = 63.3 bits (153), Expect = 8e-11
 Identities = 46/338 (13%), Positives = 98/338 (28%), Gaps = 94/338 (27%)

Query: 60  ENIISSA-RDKMKKKYSFIPDTFSSLEQVTAALRDSGLESSNLILGID--FTKSNEWTGK 116
           E ++     + ++  Y F+     + ++  + +    +E  + +   +  F K N    +
Sbjct: 76  EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135

Query: 117 VSFNNRSLHAIGDTPNPYEKAITI-----IGKT-LAP--FDEDNLIPCFGFGDATTHDQE 168
             +       +   P      + I      GKT +A        +     F         
Sbjct: 136 -PYLKLRQALLELRPAKN---VLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-------- 183

Query: 169 VF--SFHDDHTPCHGFEEVLACYRNIVPNL--RLAGPTSYAPVVEAA------------- 211
           +F  +  + ++P    E +      I PN   R    ++    + +              
Sbjct: 184 IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243

Query: 212 ------MD------IVEKSGGQYHVLVIIADGQVTRSVNTG----------DGELSSQEQ 249
                 +                 +L+     QVT  ++               L+  E 
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 250 KTI--KSI---------VAASSYPLSIVLVGVGDGPWEDMQKFDDKIPAREFDNFQFVNF 298
           K++  K +            ++ P  + ++       E ++       A  +DN++ VN 
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIA------ESIRDG----LAT-WDNWKHVNC 352

Query: 299 ----TAI-MSKNA-TPSEKETAF-ALAALME---IPIQ 326
               T I  S N   P+E    F  L+       IP  
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 48.7 bits (116), Expect = 6e-08
 Identities = 16/58 (27%), Positives = 21/58 (36%), Gaps = 5/58 (8%)

Query: 366 SRGSTPVAETQACPICLTNAKD-LAFGCGHMTCRECGSRVSN----CPICRQRITNRL 418
           S  + P      C ICL      ++  C H+ C  C    S     C +CRQ I    
Sbjct: 6   SGNTAPSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDF 63

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389

 Score = 52.1 bits (124), Expect = 1e-07
 Identities = 21/74 (28%), Positives = 26/74 (35%), Gaps = 6/74 (8%)

Query: 350 PPPAPYSRRALPERQPSRGSTPVAETQACPICLTNAKDLAF-GCGHMTCREC-----GSR 403
             P P     + + Q        +  Q C IC  N KD+    CGH+ C  C      S 
Sbjct: 307 CEPTPQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESE 366

Query: 404 VSNCPICRQRITNR 417
              CP CR  I   
Sbjct: 367 GQGCPFCRCEIKGT 380

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 46.3 bits (110), Expect = 3e-07
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 12/52 (23%)

Query: 378 CPICLTNAKDLAFG--------CGHMTCREC----GSRVSNCPICRQRITNR 417
           CPIC+    ++           CGH+ C +C        + CP CR++I ++
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 57

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 46.4 bits (110), Expect = 3e-07
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 16/70 (22%)

Query: 368 GSTPVAETQA--CPICLTNAKDLAFG--------CGHMTCRECGSRV----SNCPICRQR 413
           G+T +  +    CPIC+    ++           CGH+ C +C        + CP CR++
Sbjct: 1   GTTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 60

Query: 414 ITNR--LRLF 421
           I ++    ++
Sbjct: 61  INHKRYHPIY 70

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124

 Score = 48.0 bits (114), Expect = 3e-07
 Identities = 16/76 (21%), Positives = 25/76 (32%), Gaps = 6/76 (7%)

Query: 351 PPAPYSRRALPERQPSRGSTPVAETQACPICLTNAKD-LAFGCGHMTCREC-----GSRV 404
             A    R           + V ET  C  C       +   C H  C++C      ++V
Sbjct: 28  VLASLKDRPASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQV 87

Query: 405 SNCPICRQRITNRLRL 420
            +CP CR  +     +
Sbjct: 88  FSCPACRYDLGRSYAM 103

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 45.7 bits (108), Expect = 5e-07
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 12/52 (23%)

Query: 378 CPICLTNAKDLAFG--------CGHMTCRECGSRV----SNCPICRQRITNR 417
           CPIC+    ++           CGH+ C +C        + CP CR++I ++
Sbjct: 18  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 11/44 (25%), Positives = 13/44 (29%), Gaps = 6/44 (13%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-----GSRVSNCPICRQRIT 415
           C  C           CGH  C  C      S    C  C++ I 
Sbjct: 18  CEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIV 61

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 10/60 (16%)

Query: 366 SRGSTPVAETQACPICL-----TNAKDLAFGCGHMTCRECGSRVSN-----CPICRQRIT 415
           SR      +   CP+C+      +       CG+  CR C  R+       CP CR+   
Sbjct: 2   SRSPDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 61

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 378 CPICLTNAKDLAFG--CGHMTCREC----GSRVSNCPICRQRIT 415
           CPICL +  + +    C H  C  C      +   CP+C+  + 
Sbjct: 8   CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 372 VAETQACPICLTNAKD--LAFGCGHMTCREC-----GSRVSNCPICRQRIT 415
           +AE   C IC+   +D  L   C  + C  C       + + CP CR  + 
Sbjct: 19  IAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQ 69

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 43.2 bits (102), Expect = 5e-06
 Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 10/62 (16%)

Query: 365 PSRGSTPVAETQACPICL---TNAKDLAFGCGHMTCREC------GSRVSNCPICRQRIT 415
            S    P+ +   C IC    T+A  +   CG+  C EC       S    CP C Q   
Sbjct: 5   SSGEDDPIPDELLCLICKDIMTDAVVIP-CCGNSYCDECIRTALLESDEHTCPTCHQNDV 63

Query: 416 NR 417
           + 
Sbjct: 64  SP 65

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65

 Score = 42.2 bits (99), Expect = 8e-06
 Identities = 15/50 (30%), Positives = 17/50 (34%), Gaps = 11/50 (22%)

Query: 374 ETQACPICLTN---AKDLAF---GCGHMTCRECGSRV-----SNCPICRQ 412
           + Q CP C T       L      CGH  C  C   +      NCP C  
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGT 51

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 372 VAETQACPICLTNAKDLAFGCGHMTCRECGSRV----SNCPICRQRITN 416
           + + + C IC+    DL   C H  C++C  +      NCPICR ++T 
Sbjct: 12  LTDEEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTG 60

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 15/44 (34%), Positives = 17/44 (38%), Gaps = 6/44 (13%)

Query: 378 CPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRIT 415
           C IC     D +   C H+ CR C  R      S CP CR    
Sbjct: 26  CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 12/41 (29%), Positives = 14/41 (34%), Gaps = 6/41 (14%)

Query: 378 CPICL---TNAKDLAFGCGHMTCREC-GSRVSNCPICRQRI 414
           C  C       K L   C H  C  C  +    CPIC+   
Sbjct: 9   CQQCQAEAKCPKLLP--CLHTLCSGCLEASGMQCPICQAPW 47

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 5/67 (7%)

Query: 356 SRRALPERQPSRGSTPVAETQACPICLTNAKDLAF-GCGHMTCRECGSRV----SNCPIC 410
             +A  E   S  +  +     C IC     +     C H  C  C +        CPIC
Sbjct: 45  KMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPIC 104

Query: 411 RQRITNR 417
           R+ I ++
Sbjct: 105 RKDIKSK 111

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-----GSRVSNCPICRQRIT 415
           CPICL   ++ +   CGH  C+ C           CP+  + + 
Sbjct: 21  CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 6/48 (12%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-----GSRVSNCPICRQRITNRLR 419
           C IC+    + +   C H  C+ C           CP CR+R+++  R
Sbjct: 18  CGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTR 65

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 9/51 (17%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-------GSRVSNCPICRQRITNR-LR 419
           CPICL   +  +   CGH  C +C             CP+C+  +    +R
Sbjct: 23  CPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAIR 73

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 8/48 (16%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-------GSRVSNCPICRQRITNR 417
           CPICL   K+ ++  C H+ C+ C           S CP+C+  IT R
Sbjct: 24  CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141

 Score = 42.4 bits (99), Expect = 4e-05
 Identities = 12/55 (21%), Positives = 14/55 (25%), Gaps = 6/55 (10%)

Query: 369 STPVAETQACPICLTNAKD-LAFGCGHMTCREC-----GSRVSNCPICRQRITNR 417
            T +     C  C    +      CGH  C  C      S   NC  C       
Sbjct: 25  GTKLEAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE 79

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 5/41 (12%)

Query: 377 ACPICLTNAKD-LAFGCGHMTCREC----GSRVSNCPICRQ 412
            C IC    ++ +   C H  C  C          C IC Q
Sbjct: 17  RCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQ 57

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 11/47 (23%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC----------GSRVSNCPICRQR 413
           CPICL   K+ ++  C H  CR C               NCP+CR  
Sbjct: 22  CPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVP 68

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 11/51 (21%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC----------GSRVSNCPICRQRITNR 417
           CPICL      L+  CGH  C+ C              S+CP+CR      
Sbjct: 22  CPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE 72

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Length = 92

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 14/48 (29%), Positives = 17/48 (35%), Gaps = 8/48 (16%)

Query: 378 CPICLTNAKD--LAFGCGHMTCREC------GSRVSNCPICRQRITNR 417
           C IC     D  +   CG+  C EC       S    CP C Q   + 
Sbjct: 16  CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP 63

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165

 Score = 41.9 bits (98), Expect = 8e-05
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 15/99 (15%)

Query: 338 RTTGRAKKIAPRPPPAPYSRRALPERQPSRGSTPVAETQA------CPIC---LTNAKDL 388
             T   + ++     + Y  +  P+   + G   V   ++      CPIC   L N    
Sbjct: 11  VQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTT 70

Query: 389 AFGCGHMTCREC-----GSRVSNCPICRQRITNRLRLFA 422
              C H  C +C      S    CP CR+++ ++  L  
Sbjct: 71  K-ECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRP 108

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 117

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 4/44 (9%)

Query: 378 CPICLTNAKD--LAFGCGHMTCRECGSRV--SNCPICRQRITNR 417
           C  C    ++     GC H+ C  C S    + CP+C      +
Sbjct: 25  CSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQ 68

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-----GSRVSNCPICRQRITNRLRL 420
           C  C       +   C H  C++C      ++V +CP CR  +     +
Sbjct: 81  CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIM 129

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 12/52 (23%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-----------GSRVSNCPICRQRITNR 417
           CPICL    + L+  CGH  CR C               S+CP+C    +  
Sbjct: 15  CPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE 66

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 20/78 (25%), Positives = 27/78 (34%), Gaps = 17/78 (21%)

Query: 350 PPPAPYSR-RALPERQPSRGSTPVAETQACPICLTNAKDLAFG-------CGHMTCREC- 400
            PPA      ALPE   +     V +   CPIC +   +   G       C H   + C 
Sbjct: 14  NPPASKESIDALPEILVTEDHGAVGQEMCCPICCS---EYVKGDVATELPCHHYFHKPCV 70

Query: 401 ----GSRVSNCPICRQRI 414
                   + CP+CR   
Sbjct: 71  SIWLQKSGT-CPVCRCMF 87

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 6/46 (13%)

Query: 378 CPICLTNAKD--LAFGCGHMTCRECGSRV----SNCPICRQRITNR 417
           C IC        +   C H  C  C  +     + CP C   +T  
Sbjct: 25  CGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP 70

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 8/46 (17%)

Query: 378 CPIC---LTNAKDLAFGCGHMTCRECGSR----VSNCPICRQRITN 416
           C IC   L +A  +   C H  C+ C  R     + CP C   +  
Sbjct: 18  CSICKGYLIDATTIT-ECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ 62

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 8/41 (19%)

Query: 378 CPICLTNAKD-LAFGCGHMTCREC-------GSRVSNCPIC 410
           C +CL   K+ +   CGH  C+ C         R   CP+C
Sbjct: 18  CSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170

 Score = 39.7 bits (92), Expect = 5e-04
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 6/46 (13%)

Query: 378 CPICLTNAKD-LAFGCGHMTCRECGSRVSN-----CPICRQRITNR 417
           CPICL   ++ +   CGH  C+ C  +        CP+  + +   
Sbjct: 21  CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN 66

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 8/50 (16%)

Query: 378 CPIC---LTNAKDLAFGCGHMTCRECGSR----VSNCPICRQRITNRLRL 420
           C +C     +A  +   C H  C+ C  R       CPIC  ++     L
Sbjct: 18  CVLCGGYFIDATTII-ECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPL 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	422
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.08
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.02
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.99
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.91
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	98.88
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.86
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	98.85
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	98.83
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.82
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.81
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	98.79
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	98.77
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	98.76
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	98.76
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.75
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.74
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.73
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	98.73
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.71
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	98.71
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.7
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.7
2ect_A	78	Ring finger protein 126; metal binding protein, st	98.69
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	98.69
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	98.67
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.66
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	98.66
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.65
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.65
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	98.62
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.6
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.6
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.59
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.59
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.58
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.54
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.54
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.52
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.49
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.49
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.48
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.48
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.47
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.47
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.46
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.45
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.45
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.44
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.43
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.43
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.4
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.34
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.32
4hqo_A	266	Sporozoite surface protein 2; malaria, gliding mot	98.3
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.3
4hqf_A	281	Thrombospondin-related anonymous protein, trap; ma	98.28
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.27
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.24
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.2
3n2n_F	185	Anthrax toxin receptor 1; rossmann fold; 1.80A {Ho	98.17
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.13
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.09
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.06
3ibs_A	218	Conserved hypothetical protein BATB; structural ge	98.03
1shu_X	182	Anthrax toxin receptor 2; alpha/beta rossmann fold	98.0
4fx5_A	464	VON willebrand factor type A; structural genomics,	97.91
2xgg_A	178	Microneme protein 2; A/I domain, cell adhesion, hy	97.9
1q0p_A	223	Complement factor B; VON willebrand factor, MAC-1,	97.85
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	97.83
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	97.83
1atz_A	189	VON willebrand factor; collagen-binding, hemostasi	97.74
1ijb_A	202	VON willebrand factor; dinucleotide-binding fold,	97.71
1n3y_A	198	Integrin alpha-X; alpha/beta rossmann fold, cell a	97.69
2b2x_A	223	Integrin alpha-1; computational design, antibody-a	97.68
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	97.65
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	97.64
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	97.62
1pt6_A	213	Integrin alpha-1; cell adhesion; 1.87A {Homo sapie	97.58
2x5n_A	192	SPRPN10, 26S proteasome regulatory subunit RPN10;	97.58
2odp_A	509	Complement C2; C3/C5 convertase, complement serin	97.53
2x31_A	189	Magnesium-chelatase 60 kDa subunit; ligase, bacter	97.51
1mf7_A	194	Integrin alpha M; cell adhesion; 1.25A {Homo sapie	97.46
1v7p_C	200	Integrin alpha-2; snake venom, C-type lectin, anta	97.45
4b4t_W	268	RPN10, 26S proteasome regulatory subunit RPN10; hy	97.4
1rrk_A	497	Complement factor B; BB, hydrolase; 2.00A {Homo sa	97.3
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	97.13
3hrz_D	741	Complement factor B; serine protease, glycosilated	96.99
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	96.9
3zqk_A	199	VON willebrand factor; blood clotting, adamts-13,	96.78
1jey_A	609	KU70; double-strand DNA break repair, non-homologo	96.75
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	96.71
1mjn_A	179	Integrin alpha-L; rossmann fold, immune system; 1.	96.3
3k6s_A	1095	Integrin alpha-X; cell receptor, adhesion molecule	96.17
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.09
1jey_B	565	KU80; double-strand DNA break repair, non-homologo	95.96
1yvr_A	538	RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein,	95.59
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	95.31
2nvo_A	535	RO sixty-related protein, RSR; alpha helical repea	95.12
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	92.26
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	89.12
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	88.08
3nw0_A	238	Non-structural maintenance of chromosomes element	82.44

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=7.6e-11  Score=91.72  Aligned_cols=51  Identities=24%  Similarity=0.664  Sum_probs=45.9

Q ss_pred             CCcCCcccccccccccc-cccCCCc-cchhhhhcCCCCCCccccccCccccCC
Q 042398          372 VAETQACPICLTNAKDL-AFGCGHM-TCRECGSRVSNCPICRQRITNRLRLFA  422 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v-~l~CGH~-fC~~Ci~~~~~CP~CR~~i~~~i~vy~  422 (422)
                      ..+...|+||++...++ .+||||. +|..|+.....||+||.+|..++++|.
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~~~CP~CR~~i~~~~~i~~   64 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYFQQCPMCRQFVQESFALSG   64 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHHCSSCTTTCCCCCCEECCCS
T ss_pred             CCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhcCCCCCCCCcchhceEEeec
Confidence            34568999999999995 5599999 999999999999999999999999984

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.02  E-value=5.4e-11  Score=93.60  Aligned_cols=50  Identities=32%  Similarity=0.887  Sum_probs=45.6

Q ss_pred             CCcCCccccccccccc-ccccCCCc-cchhhhhcCCCCCCccccccCccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHM-TCRECGSRVSNCPICRQRITNRLRLF  421 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~-fC~~Ci~~~~~CP~CR~~i~~~i~vy  421 (422)
                      ++++..|+||++.+.+ +.++|||. ||..|+..+..||+||.++..++++|
T Consensus        21 ~~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~CP~Cr~~i~~~~~i~   72 (74)
T 4ic3_A           21 LQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDKCPMCYTVITFKQKIL   72 (74)
T ss_dssp             HHHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTCSBCTTTCCBCSEEEECB
T ss_pred             CccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcCccCCCcCcCccCcEEEe
Confidence            4566899999999999 55699999 99999999999999999999999987

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=9.8e-11  Score=92.17  Aligned_cols=50  Identities=34%  Similarity=0.920  Sum_probs=45.1

Q ss_pred             CCcCCccccccccccc-ccccCCCc-cchhhhhcCCCCCCccccccCccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHM-TCRECGSRVSNCPICRQRITNRLRLF  421 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~-fC~~Ci~~~~~CP~CR~~i~~~i~vy  421 (422)
                      +++...|+||++.+.+ +.++|||. ||..|+.....||+||.++..++++|
T Consensus        22 ~~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~~~~CP~Cr~~i~~~~~i~   73 (75)
T 2ecg_A           22 LQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDKCPMCYTVITFKQKIF   73 (75)
T ss_dssp             HHHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHHCSBCTTTCCBCCCCCBCC
T ss_pred             CCCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhCCCCCccCCceecCcEEEe
Confidence            3456799999999999 45699999 99999999999999999999999988

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.91  E-value=2.4e-10  Score=91.38  Aligned_cols=49  Identities=27%  Similarity=0.829  Sum_probs=44.5

Q ss_pred             CcCCcccccccccccc-cccCCCc-cchhhhhcCCCCCCccccccCccccC
Q 042398          373 AETQACPICLTNAKDL-AFGCGHM-TCRECGSRVSNCPICRQRITNRLRLF  421 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~v-~l~CGH~-fC~~Ci~~~~~CP~CR~~i~~~i~vy  421 (422)
                      ++...|+||++...++ .+||||. ||..|+..+..||+||.++...+++|
T Consensus        16 ~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~~~CP~Cr~~i~~~~~i~   66 (79)
T 2yho_A           16 KEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVY   66 (79)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTCSBCTTTCCBCCEEEECB
T ss_pred             CCCCEeEEeCcccCcEEEECCCCHHHHHHHHHhcCcCCCCCchhhCeEEEE
Confidence            4567999999999994 5599999 89999999999999999999999887

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.88  E-value=9.9e-10  Score=85.10  Aligned_cols=46  Identities=30%  Similarity=0.788  Sum_probs=39.9

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +..+...|+||++.+.+ +.++|||.||..|+..|    ..||+||..+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             cCCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            35667899999999999 66799999999999976    579999999864

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=98.86  E-value=1.7e-10  Score=88.48  Aligned_cols=52  Identities=29%  Similarity=0.743  Sum_probs=44.1

Q ss_pred             CCCcCCccccccccccc-ccc--cCCCc-cchhhhhcC----CCCCCccccccCccccCC
Q 042398          371 PVAETQACPICLTNAKD-LAF--GCGHM-TCRECGSRV----SNCPICRQRITNRLRLFA  422 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l--~CGH~-fC~~Ci~~~----~~CP~CR~~i~~~i~vy~  422 (422)
                      +..++..|+||++..++ +.+  ||||. +|..|+..+    ..||+||+++...+++|.
T Consensus         4 ~~~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i~i~~   63 (64)
T 2vje_A            4 PLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYF   63 (64)
T ss_dssp             -CGGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCCEEEEEEC
T ss_pred             CCCCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchhceEeeec
Confidence            35577899999999999 444  99999 799999976    469999999999999883

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=2.3e-09  Score=82.91  Aligned_cols=47  Identities=30%  Similarity=0.899  Sum_probs=40.2

Q ss_pred             CCCCcCCccccccccccc-ccccCCCccchhhhhcCC-------CCCCccccccC
Q 042398          370 TPVAETQACPICLTNAKD-LAFGCGHMTCRECGSRVS-------NCPICRQRITN  416 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~~-------~CP~CR~~i~~  416 (422)
                      ..+.+...|+||++.+.+ +.++|||.||..|+..+.       .||+||..+..
T Consensus        15 ~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   69 (73)
T 2ysl_A           15 NKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRK   69 (73)
T ss_dssp             CCCCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCC
T ss_pred             HhCccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCc
Confidence            346778899999999999 567999999999999653       69999999864

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.83  E-value=2.3e-09  Score=83.19  Aligned_cols=48  Identities=25%  Similarity=0.587  Sum_probs=41.2

Q ss_pred             CCCCcCCccccccccccc-ccc-cCCCccchhhhhcC----CCCCCccccccCc
Q 042398          370 TPVAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      +.+++...|+||++.+.+ +.+ +|||.||..|+..+    ..||+||..+...
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A           10 SELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             CCCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             hhcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            346778999999999998 555 99999999999865    6899999998764

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=1.8e-09  Score=82.24  Aligned_cols=46  Identities=33%  Similarity=0.913  Sum_probs=38.9

Q ss_pred             CCCcCCccccccccccc--------ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          371 PVAETQACPICLTNAKD--------LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~--------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      ...+...|+||++.+.+        +.++|||.||..|+..|    ..||+||..+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           11 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            35677899999998876        34599999999999976    689999998865

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.81  E-value=3.9e-10  Score=86.18  Aligned_cols=49  Identities=31%  Similarity=0.836  Sum_probs=43.0

Q ss_pred             CcCCccccccccccc-ccc--cCCCc-cchhhhhcCC----CCCCccccccCccccC
Q 042398          373 AETQACPICLTNAKD-LAF--GCGHM-TCRECGSRVS----NCPICRQRITNRLRLF  421 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l--~CGH~-fC~~Ci~~~~----~CP~CR~~i~~~i~vy  421 (422)
                      .....|+||++..++ +++  ||||. +|..|+.++.    .||+||+++...+++|
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i~i~   61 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVF   61 (63)
T ss_dssp             GGGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCCEEEEEE
T ss_pred             CcCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhhceEEEe
Confidence            445789999999998 444  99999 8999999774    8999999999999988

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=98.79  E-value=3.1e-09  Score=83.15  Aligned_cols=48  Identities=29%  Similarity=0.729  Sum_probs=40.4

Q ss_pred             CCCCCcCCccccccccccc-cccc-CCCccchhhhhcC------CCCCCccccccC
Q 042398          369 STPVAETQACPICLTNAKD-LAFG-CGHMTCRECGSRV------SNCPICRQRITN  416 (422)
Q Consensus       369 ~~~~~e~~~CpIC~~~~~~-v~l~-CGH~fC~~Ci~~~------~~CP~CR~~i~~  416 (422)
                      ...+.+...|+||++.+.+ ++++ |||.||..|+..+      ..||+||.++..
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A            9 DDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CCCSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             cccCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            4446788999999999999 6678 9999999999865      479999998643

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.77  E-value=4.4e-09  Score=80.16  Aligned_cols=47  Identities=23%  Similarity=0.596  Sum_probs=40.1

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccCc
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITNR  417 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~  417 (422)
                      .+.+...|+||++.+.+ +.++|||.||..|+..+     ..||+||.++...
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           11 TVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             SCCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             cCCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            35677899999999999 56799999999999954     4799999998653

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=4.5e-09  Score=83.31  Aligned_cols=46  Identities=24%  Similarity=0.521  Sum_probs=39.6

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      ...+...|+||++.+.+ ++++|||.||..|+..+    ..||+||.++..
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (81)
T 2csy_A           11 EEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTGG   61 (81)
T ss_dssp             CCCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCCS
T ss_pred             cCCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCCCcCCCcCccccc
Confidence            35667899999999999 56799999999999876    579999999863

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=2.7e-09  Score=82.08  Aligned_cols=50  Identities=32%  Similarity=0.782  Sum_probs=42.7

Q ss_pred             CCcCCcccccccccccccccCCCccchhhhhcC----CCCCCccccccCccccC
Q 042398          372 VAETQACPICLTNAKDLAFGCGHMTCRECGSRV----SNCPICRQRITNRLRLF  421 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i~vy  421 (422)
                      ..+...|+||++.+.++.++|||.||..|+..|    ..||+||.++.....+|
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   65 (70)
T 2ecn_A           12 LTDEEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESS   65 (70)
T ss_dssp             CCCCCCCSSSCCSCCSEEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCC
T ss_pred             CCCCCCCeeCCcCccCcccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCccc
Confidence            566789999999999866799999999999976    57999999998765544

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=98.75  E-value=5.8e-09  Score=81.69  Aligned_cols=47  Identities=38%  Similarity=0.869  Sum_probs=40.1

Q ss_pred             CCCCcCCccccccccccc-ccccCCCccchhhhhcC-----------CCCCCccccccC
Q 042398          370 TPVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----------SNCPICRQRITN  416 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----------~~CP~CR~~i~~  416 (422)
                      ..+.+...|+||++.+.+ +.++|||.||..|+..+           ..||+||..+..
T Consensus         7 ~~~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A            7 GNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             hhcccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            346778999999999999 66799999999999953           469999999864

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=98.74  E-value=5.5e-09  Score=83.40  Aligned_cols=51  Identities=29%  Similarity=0.809  Sum_probs=40.1

Q ss_pred             CCCcCCcccccccccc--cc-ccc--CCCccchhhhhcC-----CCCCCccccccCccccC
Q 042398          371 PVAETQACPICLTNAK--DL-AFG--CGHMTCRECGSRV-----SNCPICRQRITNRLRLF  421 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~--~v-~l~--CGH~fC~~Ci~~~-----~~CP~CR~~i~~~i~vy  421 (422)
                      .++++..|+||++.+.  ++ .++  |||.||..|+.++     ..||.||+++.....+|
T Consensus         7 ~~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~   67 (78)
T 1e4u_A            7 AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVY   67 (78)
T ss_dssp             CCCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSCC
T ss_pred             ccccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchhh
Confidence            3678899999999874  33 334  9999999999864     47999999998765444

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=98.73  E-value=1.4e-09  Score=95.01  Aligned_cols=45  Identities=29%  Similarity=0.733  Sum_probs=38.8

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccCc
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      +++..|+||++.+.+ ++++|||.||..|+..|    ..||+||.++...
T Consensus        51 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           51 ENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHHSBCTTTCSBCSSEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cccCCCcccCcccCCceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            456789999999999 56799999999999965    5799999998654

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.73  E-value=1e-08  Score=80.84  Aligned_cols=47  Identities=36%  Similarity=0.817  Sum_probs=40.1

Q ss_pred             CCCCcCCccccccccccc-ccccCCCccchhhhhc----------CCCCCCccccccC
Q 042398          370 TPVAETQACPICLTNAKD-LAFGCGHMTCRECGSR----------VSNCPICRQRITN  416 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~----------~~~CP~CR~~i~~  416 (422)
                      +.+.+...|+||++.+.+ +.++|||.||..|+..          ...||+||..+..
T Consensus        14 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           14 EMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CCCCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             HhCccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            336778999999999999 6679999999999985          3579999999864

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.71  E-value=7.1e-09  Score=77.07  Aligned_cols=45  Identities=27%  Similarity=0.522  Sum_probs=38.9

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-~~CP~CR~~i~~  416 (422)
                      ..+...|+||++.+.+ ++++|||.||..|+..+ ..||+||..+..
T Consensus         3 e~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~CP~Cr~~~~~   49 (56)
T 1bor_A            3 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPL   49 (56)
T ss_dssp             SCCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSSSSSCSSCCSSSSC
T ss_pred             cccCCCceEeCCccCCeEEcCCCCcccHHHHccCCCCCCcCCcEeec
Confidence            3567899999999999 67799999999999876 589999998764

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.71  E-value=1.3e-08  Score=80.16  Aligned_cols=47  Identities=38%  Similarity=0.883  Sum_probs=40.2

Q ss_pred             CCCCcCCccccccccccc-ccccCCCccchhhhhc----------CCCCCCccccccC
Q 042398          370 TPVAETQACPICLTNAKD-LAFGCGHMTCRECGSR----------VSNCPICRQRITN  416 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~----------~~~CP~CR~~i~~  416 (422)
                      ..+.+...|+||++.+.+ +.++|||.||..|+..          ...||+||..+..
T Consensus        14 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           14 VNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             HHccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            346778999999999999 5679999999999985          3689999999864

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=98.70  E-value=5.4e-09  Score=84.56  Aligned_cols=46  Identities=30%  Similarity=0.751  Sum_probs=39.5

Q ss_pred             CCCCcCCccccccccccc-cccc-CCCccchhhhhcC------CCCCCcccccc
Q 042398          370 TPVAETQACPICLTNAKD-LAFG-CGHMTCRECGSRV------SNCPICRQRIT  415 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~-CGH~fC~~Ci~~~------~~CP~CR~~i~  415 (422)
                      ..+.+.+.|+||++.+.+ ++++ |||.||..|+..+      ..||+||..+.
T Consensus         8 ~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A            8 DPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCCCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             ccCCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            346788999999999999 6678 9999999999855      48999999873

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=98.70  E-value=4.9e-09  Score=88.45  Aligned_cols=47  Identities=28%  Similarity=0.782  Sum_probs=40.3

Q ss_pred             CCCCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          370 TPVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      ....++..|+||++.+.+ ++++|||.||..|+..+     ..||+||..+..
T Consensus        10 ~~~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           10 IPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCCHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             cCCCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            346778999999999999 66799999999999976     379999998753

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.69  E-value=8.2e-09  Score=80.97  Aligned_cols=47  Identities=26%  Similarity=0.662  Sum_probs=38.9

Q ss_pred             CCCcCCccccccccccc----ccccCCCccchhhhhcC----CCCCCccccccCc
Q 042398          371 PVAETQACPICLTNAKD----LAFGCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      ...+...|+||++.+.+    ..++|||.||..|+.+|    ..||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           11 HVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             TSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             cCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            35677899999998875    24599999999999965    6799999998654

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=98.69  E-value=4.5e-09  Score=80.68  Aligned_cols=45  Identities=33%  Similarity=0.940  Sum_probs=38.1

Q ss_pred             CCcCCccccccccccc--------ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD--------LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~--------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      ..++..|+||++.+.+        +.++|||.||..|+..|    ..||+||..+..
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   63 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccCh
Confidence            4567899999999876        35599999999999865    689999999864

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.67  E-value=1.1e-08  Score=81.53  Aligned_cols=48  Identities=29%  Similarity=0.805  Sum_probs=39.7

Q ss_pred             CCCCCcCCccccccccccc----c-cccCCCccchhhhhcC-------CCCCCccccccC
Q 042398          369 STPVAETQACPICLTNAKD----L-AFGCGHMTCRECGSRV-------SNCPICRQRITN  416 (422)
Q Consensus       369 ~~~~~e~~~CpIC~~~~~~----v-~l~CGH~fC~~Ci~~~-------~~CP~CR~~i~~  416 (422)
                      ...+.+...|+||++.+.+    . .++|||.||..|+..+       ..||+||..+..
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   68 (88)
T 2ct2_A            9 LDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRI   68 (88)
T ss_dssp             CCCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCC
T ss_pred             hhhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccc
Confidence            3346778899999999887    4 4599999999999965       579999998753

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.66  E-value=4.6e-09  Score=105.66  Aligned_cols=50  Identities=34%  Similarity=0.963  Sum_probs=45.9

Q ss_pred             CCcCCccccccccccc-ccccCCCc-cchhhhhcCCCCCCccccccCccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHM-TCRECGSRVSNCPICRQRITNRLRLF  421 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~-fC~~Ci~~~~~CP~CR~~i~~~i~vy  421 (422)
                      ++++..|+||++.+.+ +.++|||. ||..|+..+..||+||.++..++++|
T Consensus       292 l~~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~~~CP~CR~~i~~~~~i~  343 (345)
T 3t6p_A          292 LQEERTCKVCMDKEVSVVFIPCGHLVVCQECAPSLRKCPICRGIIKGTVRTF  343 (345)
T ss_dssp             HHTTCBCTTTSSSBCCEEEETTCCEEECTTTGGGCSBCTTTCCBCCEEEECC
T ss_pred             CcCCCCCCccCCcCCceEEcCCCChhHhHHHHhcCCcCCCCCCCccCeEEee
Confidence            4567899999999999 45699999 99999999999999999999999998

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=98.66  E-value=6.6e-09  Score=81.52  Aligned_cols=45  Identities=24%  Similarity=0.428  Sum_probs=39.1

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      +.+.+.|+||++.+.+ ++++|||.||..|+..+     ..||+||.++..
T Consensus         5 ~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            5678999999999999 66799999999999854     569999999864

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=98.65  E-value=7.1e-09  Score=79.13  Aligned_cols=47  Identities=30%  Similarity=0.815  Sum_probs=39.7

Q ss_pred             cCCccccccccccc--ccccCCCccchhhhhcC----CCCCCccccccCcccc
Q 042398          374 ETQACPICLTNAKD--LAFGCGHMTCRECGSRV----SNCPICRQRITNRLRL  420 (422)
Q Consensus       374 e~~~CpIC~~~~~~--v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i~v  420 (422)
                      +...|+||++.+.+  +.++|||.||..|+..|    ..||+||.++...++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   56 (68)
T 1chc_A            4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHT   56 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCCEECC
T ss_pred             CCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHhhhhc
Confidence            45789999999988  45699999999999865    6899999999876554

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.65  E-value=1.3e-08  Score=78.95  Aligned_cols=48  Identities=23%  Similarity=0.541  Sum_probs=39.5

Q ss_pred             CCcCCccccccccccc----ccccCCCccchhhhhcC----CCCCCccccccCccc
Q 042398          372 VAETQACPICLTNAKD----LAFGCGHMTCRECGSRV----SNCPICRQRITNRLR  419 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i~  419 (422)
                      ..+...|+||++.+.+    ..++|||.||..|+..|    ..||+||.++.....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQ   67 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCS
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccccc
Confidence            5667899999999876    23499999999999976    679999999876543

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=98.62  E-value=8e-09  Score=77.41  Aligned_cols=48  Identities=29%  Similarity=0.893  Sum_probs=39.0

Q ss_pred             cCCccccccccccc--------ccccCCCccchhhhhcC----CCCCCccccccC--ccccC
Q 042398          374 ETQACPICLTNAKD--------LAFGCGHMTCRECGSRV----SNCPICRQRITN--RLRLF  421 (422)
Q Consensus       374 e~~~CpIC~~~~~~--------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~--~i~vy  421 (422)
                      +...|+||++.+.+        +.++|||.||..|+.++    ..||+||.++..  ..++|
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   63 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY   63 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEEECC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccceeeee
Confidence            46789999998876        34599999999999866    589999999874  44554

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=98.60  E-value=8.2e-09  Score=88.33  Aligned_cols=45  Identities=31%  Similarity=0.673  Sum_probs=39.0

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      +.+...|+||++.+.+ ++++|||.||..|+..+     ..||+||.++..
T Consensus        49 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           49 VEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CccCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            4567899999999999 66799999999999854     489999999875

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=98.60  E-value=2.6e-08  Score=76.22  Aligned_cols=48  Identities=29%  Similarity=0.668  Sum_probs=39.2

Q ss_pred             CCcCCccccccccccc----ccccCCCccchhhhhcC----CCCCCccccccCccc
Q 042398          372 VAETQACPICLTNAKD----LAFGCGHMTCRECGSRV----SNCPICRQRITNRLR  419 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i~  419 (422)
                      ..+...|+||++.+..    +.++|||.||..|+..|    ..||+||..+...+.
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            4566799999998753    45699999999999966    679999999876553

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.59  E-value=3e-08  Score=74.68  Aligned_cols=41  Identities=34%  Similarity=0.954  Sum_probs=35.1

Q ss_pred             CCCCcCCccccccccccc-ccccCCCccchhhhhcC-------CCCCCc
Q 042398          370 TPVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-------SNCPIC  410 (422)
Q Consensus       370 ~~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-------~~CP~C  410 (422)
                      ..++++..|+||++.+.+ ++++|||.||..|+.++       ..||+|
T Consensus        15 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HhCccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            346778999999999999 56799999999999865       379998

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.59  E-value=3.6e-08  Score=72.56  Aligned_cols=40  Identities=33%  Similarity=0.908  Sum_probs=34.6

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC-------CCCCCc
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-------SNCPIC  410 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-------~~CP~C  410 (422)
                      .+.+...|+||++.+.+ +.++|||.||..|+..+       ..||+|
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           11 NLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CSCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            36678899999999999 66799999999999865       569988

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=98.58  E-value=7.4e-09  Score=85.72  Aligned_cols=45  Identities=31%  Similarity=0.711  Sum_probs=39.6

Q ss_pred             CCcCCccccccccccc-cc-ccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LA-FGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~-l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      +.+...|+||++.+.+ +. ++|||.||..|+..|     ..||+||.++..
T Consensus        19 l~~~~~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           19 IAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCccCCccccCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            5678999999999999 56 799999999999965     589999999854

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.54  E-value=1.9e-08  Score=76.32  Aligned_cols=43  Identities=33%  Similarity=0.818  Sum_probs=35.8

Q ss_pred             cCCccccccc-ccccc-----cccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          374 ETQACPICLT-NAKDL-----AFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       374 e~~~CpIC~~-~~~~v-----~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      ++..|+||++ .+.+.     +++|||.||..|+.++     ..||+||.++..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   55 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCcccc
Confidence            4578999999 77663     4599999999999866     579999999864

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=98.54  E-value=3.4e-08  Score=72.16  Aligned_cols=44  Identities=32%  Similarity=0.761  Sum_probs=36.4

Q ss_pred             CCcCCccccccccccc----cccc-CCCccchhhhhcC----CCCCCcccccc
Q 042398          372 VAETQACPICLTNAKD----LAFG-CGHMTCRECGSRV----SNCPICRQRIT  415 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~----v~l~-CGH~fC~~Ci~~~----~~CP~CR~~i~  415 (422)
                      +++...|+||++.+.+    +.++ |||.||..|+..|    ..||+||..+.
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            3567899999999877    3455 9999999999976    57999998764

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=98.52  E-value=2e-08  Score=83.86  Aligned_cols=45  Identities=27%  Similarity=0.631  Sum_probs=39.5

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +.+...|+||++.+.+ +.+ +|||.||..|+..+    ..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHK   62 (108)
T ss_dssp             HGGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCS
T ss_pred             cCCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCccccc
Confidence            4677899999999999 566 99999999999866    679999999875

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.49  E-value=3.1e-08  Score=84.02  Aligned_cols=45  Identities=24%  Similarity=0.719  Sum_probs=39.7

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC--CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV--SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~--~~CP~CR~~i~~  416 (422)
                      +.+.+.|+||++.+.+ +++ +|||.||..|+..+  ..||+||.++..
T Consensus        19 l~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~~   67 (117)
T 1jm7_B           19 LEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWI   67 (117)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCSC
T ss_pred             chhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhcCCCcCCCCcCcc
Confidence            4678999999999999 677 99999999999987  579999999853

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=98.49  E-value=1.9e-08  Score=89.61  Aligned_cols=46  Identities=24%  Similarity=0.650  Sum_probs=39.4

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~  417 (422)
                      +.+...|+||++.+.+ ++++|||.||..|+..+     ..||+||..+...
T Consensus        75 l~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CccCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4466899999999999 66799999999999865     3799999998754

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=3.5e-08  Score=76.96  Aligned_cols=45  Identities=24%  Similarity=0.634  Sum_probs=37.6

Q ss_pred             CCcCCccccccccccc----ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD----LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~----v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      ..+...|+||++.+.+    ..++|||.||..|+..|    ..||+||..+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            4566799999998776    34699999999999976    689999998864

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=98.48  E-value=3.9e-08  Score=79.94  Aligned_cols=46  Identities=28%  Similarity=0.658  Sum_probs=38.0

Q ss_pred             CCcCCccccccccccc---c-cccCCCccchhhhhcC----CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKD---L-AFGCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~---v-~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      ..++..|+||++.+..   + .++|||.||..|+..|    ..||+||..+...
T Consensus        37 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   90 (91)
T 2l0b_A           37 VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPPP   90 (91)
T ss_dssp             SSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSCC
T ss_pred             cCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCCC
Confidence            4567799999988766   3 4699999999999976    6799999988653

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.47  E-value=3.6e-08  Score=82.18  Aligned_cols=44  Identities=36%  Similarity=0.941  Sum_probs=37.7

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhcC-------CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSRV-------SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-------~~CP~CR~~i~~  416 (422)
                      .+...|+||++.+.+ +.++|||.||..|+..+       ..||+||..+..
T Consensus        19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            456799999999999 56799999999999864       279999998864

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=98.47  E-value=2.9e-08  Score=81.54  Aligned_cols=45  Identities=24%  Similarity=0.676  Sum_probs=38.6

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +.+...|+||++.+.+ +.+ +|||.||..|+..+    ..||+||..+..
T Consensus        19 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           19 IDDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            4567899999999999 556 89999999999865    579999998864

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=98.46  E-value=6.5e-08  Score=78.05  Aligned_cols=46  Identities=22%  Similarity=0.202  Sum_probs=40.2

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      ..+.+.||||++.+.+ ++++|||.||..|+..+    ..||+||.++...
T Consensus        11 ~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CchheECcccCchhcCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            5678999999999999 67799999999999865    6899999998653

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=98.45  E-value=1.2e-07  Score=78.58  Aligned_cols=46  Identities=20%  Similarity=0.127  Sum_probs=40.1

Q ss_pred             CCcCCccccccccccc-ccccCC-CccchhhhhcC----CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKD-LAFGCG-HMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CG-H~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      +.+++.||||++.+++ ++++|| |.||..|+..+    ..||+||.++...
T Consensus        19 ~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             CcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChh
Confidence            5678999999999999 667999 99999999865    5799999998753

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=98.45  E-value=5.7e-08  Score=70.84  Aligned_cols=42  Identities=31%  Similarity=0.861  Sum_probs=35.4

Q ss_pred             cCCccccccccccc-----ccccCCCccchhhhhcC----CCCCCcccccc
Q 042398          374 ETQACPICLTNAKD-----LAFGCGHMTCRECGSRV----SNCPICRQRIT  415 (422)
Q Consensus       374 e~~~CpIC~~~~~~-----v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~  415 (422)
                      +...|+||++.+.+     +.++|||.||..|+..|    ..||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            45789999998854     34599999999999976    68999999875

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=98.44  E-value=3.5e-08  Score=88.40  Aligned_cols=45  Identities=31%  Similarity=0.824  Sum_probs=38.6

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC-----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      +.+...|+||++.+.+ +.+ +|||.||..|+..|     ..||+||.++..
T Consensus        51 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           51 LHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             CHHHHBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCCcccChHhhCcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            5667899999999999 555 99999999999865     469999999854

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=98.43  E-value=5.9e-08  Score=82.41  Aligned_cols=46  Identities=28%  Similarity=0.801  Sum_probs=40.3

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      .+.+...|+||++.+.+ +.++|||.||..|+..+     ..||+||.++..
T Consensus        14 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           14 PLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            46778999999999999 66799999999999865     489999999865

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=98.43  E-value=1.8e-08  Score=88.85  Aligned_cols=44  Identities=23%  Similarity=0.587  Sum_probs=38.7

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccc
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRI  414 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i  414 (422)
                      .+++.+.|+||++.+.+ +.++|||.||..|+..+     ..||+||.++
T Consensus        27 ~l~~~~~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~   76 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEG   76 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTT
T ss_pred             cCCcCcCCCCCChhhcCcEECCCCCccCHHHHHHHHhcCCCCCCCCCCcc
Confidence            46788999999999999 66799999999999976     3799999975

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=98.40  E-value=7.6e-08  Score=80.18  Aligned_cols=45  Identities=22%  Similarity=0.225  Sum_probs=39.6

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +.+.+.||||++.+.+ ++++|||.||..|+..+    ..||+||.++..
T Consensus        26 ~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           26 APDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             CSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             CcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            5677999999999999 66799999999999865    579999999864

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=98.34  E-value=9.3e-08  Score=80.23  Aligned_cols=43  Identities=21%  Similarity=0.484  Sum_probs=34.7

Q ss_pred             CCccccccccccc-c------------------cccCCCccchhhhhcC---------CCCCCccccccCc
Q 042398          375 TQACPICLTNAKD-L------------------AFGCGHMTCRECGSRV---------SNCPICRQRITNR  417 (422)
Q Consensus       375 ~~~CpIC~~~~~~-v------------------~l~CGH~fC~~Ci~~~---------~~CP~CR~~i~~~  417 (422)
                      +..|+||++.+.+ .                  .++|||.||..|+..|         ..||+||..+...
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3589999999754 1                  4699999999999865         3799999988543

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.32  E-value=2.1e-07  Score=88.60  Aligned_cols=43  Identities=14%  Similarity=0.075  Sum_probs=37.4

Q ss_pred             cCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          374 ETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      +.+.||||++.+.+ ++++|||+||..|+..+     ..||+||.+++.
T Consensus       207 ~~~~c~i~~~~~~dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcCCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            46799999999999 66799999999999854     349999999864

>4hqo_A Sporozoite surface protein 2; malaria, gliding motility, VWA domain, TSR domain, extensibl ribbon, receptor on sporozoite, vaccine target; HET: FUC BGC; 2.19A {Plasmodium vivax} PDB: 4hql_A* 4hqn_A*

Probab=98.30  E-value=2.4e-06  Score=81.69  Aligned_cols=151  Identities=13%  Similarity=0.216  Sum_probs=103.0

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHH-HHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPY-EKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFH  173 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y-~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~  173 (422)
                      .+++++.||-|+|.+.                  ..+ +++...+-.++..++   ++-.+-++.|+....   .+|+|+
T Consensus        18 ~~DivfvlD~SgSM~~------------------~~~~~~~k~~~~~lv~~l~~~~~~~rvglv~Fs~~~~---~~~~l~   76 (266)
T 4hqo_A           18 QVDLYLLVDGSGSIGY------------------PNWITKVIPMLNGLINSLSLSRDTINLYMNLFGSYTT---ELIRLG   76 (266)
T ss_dssp             CEEEEEEEECSTTTCH------------------HHHHHTHHHHHHHHHHTCCBCTTSEEEEEEEESSSEE---EEECTT
T ss_pred             ceeEEEEEECCCCcCh------------------hHHHHHHHHHHHHHHHHcccCCCCcEEEEEEecCCcc---eEEecC
Confidence            3789999999999852                  223 356666666667776   566789999998632   245543


Q ss_pred             CCCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc---CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          174 DDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       174 ~~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                      ...  -...+.++++-...-......|-|+...-|+.|.+.....   .+.-.++++||||..+|            ...
T Consensus        77 ~~~--~~~~~~~~~~i~~l~~~~~~~G~T~~~~AL~~a~~~l~~~~~r~~~~~~iIllTDG~~~d------------~~~  142 (266)
T 4hqo_A           77 SGQ--SIDKRQALSKVTELRKTYTPYGTTSMTAALDEVQKHLNDRVNREKAIQLVILMTDGVPNS------------KYR  142 (266)
T ss_dssp             SHH--HHCHHHHHHHHHHHHHHCCCCSCCCHHHHHHHHHHHHHTTCSCTTSEEEEEEEECSCCSC------------HHH
T ss_pred             CCC--ccCHHHHHHHHHHhhhccCCCCCCCHHHHHHHHHHHHhhccccCCCCeEEEEEccCCCCC------------chH
Confidence            221  0124555554444322235679999999999998776654   23468999999999987            456


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCCC-ccccccccC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDGP-WEDMQKFDD  283 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~~-f~~m~~LD~  283 (422)
                      ..+++..+.+..+.|..||||++. -+.|+.+-+
T Consensus       143 ~~~~a~~l~~~gi~i~~iGiG~~~~~~~L~~iA~  176 (266)
T 4hqo_A          143 ALEVANKLKQRNVRLAVIGIGQGINHQFNRLIAG  176 (266)
T ss_dssp             HHHHHHHHHHTTCEEEEEECSSSCCHHHHHHHHT
T ss_pred             HHHHHHHHHHCCCEEEEEecCcccCHHHHHHhhC
Confidence            777777787888999999999854 333455543

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=98.30  E-value=1.3e-07  Score=79.70  Aligned_cols=45  Identities=33%  Similarity=0.694  Sum_probs=39.0

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      +.+...|+||++.+.+ +.++|||.||..|+..+     ..||+||.++..
T Consensus        20 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           20 FVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             ccCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            5567899999999999 56799999999999854     579999999864

>4hqf_A Thrombospondin-related anonymous protein, trap; malaria, parasite motility, I domain, TSR domain, receptor O sporozoite, vaccine target; 2.20A {Plasmodium falciparum} PDB: 4hqk_A 2bbx_A

Probab=98.28  E-value=4.7e-06  Score=80.06  Aligned_cols=151  Identities=17%  Similarity=0.204  Sum_probs=104.6

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHH-HHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPY-EKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFH  173 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y-~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~  173 (422)
                      .+++++.||-|+|.+.                  ..+ +++...+..++..++.   +-.+-++.|+....   .+|+++
T Consensus        21 ~~div~vlD~SgSM~~------------------~~~~~~~k~~~~~~v~~l~~~~~~~rvglv~Fs~~~~---~~~~l~   79 (281)
T 4hqf_A           21 EVDLYLLMDGSGSIRR------------------HNWVNHAVPLAMKLIQQLNLNDNAIHLYASVFSNNAR---EIIRLH   79 (281)
T ss_dssp             CEEEEEEEECCCCSST------------------HHHHHHHHHHHHHHHTTCCCCTTSEEEEEEEEETTEE---EEEEEC
T ss_pred             ceeEEEEEeCCCCcCH------------------HHHHHHHHHHHHHHHHHhccCCCCcEEEEEEcCCCce---EEEEcc
Confidence            4889999999999852                  123 5566666666666654   66799999987642   345554


Q ss_pred             CCCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC---CceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          174 DDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG---GQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       174 ~~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~---~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                      ....  ...+.++++-...-......|-|+....|+.|.+.....+   +.-.++|+||||..+|            ...
T Consensus        80 ~~~~--~~~~~l~~~i~~l~~~~~~~G~T~~~~aL~~a~~~l~~~~~r~~~~~~iillTDG~~~d------------~~~  145 (281)
T 4hqf_A           80 SDAS--KNKEKALIIIKSLLSTNLPYGKTSLTDALLQVRKHLNDRINRENANQLVVILTDGIPDS------------IQD  145 (281)
T ss_dssp             SSCS--SCHHHHHHHHHHHHHTTGGGCSCCHHHHHHHHHHHHHTSCCCTTCEEEEEEEESSCCSC------------HHH
T ss_pred             ccCc--cCHHHHHHHHHHHhhccCCCCCccHHHHHHHHHHHHHhccCCCCCCEEEEEEecCCCCC------------cHH
Confidence            3321  2345565554443334456899999999999987766542   2568899999999887            346


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC-CccccccccC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG-PWEDMQKFDD  283 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~-~f~~m~~LD~  283 (422)
                      ..+++..+...-+-|..||||++ +-+.|+.+-+
T Consensus       146 ~~~~~~~l~~~gv~i~~igiG~~~~~~~L~~iA~  179 (281)
T 4hqf_A          146 SLKESRKLSDRGVKIAVFGIGQGINVAFNRFLVG  179 (281)
T ss_dssp             HHHHHHHHHHTTCEEEEEEESSSCCHHHHHHHTT
T ss_pred             HHHHHHHHHHCCCEEEEEeCCCccCHHHHHhhhC
Confidence            66777777778899999999995 5555666654

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=98.27  E-value=2.9e-07  Score=93.75  Aligned_cols=46  Identities=37%  Similarity=0.792  Sum_probs=38.8

Q ss_pred             CCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccCcccc
Q 042398          375 TQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITNRLRL  420 (422)
Q Consensus       375 ~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~i~v  420 (422)
                      ...|+||++...+ +.++|||.||..|+..+     ..||+||.++.....+
T Consensus       332 ~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          332 FQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI  383 (389)
T ss_dssp             SSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEEC
T ss_pred             CCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCceeE
Confidence            4699999999999 55699999999999854     6899999999765433

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.24  E-value=5.7e-07  Score=71.63  Aligned_cols=45  Identities=29%  Similarity=0.637  Sum_probs=35.0

Q ss_pred             CCcCCccccccccccc--------------c-cc-cCCCccchhhhhcC----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD--------------L-AF-GCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~--------------v-~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      ..++..|+||++.+.+              + ++ +|||.||..|+.++    ..||+||.++..
T Consensus        12 ~~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           12 DVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             SCCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             cCCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            3456789999987743              2 44 59999999999965    579999998753

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.20  E-value=3.2e-07  Score=77.93  Aligned_cols=44  Identities=34%  Similarity=0.975  Sum_probs=37.1

Q ss_pred             CcCCccccccccccc--------ccccCCCccchhhhhcC----CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD--------LAFGCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~--------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      .+...|+||++.+.+        +.++|||.||..|+..+    ..||+||..+..
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   60 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   60 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcc
Confidence            456899999999876        34599999999999865    579999999864

>3n2n_F Anthrax toxin receptor 1; rossmann fold; 1.80A {Homo sapiens} SCOP: c.62.1.1

Probab=98.17  E-value=2.2e-05  Score=69.58  Aligned_cols=148  Identities=14%  Similarity=0.137  Sum_probs=94.8

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      .+++++.||-|+|.+.           .+     ....+++..+..-+  ...+-.+-++.|+....   .++++..   
T Consensus         7 ~~div~vlD~SgSM~~-----------~~-----~~~~~~~~~~~~~~--~~~~~~v~lv~f~~~~~---~~~~l~~---   62 (185)
T 3n2n_F            7 GFDLYFILDKSGSVLH-----------HW-----NEIYYFVEQLAHKF--ISPQLRMSFIVFSTRGT---TLMKLTE---   62 (185)
T ss_dssp             EEEEEEEEECSGGGGG-----------GH-----HHHHHHHHHHHHHC--CCTTEEEEEEEESSSEE---EEEEEEC---
T ss_pred             CeeEEEEEeCCCChhh-----------hH-----HHHHHHHHHHHHHh--CCCCcEEEEEEEecCce---EEeccCC---
Confidence            3689999999999851           00     12223333333322  23356899999987642   2345542   


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHH--HcC--CceEEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE--KSG--GQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~--~~~--~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                         ..+.+.++-.+. +.+...|-|+...-|+.+.+...  ...  ..-.++++||||..++..          .....+
T Consensus        63 ---~~~~~~~~i~~l-~~~~~~g~T~~~~al~~a~~~l~~~~~~~~~~~~~iillTDG~~~~~~----------~~~~~~  128 (185)
T 3n2n_F           63 ---DREQIRQGLEEL-QKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDL----------FFYSER  128 (185)
T ss_dssp             ---CHHHHHHHHHHH-HTCCCCSCCCHHHHHHHHHHHHHHHHTTCBCEEEEEEEEECCCCCHHH----------HHHHHH
T ss_pred             ---CHHHHHHHHHHH-hhhcCCCCccHHHHHHHHHHHHhhccccCCCCCcEEEEEcCCCCCCCc----------ccchHH
Confidence               344444433332 22345799999999999998652  222  246789999999988721          123456


Q ss_pred             HHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          254 SIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       254 aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      ++..+.+..+-|..||||+.+...|+.+-+
T Consensus       129 ~~~~~~~~gi~i~~igvg~~~~~~L~~iA~  158 (185)
T 3n2n_F          129 EANRSRDLGAIVYAVGVKDFNETQLARIAD  158 (185)
T ss_dssp             HHHHHHHTTEEEEEEECSSCCHHHHTTTSS
T ss_pred             HHHHHHHCCCEEEEEEeccCCHHHHHHHhC
Confidence            667777788999999999888777777654

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.13  E-value=6.7e-07  Score=80.28  Aligned_cols=46  Identities=28%  Similarity=0.801  Sum_probs=40.4

Q ss_pred             CCCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          371 PVAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       371 ~~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      ++.+.+.|+||++.+.+ +.++|||.||..|+.++     ..||+||.++..
T Consensus        14 ~~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           14 PLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcch
Confidence            46788999999999999 56799999999999875     489999999865

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.09  E-value=9.3e-07  Score=81.20  Aligned_cols=44  Identities=14%  Similarity=0.061  Sum_probs=37.9

Q ss_pred             cCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccCc
Q 042398          374 ETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITNR  417 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~  417 (422)
                      +.+.||||++.+.+ ++++|||.||..|+..+     ..||+||.++...
T Consensus       105 ~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          105 DYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             GGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             HhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            56899999999999 66799999999999854     3599999998653

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.09  E-value=9.5e-07  Score=72.32  Aligned_cols=42  Identities=26%  Similarity=0.545  Sum_probs=35.6

Q ss_pred             CCcCCccccccccccc-cccc-CCCccchhhhhcC----------CCCCC--cccc
Q 042398          372 VAETQACPICLTNAKD-LAFG-CGHMTCRECGSRV----------SNCPI--CRQR  413 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~-CGH~fC~~Ci~~~----------~~CP~--CR~~  413 (422)
                      ..+.+.||||++.+.+ ++++ |||.||..|+..+          ..||+  |+..
T Consensus         4 ~~~~~~CPI~~~~~~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             CSSCCBCTTTCSBCSSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CCcEeECcCcCchhcCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            3567899999999999 6675 9999999999854          28999  9865

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.06  E-value=8.5e-07  Score=75.25  Aligned_cols=49  Identities=31%  Similarity=0.929  Sum_probs=39.6

Q ss_pred             CcCCccccccccccc--------ccccCCCccchhhhhcC----CCCCCccccccCc--cccC
Q 042398          373 AETQACPICLTNAKD--------LAFGCGHMTCRECGSRV----SNCPICRQRITNR--LRLF  421 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~--------v~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~--i~vy  421 (422)
                      .+...|+||++.+.+        +.++|||.||..|+..|    ..||+||..+...  +++|
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  132 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY  132 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEEEEC
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcceeee
Confidence            456789999998876        44599999999999965    7899999998753  4444

>3ibs_A Conserved hypothetical protein BATB; structural genomics, protein structure, midwest center for S genomics, MCSG, PSI-2; HET: MSE; 2.10A {Bacteroides thetaiotaomicron}

Probab=98.03  E-value=1.4e-05  Score=72.79  Aligned_cols=139  Identities=17%  Similarity=0.277  Sum_probs=97.4

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .++++.||-|+|+...             +..++..+.|...+..++..+. +..+-++.|+....   .++++..    
T Consensus        12 ~~iv~vlD~SgSM~~~-------------d~~~~r~~~ak~~~~~~~~~~~-~~~v~lv~F~~~~~---~~~~~~~----   70 (218)
T 3ibs_A           12 VEVIIALDISNSMLAQ-------------DVQPSRLEKAKRLISRLVDELD-NDKVGMIVFAGDAF---TQLPITS----   70 (218)
T ss_dssp             CEEEEEEECSGGGGCC-------------SSSSCHHHHHHHHHHHHHHTCS-SCEEEEEEESSSEE---EEEEEES----
T ss_pred             CcEEEEEECCcCcccc-------------cCCcCHHHHHHHHHHHHHHhCC-CCeEEEEEECCCce---EeCCCCC----
Confidence            6799999999999642             1125788888888888888887 45899999997632   2344432    


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                        +.+.+.+.-...-+.....|.|++..-|+.+.+........-.++++||||..++.             ...+++..+
T Consensus        71 --~~~~~~~~l~~l~~~~~~~g~T~l~~al~~a~~~l~~~~~~~~~ivllTDG~~~~~-------------~~~~~~~~~  135 (218)
T 3ibs_A           71 --DYISAKMFLESISPSLISKQGTAIGEAINLATRSFTPQEGVGRAIIVITDGENHEG-------------GAVEAAKAA  135 (218)
T ss_dssp             --CHHHHHHHHHTCCGGGCCSCSCCHHHHHHHHHTTSCSCSSCCEEEEEEECCTTCCS-------------CHHHHHHHH
T ss_pred             --CHHHHHHHHHhcCcccCCCCCCcHHHHHHHHHHHHhhCCCCCcEEEEEcCCCCCCC-------------cHHHHHHHH
Confidence              34444443333333344579999999999988766554345678899999988761             234555666


Q ss_pred             cCCCeeEEEEecCCC
Q 042398          259 SSYPLSIVLVGVGDG  273 (422)
Q Consensus       259 S~~PlSIiiVGVG~~  273 (422)
                      ....+.|..||||+.
T Consensus       136 ~~~~i~v~~igig~~  150 (218)
T 3ibs_A          136 AEKGIQVSVLGVGMP  150 (218)
T ss_dssp             HTTTEEEEEEEESCT
T ss_pred             HhcCCEEEEEEecCC
Confidence            677899999999984

>1shu_X Anthrax toxin receptor 2; alpha/beta rossmann fold, membrane protein; 1.50A {Homo sapiens} SCOP: c.62.1.1 PDB: 1tzn_a 1sht_X 1t6b_Y*

Probab=98.00  E-value=7.1e-06  Score=72.55  Aligned_cols=147  Identities=14%  Similarity=0.124  Sum_probs=96.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .++++.||-|+|.+.           ..    ....+.|...+..++.   .+-.+-++.|+....   .++++.     
T Consensus         7 ~dvv~vlD~SgSM~~-----------~~----~~~~~~~~~~~~~~~~---~~~~v~lv~f~~~~~---~~~~~~-----   60 (182)
T 1shu_X            7 FDLYFVLDKSGSVAN-----------NW----IEIYNFVQQLAERFVS---PEMRLSFIVFSSQAT---IILPLT-----   60 (182)
T ss_dssp             EEEEEEEECSGGGGG-----------GH----HHHHHHHHHHHHHCCC---TTEEEEEEEESSSEE---EEEEEE-----
T ss_pred             eeEEEEEECCCCccc-----------CH----HHHHHHHHHHHHHhcC---CCceEEEEEeCCCce---EEECCC-----
Confidence            689999999999852           00    1123334444444444   466799999987632   234443     


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHH
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIV  256 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv  256 (422)
                       .+.+.+.++-. .+..+...|.|+....|+.+.+.....  ...-.++++||||..++.          ......+++.
T Consensus        61 -~~~~~~~~~l~-~l~~~~~~g~T~~~~al~~a~~~l~~~~~~~~~~~iiliTDG~~~~~----------~~~~~~~~~~  128 (182)
T 1shu_X           61 -GDRGKISKGLE-DLKRVSPVGETYIHEGLKLANEQIQKAGGLKTSSIIIALTDGKLDGL----------VPSYAEKEAK  128 (182)
T ss_dssp             -CCHHHHHHHHH-HHHTCCCCSCCCHHHHHHHHHHHHHHHTGGGSCEEEEEEECCCCCTT----------HHHHHHHHHH
T ss_pred             -CCHHHHHHHHH-hcccCCCCCCchHHHHHHHHHHHHHhccCCCCCeEEEEECCCCcCCC----------CchhHHHHHH
Confidence             22333333222 223345679999999999999887654  234688899999998762          1233455666


Q ss_pred             HhcCCCeeEEEEecCCCCccccccccC
Q 042398          257 AASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       257 ~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      .+....+.|..||||+.+...|+.+-+
T Consensus       129 ~~~~~~i~i~~igvg~~~~~~L~~ia~  155 (182)
T 1shu_X          129 ISRSLGASVYCVGVLDFEQAQLERIAD  155 (182)
T ss_dssp             HHHHTTCEEEEEECSSCCHHHHHHHSS
T ss_pred             HHHhCCCEEEEEeCCcCCHHHHHHHhC
Confidence            677788999999999888777777754

>4fx5_A VON willebrand factor type A; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, blood clotting; HET: MSE; 1.73A {Catenulispora acidiphila}

Probab=97.91  E-value=2.4e-05  Score=81.31  Aligned_cols=156  Identities=12%  Similarity=0.144  Sum_probs=105.9

Q ss_pred             CccccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCC
Q 042398           96 LESSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        96 ~~~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      ...+++++.||.|+|+.++                .+..+.|..++..++..+.++..|-++.|+....   .++++...
T Consensus        75 ~~~~dvv~VLD~SGSM~~~----------------~~rl~~ak~a~~~ll~~L~~~drv~lV~Fs~~a~---~~~p~t~~  135 (464)
T 4fx5_A           75 GSENVEVIIIDCSGSMDYP----------------RTKMMAAKEATKVAIDTLTDGAFFAVVAGTEGAR---VVYPTGGQ  135 (464)
T ss_dssp             -CCEEEEEEEECCGGGGTT----------------THHHHHHHHHHHHHHHHSCTTCEEEEEEESSSEE---EEESSSSS
T ss_pred             CCCceEEEEEEcCcccCCC----------------CchHHHHHHHHHHHHHhCCCCCEEEEEEEcCceE---EEecCCcc
Confidence            3458999999999999531                3567788888888888887777899999987642   13333210


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSI  255 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aI  255 (422)
                        ....-..-.+.-.+.+..++..|-|++..-|+.+.+...+..+.-.++++||||+.++.           ....+...
T Consensus       136 --l~~~~~~~~~~l~~~I~~L~~~GgT~l~~aL~~A~~~l~~~~~~~~~IILLTDG~~~~~-----------~~~~l~~~  202 (464)
T 4fx5_A          136 --LLRADYQSRAAAKEAVGRLHANGGTAMGRWLAQAGRIFDTAPSAIKHAILLTDGKDESE-----------TPADLARA  202 (464)
T ss_dssp             --CEECSHHHHHHHHHHHHTCCCCSCCCHHHHHHHHHHHHTTCTTSEEEEEEEESSCCTTS-----------CHHHHHHH
T ss_pred             --cccCCHHHHHHHHHHHHcCCCCCCCcHHHHHHHHHHHHhcCCCCCCEEEEEcCCCCCCC-----------ChHHHHHH
Confidence              00000112233344456677789999999999999887765555678899999998752           12334445


Q ss_pred             HHhcCCCeeEEEEecCCC-CccccccccC
Q 042398          256 VAASSYPLSIVLVGVGDG-PWEDMQKFDD  283 (422)
Q Consensus       256 v~AS~~PlSIiiVGVG~~-~f~~m~~LD~  283 (422)
                      .++....+.|..||||.. +...|+++-.
T Consensus       203 ~~a~~~~i~i~tiGiG~~~d~~~L~~IA~  231 (464)
T 4fx5_A          203 IQSSIGNFTADCRGIGEDWEPKELRKIAD  231 (464)
T ss_dssp             HHHHTTTCEEEEEEESSSSCHHHHHHHHH
T ss_pred             HHHhcCCCeEEEEEeCCccCHHHHHHHHH
Confidence            556677899999999954 6666776643

>2xgg_A Microneme protein 2; A/I domain, cell adhesion, hydrolase; 2.05A {Toxoplasma gondii}

Probab=97.90  E-value=2.9e-05  Score=69.31  Aligned_cols=138  Identities=10%  Similarity=0.107  Sum_probs=91.8

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCC---CCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDE---DNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~---D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||-|+|.+.                  ..++.+...+..++..++.   .-.+-++.|+....   .+|+|+.
T Consensus        17 ~~divfvlD~SgSm~~------------------~~~~~~k~~~~~~i~~l~~~~~~~rv~vv~F~~~~~---~~~~l~~   75 (178)
T 2xgg_A           17 QLDICFLIDSSGSIGI------------------QNFRLVKQFLHTFLMVLPIGPEEVNNAVVTYSTDVH---LQWDLQS   75 (178)
T ss_dssp             CEEEEEEEECCTTTCH------------------HHHHHHHHHHHHHHHHSCBSTTSEEEEEEEESSSEE---EEECTTS
T ss_pred             CeeEEEEEECCCCCCH------------------HHHHHHHHHHHHHHHhcCCCCCCeEEEEEEeCCceE---EEEeCCC
Confidence            3789999999999852                  2466777777777777763   36899999998642   2355532


Q ss_pred             CCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCCchhHH
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQ  249 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~  249 (422)
                      ..  ....+.++++-.. ++.  ..|.|+...-|+.|.+.....     ...-.++++||||..++            ..
T Consensus        76 ~~--~~~~~~~~~~i~~-l~~--~~g~T~~~~aL~~a~~~l~~~~~g~r~~~~~~iillTDG~~~~------------~~  138 (178)
T 2xgg_A           76 PN--AVDKQLAAHAVLD-MPY--KKGSTNTSDGLKACKQILFTGSRPGREHVPKLVIGMTDGESDS------------DF  138 (178)
T ss_dssp             GG--GSCHHHHHHHHHH-CCC--CCCCCCHHHHHHHHHHHHHHCCCTTCTTSCEEEEEEESSCCCH------------HH
T ss_pred             CC--ccCHHHHHHHHHh-CCC--CCCCccHHHHHHHHHHHhcCcccCCCCCCCEEEEEEcCCCCCC------------Cc
Confidence            11  1145555554333 221  568999999999999864321     12457899999999887            22


Q ss_pred             HHHHHHHHhcCCCeeEEEEecCCC
Q 042398          250 KTIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       250 ~T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      ...+++..+.+..+-|..||||+.
T Consensus       139 ~~~~~~~~l~~~gi~v~~igvG~~  162 (178)
T 2xgg_A          139 RTVRAAKEIRELGGIVTVLAVGHY  162 (178)
T ss_dssp             HHSHHHHHHHHTTCEEEEEECC--
T ss_pred             cHHHHHHHHHHCCCEEEEEEcCCc
Confidence            344555555566889999999975

>1q0p_A Complement factor B; VON willebrand factor, MAC-1, I domain, A domain, hydrolase; 1.80A {Homo sapiens} SCOP: c.62.1.1

Probab=97.85  E-value=1.6e-05  Score=72.33  Aligned_cols=157  Identities=14%  Similarity=0.120  Sum_probs=96.8

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      .+++++.||-|+|.++.               ......+++..+..-+..++.+-.+-++.|+....   .++++.  .+
T Consensus        15 ~~div~vlD~SgSM~~~---------------~~~~~k~~~~~~i~~l~~~~~~~~v~lv~f~~~~~---~~~~~~--~~   74 (223)
T 1q0p_A           15 SMNIYLVLDGSDSIGAS---------------NFTGAKKSLVNLIEKVASYGVKPRYGLVTYATYPK---IWVKVS--EA   74 (223)
T ss_dssp             CEEEEEEEECSTTTCHH---------------HHHHHHHHHHHHHHHHHTTTCCCEEEEEEESSSEE---EEECTT--SG
T ss_pred             ceeEEEEEeCCCCCchH---------------HHHHHHHHHHHHHHHHhcCCCCceEEEEEecCccc---eeeccc--cC
Confidence            47899999999999631               01233344444444455566667899999998642   223332  22


Q ss_pred             CCCCHHHHHHHHHhhCCcc-cccCCCChHHHHHHHHHHHHHcC--------CceEEEEEEeCCcccccCCCCCCCCchhH
Q 042398          178 PCHGFEEVLACYRNIVPNL-RLAGPTSYAPVVEAAMDIVEKSG--------GQYHVLVIIADGQVTRSVNTGDGELSSQE  248 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v-~l~GPT~fapiI~~a~~~~~~~~--------~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~  248 (422)
                      .-...+.+.++-...-+.. ...|.|+...-|+.+.+......        ..-.++++||||..+...|         .
T Consensus        75 ~~~~~~~~~~~i~~l~~~~~~~~g~T~~~~aL~~a~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g~~---------~  145 (223)
T 1q0p_A           75 DSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGD---------P  145 (223)
T ss_dssp             GGGCHHHHHHHHHTCCTTSCSCTTCCCHHHHHHHHHHHHCCTTSSCCTTGGGCEEEEEEEECSCCCSSSC---------T
T ss_pred             CCCCHHHHHHHHHhcccccccCCCCccHHHHHHHHHHHhhccccccccccccCCeEEEEECCCCCCCCCC---------h
Confidence            2234555555443332221 24799999999999998765321        3457889999998873111         2


Q ss_pred             HHHHHHHHHh----------cCCCeeEEEEecCC-CCccccccccC
Q 042398          249 QKTIKSIVAA----------SSYPLSIVLVGVGD-GPWEDMQKFDD  283 (422)
Q Consensus       249 ~~T~~aIv~A----------S~~PlSIiiVGVG~-~~f~~m~~LD~  283 (422)
                      ....+.+.+.          ....+-|..||||+ .+...|+.+=.
T Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~~igvG~~~~~~~L~~iA~  191 (223)
T 1q0p_A          146 ITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALAS  191 (223)
T ss_dssp             HHHHHHHHHHTTCSCBTTBCCGGGEEEEEEECSSCCCHHHHHHHSC
T ss_pred             HHHHHHHHHHHhhhhhhhhcccCCcEEEEEEecCcCCHHHHHHHhc
Confidence            3444455432          34578899999996 46666766654

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=97.83  E-value=7.8e-06  Score=79.15  Aligned_cols=45  Identities=24%  Similarity=0.437  Sum_probs=38.2

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC------CCCCC--ccccccC
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV------SNCPI--CRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~------~~CP~--CR~~i~~  416 (422)
                      ......||||++.+.+ |+. .|||.||..|+..+      ..||+  ||..+..
T Consensus       178 ~~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          178 GKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             SBCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             CceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            5778999999999999 544 99999999999954      36999  9998754

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=97.83  E-value=5.4e-06  Score=69.75  Aligned_cols=42  Identities=29%  Similarity=0.470  Sum_probs=34.1

Q ss_pred             cCCcccccccccccc-------------------cccCCCccchhhhhcC----CCCCCcccccc
Q 042398          374 ETQACPICLTNAKDL-------------------AFGCGHMTCRECGSRV----SNCPICRQRIT  415 (422)
Q Consensus       374 e~~~CpIC~~~~~~v-------------------~l~CGH~fC~~Ci~~~----~~CP~CR~~i~  415 (422)
                      ++..|.||++.+.+.                   .++|+|.||..|+..+    ..||+||+.+.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            557899999887641                   2599999999999975    67999999853

>1atz_A VON willebrand factor; collagen-binding, hemostasis, dinucleotide binding fold; 1.80A {Homo sapiens} SCOP: c.62.1.1 PDB: 4dmu_B 2adf_A 1fe8_A 1ao3_A

Probab=97.74  E-value=8.2e-05  Score=66.60  Aligned_cols=143  Identities=14%  Similarity=0.188  Sum_probs=94.8

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|+|.+.                  +.++++...+..++..++   .+-.+-++.|+....   .+|+++. 
T Consensus         6 ~div~vlD~SgSm~~------------------~~~~~~k~~~~~~~~~l~~~~~~~rv~lv~f~~~~~---~~~~l~~-   63 (189)
T 1atz_A            6 LDVILLLDGSSSFPA------------------SYFDEMKSFAKAFISKANIGPRLTQVSVLQYGSITT---IDVPWNV-   63 (189)
T ss_dssp             EEEEEEEECSSSSCH------------------HHHHHHHHHHHHHHHHSCBSTTSEEEEEEEESSSEE---EEECTTC-
T ss_pred             eeEEEEEeCCCCCCh------------------hhHHHHHHHHHHHHHhcCcCCCCeEEEEEEECCcce---EEEecCC-
Confidence            689999999999851                  356667777777777765   235789999987642   2355532 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                         -...+.+.++-.. ++.  ..|.|+...-|+.|.+.....     .+.-.+++|||||..+|.           ..+
T Consensus        64 ---~~~~~~~~~~i~~-l~~--~~g~T~~~~aL~~a~~~l~~~~~g~r~~~~~~vivltdg~~~~~-----------~~~  126 (189)
T 1atz_A           64 ---VPEKAHLLSLVDV-MQR--EGGPSQIGDALGFAVRYLTSEMHGARPGASKAVVILVTDVSVDS-----------VDA  126 (189)
T ss_dssp             ---CCCHHHHHHHHHT-CCC--CCCCCCHHHHHHHHHHHHHSCCTTCCTTSEEEEEEEECSCCSSC-----------CHH
T ss_pred             ---CCCHHHHHHHHHh-CcC--CCCcchHHHHHHHHHHHHhccccCCCCCCCcEEEEEeCCCCCch-----------HHH
Confidence               1345566555443 222  368899999999999876542     234577888999987651           233


Q ss_pred             HHHHHHHhcCCCeeEEEEecCC-CCccccccccC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGD-GPWEDMQKFDD  283 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~-~~f~~m~~LD~  283 (422)
                      ..+.   +....+-|..||||+ .+-..|+.+=+
T Consensus       127 ~~~~---~~~~gi~v~~igvG~~~~~~~L~~iA~  157 (189)
T 1atz_A          127 AADA---ARSNRVTVFPIGIGDRYDAAQLRILAG  157 (189)
T ss_dssp             HHHH---HHHTTEEEEEEEESSSSCHHHHHHHTG
T ss_pred             HHHH---HHHCCCEEEEEEcCCcCCHHHHHHHHC
Confidence            3443   445688999999998 45555655543

>1ijb_A VON willebrand factor; dinucleotide-binding fold, blood clotting; 1.80A {Homo sapiens} SCOP: c.62.1.1 PDB: 1ijk_A 1auq_A 1u0n_A 3hxo_A 1uex_C 3hxq_A 1sq0_A 1m10_A 1fns_A 1oak_A 1u0o_C

Probab=97.71  E-value=6.2e-05  Score=68.55  Aligned_cols=145  Identities=9%  Similarity=0.159  Sum_probs=94.9

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|+|.+.                  +.++++...+..++..++   ++-.+-+..|+....   ..|+|+.-
T Consensus        14 ~divfvlD~SgSm~~------------------~~~~~~k~~~~~~v~~l~~~~~~~rv~vv~fs~~~~---~~~~l~~~   72 (202)
T 1ijb_A           14 LDLVFLLDGSSRLSE------------------AEFEVLKAFVVDMMERLRVSQKWVRVAVVEYHDGSH---AYIGLKDR   72 (202)
T ss_dssp             EEEEEEEECBTTSCH------------------HHHHHHHHHHHHHHHTBCBSTTSEEEEEEEESSSEE---EEECTTCC
T ss_pred             ccEEEEEECCCCCCH------------------HHHHHHHHHHHHHHHhcccCCCceEEEEEEECCCce---EEEecCCC
Confidence            789999999999851                  246677777777787776   445899999987642   23555421


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccc-cC-CCChHHHHHHHHHHH-HHc--CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRL-AG-PTSYAPVVEAAMDIV-EKS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l-~G-PT~fapiI~~a~~~~-~~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                          ...+.+.++-.    .++. .| -|+....|+++.+.. .+.  .+.-.++++||||.-++..          .+.
T Consensus        73 ----~~~~~~~~~i~----~l~~~gg~~T~~~~aL~~a~~~~~~~~~r~~~~~~iillTDG~~~~~~----------~~~  134 (202)
T 1ijb_A           73 ----KRPSELRRIAS----QVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRM----------SRN  134 (202)
T ss_dssp             ----CCHHHHHHHHH----TCCCCCBSCCCHHHHHHHHHHHTSSSCSCTTSEEEEEEEECCCCCGGG----------CTT
T ss_pred             ----CCHHHHHHHHH----hCcCCCCCcCcHHHHHHHHHHHHhccCCCCCCCeEEEEEccCCCCccc----------hHH
Confidence                23455544432    3333 44 399999999887543 211  2346899999999987510          112


Q ss_pred             HHHHHHHhcCCCeeEEEEecCC-CCcccccccc
Q 042398          251 TIKSIVAASSYPLSIVLVGVGD-GPWEDMQKFD  282 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~-~~f~~m~~LD  282 (422)
                      ..+++..+-+..+-|..||||+ .+.+.|+.+-
T Consensus       135 ~~~~a~~l~~~gi~i~~igvG~~~~~~~L~~iA  167 (202)
T 1ijb_A          135 FVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIE  167 (202)
T ss_dssp             HHHHHHHHHHTTEEEEEEEESTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCEEEEEecCCcCCHHHHHHHh
Confidence            3444445555789999999996 5666777664

>1n3y_A Integrin alpha-X; alpha/beta rossmann fold, cell adhesion; 1.65A {Homo sapiens} SCOP: c.62.1.1

Probab=97.69  E-value=1.2e-05  Score=72.12  Aligned_cols=144  Identities=17%  Similarity=0.307  Sum_probs=92.0

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc-CCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF-DEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y-D~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +++++.||-|+|.+.                  ..++.+...+-.++..+ ..+-.+-++.|+....   .+++++.   
T Consensus        10 ~div~vlD~SgSM~~------------------~~~~~~~~~~~~~~~~l~~~~~~v~lv~f~~~~~---~~~~~~~---   65 (198)
T 1n3y_A           10 QDIVFLIDGSGSISS------------------RNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQ---THFTFEE---   65 (198)
T ss_dssp             EEEEEEEECCTTSCH------------------HHHHHHHHHHHHHHTTSCTTTEEEEEEEESSSEE---EEECHHH---
T ss_pred             eeEEEEEECCCCCCH------------------HHHHHHHHHHHHHHHhcCCCCcEEEEEEeCCCcc---EEEecCc---
Confidence            689999999999852                  13456666666677777 5777899999998632   2233321   


Q ss_pred             CCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHH-HHHc----CCceEEEEEEeCCccc-ccCCCCCCCCchhHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDI-VEKS----GGQYHVLVIIADGQVT-RSVNTGDGELSSQEQK  250 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~-~~~~----~~~Y~VLlIiTDG~i~-d~~~~~~~~~~~~~~~  250 (422)
                          ... .+...+.+..+. ..|.|+....|+.+.+. ....    .+.-.++++||||..+ |..            .
T Consensus        66 ----~~~-~~~~~~~i~~l~~~~g~T~~~~al~~a~~~l~~~~~~~r~~~~~~iillTDG~~~~~~~------------~  128 (198)
T 1n3y_A           66 ----FRR-SSNPLSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITDGKKEGDSL------------D  128 (198)
T ss_dssp             ----HHH-CSSGGGGGTTCCCCCSCBCHHHHHHHHHTTTTSGGGTCCTTSEEEEEEEESSCCBSCSS------------C
T ss_pred             ----cCC-HHHHHHHHhcCcCCCCCchHHHHHHHHHHHHhCcccCCCCCCceEEEEECCCCCCCCcc------------c
Confidence                000 011223344443 67899999999999843 2321    2346889999999987 411            1


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCCC-----ccccccccC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDGP-----WEDMQKFDD  283 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~~-----f~~m~~LD~  283 (422)
                      ..+++..+....+-|..||||+..     ...|+.+-.
T Consensus       129 ~~~~~~~~~~~gi~i~~igvG~~~~~~~~~~~L~~iA~  166 (198)
T 1n3y_A          129 YKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIAS  166 (198)
T ss_dssp             HHHHHHHHHHTTCEEEEEEESGGGGSSTTHHHHHHHSC
T ss_pred             HHHHHHHHHHCCCEEEEEEccccccccccHHHHHHHHc
Confidence            234445556678899999999864     455555543

>2b2x_A Integrin alpha-1; computational design, antibody-antigen complex, immune syste; 2.20A {Rattus norvegicus} SCOP: c.62.1.1

Probab=97.68  E-value=0.00022  Score=65.74  Aligned_cols=133  Identities=19%  Similarity=0.295  Sum_probs=90.3

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||-|+|.+                    .++++...+..++..++   .+-.+-++.|+....   .+|+++ 
T Consensus        22 ~~div~vlD~SgSM~--------------------~~~~~k~~~~~~~~~l~~~~~~~rv~lv~F~~~~~---~~~~l~-   77 (223)
T 2b2x_A           22 QLDIVIVLDGSNSIY--------------------PWESVIAFLNDLLKRMDIGPKQTQVGIVQYGENVT---HEFNLN-   77 (223)
T ss_dssp             CEEEEEEEECSTTCC--------------------CHHHHHHHHHHHHTTSCCSTTSCCEEEEEESSSEE---EEECTT-
T ss_pred             cceEEEEEECCCChh--------------------hHHHHHHHHHHHHHhcccCCCCeEEEEEEeCCCcc---EEEecC-
Confidence            378999999999984                    05677777777777775   577899999987642   234542 


Q ss_pred             CCCCCCCHHHHHHHHHhhCCcccc-cC-CCChHHHHHHHHHH-HHH----cCCceEEEEEEeCCcccccCCCCCCCCchh
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLRL-AG-PTSYAPVVEAAMDI-VEK----SGGQYHVLVIIADGQVTRSVNTGDGELSSQ  247 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~l-~G-PT~fapiI~~a~~~-~~~----~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~  247 (422)
                       +  ....+.++++    +..+.. .| -|+...-|+++.+. ...    ..+.-.++++||||.-++.           
T Consensus        78 -~--~~~~~~~~~~----i~~l~~~gG~~T~~~~aL~~a~~~l~~~~~~~~~~~~~~iillTDG~~~~~-----------  139 (223)
T 2b2x_A           78 -K--YSSTEEVLVA----ANKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDN-----------  139 (223)
T ss_dssp             -T--CCSHHHHHHH----HTTCCCCCCSSCCHHHHHHHHHHTTSSGGGTCCTTSEEEEEEEESSCCTTG-----------
T ss_pred             -C--CCCHHHHHHH----HHhhhccCCCCccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEcCCCCCCC-----------
Confidence             1  1345555543    334443 45 49999999999875 221    1234678999999998872           


Q ss_pred             HHHHHHHHHHhcCCCeeEEEEecCCC
Q 042398          248 EQKTIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       248 ~~~T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                       ....+++..+....+-|..||||+.
T Consensus       140 -~~~~~~~~~~~~~gi~v~~igvG~~  164 (223)
T 2b2x_A          140 -YRLKQVIQDCEDENIQRFSIAILGH  164 (223)
T ss_dssp             -GGHHHHHHHHHTTTEEEEEEEECGG
T ss_pred             -ccHHHHHHHHHHCCCEEEEEEecCc
Confidence             1234455556677899999999974

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=97.65  E-value=7.4e-06  Score=70.27  Aligned_cols=42  Identities=26%  Similarity=0.453  Sum_probs=0.9

Q ss_pred             cCCccccccccccc------------------c-cccCCCccchhhhhcC----CCCCCcccccc
Q 042398          374 ETQACPICLTNAKD------------------L-AFGCGHMTCRECGSRV----SNCPICRQRIT  415 (422)
Q Consensus       374 e~~~CpIC~~~~~~------------------v-~l~CGH~fC~~Ci~~~----~~CP~CR~~i~  415 (422)
                      ++..|.||++.+.+                  + .++|+|.||..|+..|    ..||+||.++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            44689999988754                  1 2489999999999986    57999999853

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.64  E-value=2.8e-05  Score=62.13  Aligned_cols=47  Identities=21%  Similarity=0.535  Sum_probs=36.8

Q ss_pred             CCcCCccccccccccc---ccccCC-----CccchhhhhcC------CCCCCccccccCcc
Q 042398          372 VAETQACPICLTNAKD---LAFGCG-----HMTCRECGSRV------SNCPICRQRITNRL  418 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~---v~l~CG-----H~fC~~Ci~~~------~~CP~CR~~i~~~i  418 (422)
                      ..+...|.||++.+.+   +++||.     |.|+..|+.+|      ..||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            3456789999987643   456996     99999999977      47999999986543

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=97.62  E-value=1.1e-05  Score=65.48  Aligned_cols=40  Identities=23%  Similarity=0.644  Sum_probs=32.2

Q ss_pred             cCCccccccccccc-c--cc-cCCCccchhhhhcC------------CCCCC--cccc
Q 042398          374 ETQACPICLTNAKD-L--AF-GCGHMTCRECGSRV------------SNCPI--CRQR  413 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v--~l-~CGH~fC~~Ci~~~------------~~CP~--CR~~  413 (422)
                      +...|+||++.+.. .  .+ +|||.||..|+...            ..||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            46789999998876 2  22 79999999998732            36999  9988

>1pt6_A Integrin alpha-1; cell adhesion; 1.87A {Homo sapiens} SCOP: c.62.1.1 PDB: 4a0q_A 1qcy_A 1qc5_A 1qc5_B 1ck4_A 1mhp_A

Probab=97.58  E-value=0.00042  Score=63.21  Aligned_cols=133  Identities=18%  Similarity=0.292  Sum_probs=89.3

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||-|+|.+                    .++.+...+-.++..++   .+-.+-++.|+....   .+|+++ 
T Consensus         7 ~~div~vlD~SgSm~--------------------~~~~~k~~~~~~~~~l~~~~~~~~v~lv~F~~~~~---~~~~l~-   62 (213)
T 1pt6_A            7 QLDIVIVLDGSNSIY--------------------PWDSVTAFLNDLLKRMDIGPKQTQVGIVQYGENVT---HEFNLN-   62 (213)
T ss_dssp             CEEEEEEEECCTTCC--------------------CHHHHHHHHHHHHTTSCBSTTSBEEEEEEESSSEE---EEECTT-
T ss_pred             CccEEEEEECCCChh--------------------hHHHHHHHHHHHHHhcCCCCCCeEEEEEEeCCCcc---EEEecc-
Confidence            368999999999984                    04566666666666664   677899999997642   235542 


Q ss_pred             CCCCCCCHHHHHHHHHhhCCccc-ccC-CCChHHHHHHHHHHH-HH----cCCceEEEEEEeCCcccccCCCCCCCCchh
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLR-LAG-PTSYAPVVEAAMDIV-EK----SGGQYHVLVIIADGQVTRSVNTGDGELSSQ  247 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~-l~G-PT~fapiI~~a~~~~-~~----~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~  247 (422)
                       +  ....+.++++-.    .+. ..| -|+....|+.|.+.. ..    ....-.++++||||..++.           
T Consensus        63 -~--~~~~~~~~~~i~----~l~~~~G~~T~~~~aL~~a~~~l~~~~~~~r~~~~~~iillTDG~~~~~-----------  124 (213)
T 1pt6_A           63 -K--YSSTEEVLVAAK----KIVQRGGRQTMTALGTDTARKEAFTEARGARRGVKKVMVIVTDGESHDN-----------  124 (213)
T ss_dssp             -T--CSSHHHHHHHHH----TCCCCCCSSCCHHHHHHHHHHTTTSGGGTCCTTCEEEEEEEESSCCSCS-----------
T ss_pred             -c--cCCHHHHHHHHH----hccCCCCCcccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEcCCCCCCC-----------
Confidence             1  134566655443    333 356 499999999998752 21    1235788999999998872           


Q ss_pred             HHHHHHHHHHhcCCCeeEEEEecCCC
Q 042398          248 EQKTIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       248 ~~~T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                       ....+++..+.+..+-|..||||+.
T Consensus       125 -~~~~~~~~~~~~~gi~i~~igig~~  149 (213)
T 1pt6_A          125 -HRLKKVIQDCEDENIQRFSIAILGS  149 (213)
T ss_dssp             -HHHHHHHHHHHHTTEEEEEEEECHH
T ss_pred             -ccHHHHHHHHHHCCCEEEEEEeccc
Confidence             2344555556667899999999963

>2x5n_A SPRPN10, 26S proteasome regulatory subunit RPN10; nuclear protein, nucleus, ubiquitin; 1.30A {Schizosaccharomyces pombe}

Probab=97.58  E-value=0.0005  Score=63.09  Aligned_cols=160  Identities=14%  Similarity=0.213  Sum_probs=103.6

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCCCCcccCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQEVFSFHDDH  176 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~~vf~~~~~~  176 (422)
                      .++++||-|.|+...             +-.+|..+.|...+-.++..|   .....+-+..|++...+  -+.+++.  
T Consensus         4 ~lvlvlD~S~SM~~~-------------D~~psRl~~ak~~~~~~~~~~~~~~~~d~vGLV~fa~~~a~--~~~plT~--   66 (192)
T 2x5n_A            4 ATMILIDNSEWMING-------------DYIPTRFEAQKDTVHMIFNQKINDNPENMCGLMTIGDNSPQ--VLSTLTR--   66 (192)
T ss_dssp             EEEEEECCSGGGGCT-------------TSSSCHHHHHHHHHHHHHHHHHHHCTTCEEEEEECCTTSCC--EEEEEES--
T ss_pred             EEEEEEECCHhhccC-------------CCCCCHHHHHHHHHHHHHHHHHhcCCCCeEEEEEEcCCCcE--EecCCCC--
Confidence            589999999998632             113688998888777766544   34568889999874221  1223332  


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC--Cce-EEEEEEeCCcccccCCCCCCCCchhHHHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG--GQY-HVLVIIADGQVTRSVNTGDGELSSQEQKTIK  253 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~--~~Y-~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~  253 (422)
                          +.+.+++    .+..+...|.|++..-|+.|.+..++..  ... -|+|+++|+.-.|            ..+..+
T Consensus        67 ----d~~~i~~----~L~~l~~~g~t~l~~aL~~A~~~l~~~~~~~~~~riiil~~~~~~~~------------~~~~~~  126 (192)
T 2x5n_A           67 ----DYGKFLS----AMHDLPVRGNAKFGDGIQIAQLALKHRENKIQRQRIVAFVGSPIVED------------EKNLIR  126 (192)
T ss_dssp             ----CHHHHHH----HHTTCCCCSCCCHHHHHHHHHHHHHTCSCTTSEEEEEEEECSCCSSC------------HHHHHH
T ss_pred             ----CHHHHHH----HHHcCCCCCCchHHHHHHHHHHHHHhccccCCCceEEEEEECCCCCC------------chhHHH
Confidence                2444443    4455778899999999999998877643  223 3555555544222            456677


Q ss_pred             HHHHhcCCCeeEEEEecCCCCccc-cccccCCCCCcccccceecch
Q 042398          254 SIVAASSYPLSIVLVGVGDGPWED-MQKFDDKIPAREFDNFQFVNF  298 (422)
Q Consensus       254 aIv~AS~~PlSIiiVGVG~~~f~~-m~~LD~~~~~r~rDnvqFV~f  298 (422)
                      ++..+.+.-+.|.+||+|..+... |+.|=+...  .-|+-+||..
T Consensus       127 ~a~~lk~~gi~v~~Ig~G~~~~~~~l~~la~~~n--~~~~s~~~~~  170 (192)
T 2x5n_A          127 LAKRMKKNNVAIDIIHIGELQNESALQHFIDAAN--SSDSCHLVSI  170 (192)
T ss_dssp             HHHHHHHTTEEEEEEEESCC---CHHHHHHHHHC--STTCCEEEEE
T ss_pred             HHHHHHHCCCEEEEEEeCCCCccHHHHHHHHhcc--CCCceEEEEe
Confidence            788888889999999999876532 777643222  1267788754

>2odp_A Complement C2; C3/C5 convertase, complement serin protease, human complement system, glycoprotein, SP, VWFA,; HET: NAG; 1.90A {Homo sapiens} PDB: 2odq_A* 2i6q_A* 2i6s_A*

Probab=97.53  E-value=0.00012  Score=75.41  Aligned_cols=155  Identities=15%  Similarity=0.206  Sum_probs=100.2

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||-|.|.+.                  ..+++|...+..++..+   ..+-.+-++.|+....   .+|++..
T Consensus         9 ~~divfvlD~SgSM~~------------------~~~~~~k~~~~~l~~~l~~~~~~~rv~lv~f~~~~~---~~~~l~~   67 (509)
T 2odp_A            9 HLNLYLLLDASQSVSE------------------NDFLIFKESASLMVDRIFSFEINVSVAIITFASEPK---VLMSVLN   67 (509)
T ss_dssp             EEEEEEEEECSTTSCH------------------HHHHHHHHHHHHHHHHHHTTCCCEEEEEEEESSSEE---EEECTTS
T ss_pred             CeeEEEEEeCCCccch------------------hhHHHHHHHHHHHHHHhhccCCCceEEEEEccCCCc---eeEeccC
Confidence            4789999999999851                  23466666666666555   6778899999987642   2344421


Q ss_pred             CCCCCCCHHHHHHHHHhhCCcccc-cCCCChHHHHHHHHHHHHHcC-----------CceEEEEEEeCCcccccCCCCCC
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLRL-AGPTSYAPVVEAAMDIVEKSG-----------GQYHVLVIIADGQVTRSVNTGDG  242 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~l-~GPT~fapiI~~a~~~~~~~~-----------~~Y~VLlIiTDG~i~d~~~~~~~  242 (422)
                        +.-...+.++++-..+-..... .|.|+...-|+.|.+......           ..-.++++||||.-++..+    
T Consensus        68 --~~~~~~~~~~~~l~~l~~~~~~~~ggT~~~~aL~~a~~~l~~~~~~~~~~~~~~~~~~~~iillTDG~~~~~~~----  141 (509)
T 2odp_A           68 --DNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGS----  141 (509)
T ss_dssp             --GGGGCHHHHHHHHHTCCGGGGTTCCSCCHHHHHHHHHHHHHHHHHHHCTTSHHHHTEEEEEEEESCSCCCSSSC----
T ss_pred             --CCCCCHHHHHHHHHhcccccCCCCCCccHHHHHHHHHHHHhhcccccccccccccccceEEEEECCCCccCCCC----
Confidence              1122455665543332221111 388999999999987764321           1347889999998876221    


Q ss_pred             CCchhHHHHHHHHHHh------cCCCeeEEEEecCC--CCccccccccCC
Q 042398          243 ELSSQEQKTIKSIVAA------SSYPLSIVLVGVGD--GPWEDMQKFDDK  284 (422)
Q Consensus       243 ~~~~~~~~T~~aIv~A------S~~PlSIiiVGVG~--~~f~~m~~LD~~  284 (422)
                           ..+..+.+.+.      .+..+-|..||||+  .+...|+++-+.
T Consensus       142 -----~~~~~~~~~~~~~~~~~~~~~i~i~~iGvG~~~~~~~~L~~iA~~  186 (509)
T 2odp_A          142 -----PKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSK  186 (509)
T ss_dssp             -----THHHHHHHHHHTTCCSTTGGGEEEEEEEESSSCCCHHHHHHHSCC
T ss_pred             -----hhHHHHHHHHHhhccccccCceEEEEEEcCCCcccHHHHHhhccC
Confidence                 24455555542      26678899999998  578888887653

>2x31_A Magnesium-chelatase 60 kDa subunit; ligase, bacteriochlorophyll biosynthesis, photosynthesis; 7.50A {Rhodobacter capsulatus}

Probab=97.51  E-value=1.1e-05  Score=72.16  Aligned_cols=150  Identities=15%  Similarity=0.203  Sum_probs=89.9

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc-cCCCCCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP-FDEDNLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~-yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      .++++.||-|+|+.  |                +..+.|...+..++.. +..+..+-++.|+....  ..++++.    
T Consensus         6 ~~vv~vlD~SgSM~--~----------------~~~~~~k~~~~~~~~~~~~~~~~v~lv~f~~~~~--~~~~~~~----   61 (189)
T 2x31_A            6 RVLIFAVDASGSAA--V----------------ARLSEAKGAVELLLGRAYAARDHVSLITFRGTAA--QVLLQPS----   61 (189)
T ss_dssp             CEEEEEEECCTTSC--C------------------CHHHHHHHHHHHHHSCTTTSCCCEEEESBSCC--CBCTTTC----
T ss_pred             eEEEEEEECCCCCC--c----------------hHHHHHHHHHHHHHHHhcCCCcEEEEEEECCCCc--eEecCCC----
Confidence            57999999999984  1                1233344444444433 36666899999996321  1223222    


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcC--CceEEEEEEeCCcccccCCCCCCCCchh----HHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSG--GQYHVLVIIADGQVTRSVNTGDGELSSQ----EQKT  251 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~--~~Y~VLlIiTDG~i~d~~~~~~~~~~~~----~~~T  251 (422)
                        .+.+.+.+    .+..+...|-|++..-|+.+.+...+..  +.-.++++||||..++..+.     +|.    .++.
T Consensus        62 --~~~~~~~~----~i~~l~~~g~T~~~~al~~a~~~l~~~~~~~~~~~ivliTDG~~~~~~~~-----~~~~~~~~~~~  130 (189)
T 2x31_A           62 --RSLTQTKR----QLQGLPGGGGTPLASGMEMAMVTAKQARSRGMTPTIALLTDGRGNIALDG-----TANRELAGEQA  130 (189)
T ss_dssp             --SCHHHHHH----HHHHCCCCBCCCCHHHHHHHHHHHHTCTTTCSSEEEEECCBSCCSSCCTH-----HHHHGGGTCCC
T ss_pred             --CCHHHHHH----HHhcCCCCCCCCHHHHHHHHHHHHHhccCCCCceEEEEECCCCCCCCCCc-----cccccchhHHH
Confidence              24555443    3334556799999999999998877542  23578899999998762110     000    0011


Q ss_pred             HHHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          252 IKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      .+++..+....+.|..||+|+.+...|++|-.
T Consensus       131 ~~~~~~~~~~gi~v~~ig~g~~~~~~L~~iA~  162 (189)
T 2x31_A          131 TKVARAIRASGMPAVIIDTAMRPNPALVDLAR  162 (189)
T ss_dssp             EEEEECTGGGGSCCTHHHHHHSSCSSSCSTTT
T ss_pred             HHHHHHHHHcCCeEEEEecCCCCHHHHHHHHH
Confidence            12222333456788889999887777766643

>1mf7_A Integrin alpha M; cell adhesion; 1.25A {Homo sapiens} SCOP: c.62.1.1 PDB: 1na5_A 1jlm_A 1ido_A 1m1u_A 3q3g_G 1n9z_A 1bhq_1 1bho_1 1idn_1 3qa3_G

Probab=97.46  E-value=1.5e-05  Score=71.63  Aligned_cols=143  Identities=17%  Similarity=0.265  Sum_probs=91.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC-CCCCcceeeecCCCCCCCCCcccCCC-C
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD-EDNLIPCFGFGDATTHDQEVFSFHDD-H  176 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD-~D~~ip~~GFGa~~~~~~~vf~~~~~-~  176 (422)
                      +++++.||-|+|.+.                  ..++++...+..++..++ .+-.+-++.|+....   .+|+++.. +
T Consensus         6 ~div~vlD~SgSm~~------------------~~~~~~k~~~~~~~~~l~~~~~~v~vv~f~~~~~---~~~~l~~~~~   64 (194)
T 1mf7_A            6 SDIAFLIDGSGSIIP------------------HDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFR---IHFTFKEFQN   64 (194)
T ss_dssp             EEEEEEEECCTTSCH------------------HHHHHHHHHHHHHHHHHCCTTEEEEEEEESSSEE---EEECHHHHHH
T ss_pred             eeEEEEEeCCCCCCH------------------HHHHHHHHHHHHHHHhcCCCCeEEEEEEecCCce---EEEecCCcCC
Confidence            689999999999851                  245666666667777775 345799999988642   23444321 1


Q ss_pred             CCCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHH-HH-c---CCceEEEEEEeCCccc-ccCCCCCCCCchhHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIV-EK-S---GGQYHVLVIIADGQVT-RSVNTGDGELSSQEQ  249 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~-~~-~---~~~Y~VLlIiTDG~i~-d~~~~~~~~~~~~~~  249 (422)
                      .  ..+       .+.+..+. ..|.|+...-|+.+.+.. .. .   .+.-.++++||||..+ |..            
T Consensus        65 ~--~~~-------~~~i~~l~~~~g~T~~~~aL~~a~~~l~~~~~~~r~~~~~~iillTDG~~~~d~~------------  123 (194)
T 1mf7_A           65 N--PNP-------RSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPL------------  123 (194)
T ss_dssp             S--CCH-------HHHHTTCCCCCSCBCHHHHHHHHHHTTTSGGGTCCTTSEEEEEEEESSCCBSCSS------------
T ss_pred             H--HHH-------HHHHHhCcCCCCCchHHHHHHHHHHHhcCcccCCCCCCCeEEEEEcCCCCCCCch------------
Confidence            0  112       22334444 479999999999998643 21 1   1246889999999988 521            


Q ss_pred             HHHHHHHHhcCCCeeEEEEecCCCC-----ccccccccC
Q 042398          250 KTIKSIVAASSYPLSIVLVGVGDGP-----WEDMQKFDD  283 (422)
Q Consensus       250 ~T~~aIv~AS~~PlSIiiVGVG~~~-----f~~m~~LD~  283 (422)
                      ...+++.++....+.|..||||+..     ...|+.+-+
T Consensus       124 ~~~~~~~~~~~~gi~v~~igvG~~~~~~~~~~~L~~iA~  162 (194)
T 1mf7_A          124 GYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIAS  162 (194)
T ss_dssp             CGGGTHHHHHHTTEEEEEEEESGGGCSHHHHHHHHHHSC
T ss_pred             hhHHHHHHHHHCCCEEEEEEecccccccccHHHHHHHhC
Confidence            1123344445578999999999853     455555543

>1v7p_C Integrin alpha-2; snake venom, C-type lectin, antagonist, cell adhes glycoprotein, toxin-cell adhesion complex; HET: NAG; 1.90A {Homo sapiens} SCOP: c.62.1.1 PDB: 1aox_A 1dzi_A

Probab=97.45  E-value=0.001  Score=60.04  Aligned_cols=131  Identities=13%  Similarity=0.156  Sum_probs=89.0

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|.|.+                   | ++++...+..++..++   .+-.+-++.|+....   .+|+|+. 
T Consensus         7 ~div~vlD~SgSm~-------------------~-~~~~k~~~~~~~~~l~~~~~~~rvglv~f~~~~~---~~~~l~~-   62 (200)
T 1v7p_C            7 IDVVVVCDESNSIY-------------------P-WDAVKNFLEKFVQGLDIGPTKTQVGLIQYANNPR---VVFNLNT-   62 (200)
T ss_dssp             EEEEEEEECCTTCC-------------------C-HHHHHHHHHHHHHTSCBSTTSEEEEEEEESSSEE---EEECTTT-
T ss_pred             ccEEEEEECCCCcc-------------------c-HHHHHHHHHHHHHhcCCCCCceEEEEEEECCCce---EEEeCCC-
Confidence            68999999999983                   0 5666777777777776   567899999987642   2455541 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccc-cC-CCChHHHHHHHHHH-HHHc----CCceEEEEEEeCCcccccCCCCCCCCchhH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRL-AG-PTSYAPVVEAAMDI-VEKS----GGQYHVLVIIADGQVTRSVNTGDGELSSQE  248 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l-~G-PT~fapiI~~a~~~-~~~~----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~  248 (422)
                         -...+.++++-..    +.. .| -|+...-|+.+.+. ....    .+.-.++++||||..+|.            
T Consensus        63 ---~~~~~~~~~~i~~----l~~~~G~~T~~~~al~~a~~~~~~~~~g~r~~~~~~ivllTDG~~~~~------------  123 (200)
T 1v7p_C           63 ---YKTKEEMIVATSQ----TSQYGGDLTNTFGAIQYARKYAYSAASGGRRSATKVMVVVTDGESHDG------------  123 (200)
T ss_dssp             ---CSSHHHHHHHHHH----CCCCCCSCCCHHHHHHHHHHHTTSGGGTCCTTSEEEEEEEESSCCSCG------------
T ss_pred             ---cCCHHHHHHHHHh----hhccCCCCCcHHHHHHHHHHhhcccccCCCCCCCeEEEEEccCCCCCc------------
Confidence               1346666665443    333 35 59999999999875 2221    234678999999998872            


Q ss_pred             HHHHHHHHHhcCCCeeEEEEecCC
Q 042398          249 QKTIKSIVAASSYPLSIVLVGVGD  272 (422)
Q Consensus       249 ~~T~~aIv~AS~~PlSIiiVGVG~  272 (422)
                      ....+++..+.+..+-|..||||+
T Consensus       124 ~~~~~~~~~~~~~gi~i~~igvg~  147 (200)
T 1v7p_C          124 SMLKAVIDQCNHDNILRFGIAVLG  147 (200)
T ss_dssp             GGHHHHHHHHHHTTEEEEEEEECH
T ss_pred             ccHHHHHHHHHHCCCEEEEEEecc
Confidence            122344455556789999999964

>4b4t_W RPN10, 26S proteasome regulatory subunit RPN10; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.40  E-value=0.00062  Score=66.08  Aligned_cols=161  Identities=14%  Similarity=0.175  Sum_probs=109.9

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCCCCc-ccCCCC
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQEVF-SFHDDH  176 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~~vf-~~~~~~  176 (422)
                      .+|.||-|.|+...             +-.||.++.+..++-.++..+   +....+-+..|++...   .|. ++.   
T Consensus         6 tViviD~S~SM~~~-------------D~~PsRl~a~k~Av~~li~~~~~~nPed~VGLVtfag~~~---~vl~plT---   66 (268)
T 4b4t_W            6 TVLVIDNSEYSRNG-------------DFPRTRFEAQIDSVEFIFQAKRNSNPENTVGLISGAGANP---RVLSTFT---   66 (268)
T ss_dssp             EEEEECCSSTTSST-------------TSSSCHHHHHHHHHHHHHHHHHHHCTTCEEEEEECCTTSC---EEEEEEE---
T ss_pred             EEEEEECCHHHhCC-------------CCCCcHHHHHHHHHHHHHHHHhhCCCcceEEEEEecCCcc---eeccCCc---
Confidence            68899999998521             113688887777776666643   4556888888976432   221 221   


Q ss_pred             CCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHH
Q 042398          177 TPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKS  254 (422)
Q Consensus       177 ~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~a  254 (422)
                         .....++.    .+..++..|-|++..-|+.|....+..  ...-..++|+|||.+.+.           .++.+++
T Consensus        67 ---~D~~~il~----aL~~l~~~G~T~l~~gL~~A~~aLk~~~~k~~~~rIIlf~ds~~~~~-----------~~~l~~l  128 (268)
T 4b4t_W           67 ---AEFGKILA----GLHDTQIEGKLHMATALQIAQLTLKHRQNKVQHQRIVAFVCSPISDS-----------RDELIRL  128 (268)
T ss_dssp             ---SCHHHHHH----HHTTCCCCSCCCHHHHHHHHHHHHHTCSCTTSEEEEEEEECSCCSSC-----------HHHHHHH
T ss_pred             ---chHHHHHH----HhhhcCcCCCCChHHHHHHHHHHHHhcccCCCceEEEEEECCCCCCC-----------HHHHHHH
Confidence               23455544    466788999999999999999888754  234566678889887752           6778888


Q ss_pred             HHHhcCCCeeEEEEecCCCCc--cccccccCCCCCcccccceecch
Q 042398          255 IVAASSYPLSIVLVGVGDGPW--EDMQKFDDKIPAREFDNFQFVNF  298 (422)
Q Consensus       255 Iv~AS~~PlSIiiVGVG~~~f--~~m~~LD~~~~~r~rDnvqFV~f  298 (422)
                      +..+.+.-++|=+||+|.+++  +.|+.|=+......-|+-+||..
T Consensus       129 ak~lkk~gI~v~vIgFG~~~~n~~kLe~l~~~~Ng~~~~~s~~v~v  174 (268)
T 4b4t_W          129 AKTLKKNNVAVDIINFGEIEQNTELLDEFIAAVNNPQEETSHLLTV  174 (268)
T ss_dssp             HHHHHHHTEEEEEEEESSCCSSCCHHHHHHHHHCSSTTTSCEEEEE
T ss_pred             HHHHHHcCCEEEEEEeCCCccchHHHHHHHHHhcCCCCCceeEEEe
Confidence            888888889999999987654  55777632222212367777764

>1rrk_A Complement factor B; BB, hydrolase; 2.00A {Homo sapiens} SCOP: b.47.1.2 c.62.1.1 PDB: 1rs0_A* 1rtk_A* 2win_I* 1dle_A

Probab=97.30  E-value=0.00042  Score=70.98  Aligned_cols=153  Identities=13%  Similarity=0.124  Sum_probs=98.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc---cCCCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP---FDEDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~---yD~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|+|.+.                  +.++.|...+..++..   +..+-.+-++.|+....   .++.++  
T Consensus         2 ~div~vlD~SgSM~~------------------~~~~~~k~~~~~~~~~l~~~~~~~~v~lv~f~~~~~---~~~~~~--   58 (497)
T 1rrk_A            2 MNIYLVLDGSDSIGA------------------SNFTGAKKVLVNLIEKVASYGVKPRYGLVTYATYPK---IWVKVS--   58 (497)
T ss_dssp             EEEEEEEECSTTTCH------------------HHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESSSEE---EEECTT--
T ss_pred             eeEEEEEECCCCcch------------------hhHHHHHHHHHHHHHHhhccCCCceEEEEEecCCce---Eeeccc--
Confidence            578999999999851                  4456665555555554   55567899999997532   223332  


Q ss_pred             CCCCCCHHHHHHHHHhhCCcc-cccCCCChHHHHHHHHHHHHHc--------CCceEEEEEEeCCcccccCCCCCCCCch
Q 042398          176 HTPCHGFEEVLACYRNIVPNL-RLAGPTSYAPVVEAAMDIVEKS--------GGQYHVLVIIADGQVTRSVNTGDGELSS  246 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v-~l~GPT~fapiI~~a~~~~~~~--------~~~Y~VLlIiTDG~i~d~~~~~~~~~~~  246 (422)
                      .+.-...+.+.++-..+-+.- ...|.|+...-|+.|.+.....        ...-.++++||||.-++..|        
T Consensus        59 ~~~~~~~~~~~~~l~~l~~~~~~~~g~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g~~--------  130 (497)
T 1rrk_A           59 EADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGD--------  130 (497)
T ss_dssp             SGGGGCHHHHHHHHHHCCGGGSCCTTCCCHHHHHHHHHHHHCCC------CGGGCEEEEEEEECSCCCSSSC--------
T ss_pred             cccccCHHHHHHHHHhCcCccccccCccCHHHHHHHHHHHhhhhhccccccccccceEEEEEeCCCcccCCC--------
Confidence            222345666666554443222 2568899999999999876321        12457889999998875221        


Q ss_pred             hHHHHHHHHHHhc----------CCCeeEEEEecCC-CCccccccccC
Q 042398          247 QEQKTIKSIVAAS----------SYPLSIVLVGVGD-GPWEDMQKFDD  283 (422)
Q Consensus       247 ~~~~T~~aIv~AS----------~~PlSIiiVGVG~-~~f~~m~~LD~  283 (422)
                       ..+..+.+.+..          +..+-|..||||+ .+...|+.|-+
T Consensus       131 -~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~igvG~~~~~~~L~~iA~  177 (497)
T 1rrk_A          131 -PITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALAS  177 (497)
T ss_dssp             -THHHHHHHHHHTTCSSCC-CCCGGGEEEEEEECSSSCCHHHHHHHSC
T ss_pred             -hhHHHHHHHHHhhhhcccccchhcCeeEEEecCCCccCHHHHHHHhc
Confidence             345555555542          2278899999997 46667777654

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=97.13  E-value=0.00012  Score=55.48  Aligned_cols=43  Identities=12%  Similarity=0.119  Sum_probs=36.9

Q ss_pred             CCccccccccccc-ccc-cCCCccchhhhhcC----CCCCCccccccCc
Q 042398          375 TQACPICLTNAKD-LAF-GCGHMTCRECGSRV----SNCPICRQRITNR  417 (422)
Q Consensus       375 ~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~~  417 (422)
                      .+.|+||++.+.+ ++. +|||.||..|+.+|    ..||+++.++...
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            3689999999999 666 89999999999976    5699999998643

>3hrz_D Complement factor B; serine protease, glycosilated, multi-domain, complement SYST convertase, complement alternate pathway; HET: NAG P6G; 2.20A {Homo sapiens} PDB: 2xwj_I* 3hs0_D* 2ok5_A* 2xwb_F*

Probab=96.99  E-value=0.00079  Score=72.44  Aligned_cols=150  Identities=14%  Similarity=0.133  Sum_probs=95.6

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcc---ccccCCCCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKT---LAPFDEDNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~i---l~~yD~D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      .+++++.||-|.|.+.                  +.+++|...+..+   |..++..-.|-++-|+....   .+++|+.
T Consensus       243 ~~div~vlD~SgSM~~------------------~~~~~~k~~~~~~i~~l~~~~~~~rv~lv~f~~~~~---~~~~l~~  301 (741)
T 3hrz_D          243 SMNIYLVLDGSGSIGA------------------SDFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPK---IWVKVSE  301 (741)
T ss_dssp             EEEEEEEEECSTTTCH------------------HHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESSSEE---EEECTTS
T ss_pred             ceeEEEEeccCCcccc------------------cchHHHHHHHHHHHHhhhccCCCceEEEEEeccCCc---eeEeecc
Confidence            4789999999999852                  1244444444444   44445556799999987532   2344433


Q ss_pred             CCCCCCCHHHHHHHHHhhCCccc-----ccCCCChHHHHHHHHHHHHH--------cCCceEEEEEEeCCcccccCCCCC
Q 042398          175 DHTPCHGFEEVLACYRNIVPNLR-----LAGPTSYAPVVEAAMDIVEK--------SGGQYHVLVIIADGQVTRSVNTGD  241 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~l~~v~-----l~GPT~fapiI~~a~~~~~~--------~~~~Y~VLlIiTDG~i~d~~~~~~  241 (422)
                      .+  -...+.++++-    ..+.     ..|-|+...-|+.|.+....        ....-.++|+||||+-++-.    
T Consensus       302 ~~--~~~~~~~~~~i----~~l~~~~~~~~ggT~~~~aL~~a~~~l~~~~~~~~~~~~~~~~~iillTDG~~n~g~----  371 (741)
T 3hrz_D          302 AD--SSNADWVTKQL----NEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGG----  371 (741)
T ss_dssp             GG--GGCHHHHHHHH----TTCCGGGGSSSCCCCHHHHHHHHHHHHCCC--CCCTTGGGEEEEEEEEECSCCCSSS----
T ss_pred             cC--CcCHHHHHHHH----HhcccccccCCCChHHHHHHHHHHHHHhhhhhccccchhccCeEEEEECCCccccCC----
Confidence            11  13455565543    4444     68899999999999987621        11245789999999876421    


Q ss_pred             CCCchhHHHHHHHHHH----------hcCCCeeEEEEecCC-CCccccccccC
Q 042398          242 GELSSQEQKTIKSIVA----------ASSYPLSIVLVGVGD-GPWEDMQKFDD  283 (422)
Q Consensus       242 ~~~~~~~~~T~~aIv~----------AS~~PlSIiiVGVG~-~~f~~m~~LD~  283 (422)
                         +  .....+.|.+          +.+..+-|..||||+ .+...|++|-.
T Consensus       372 ---~--p~~~~~~i~~~~~~~~~a~~~~~~gi~i~~igvG~~~~~~~L~~ia~  419 (741)
T 3hrz_D          372 ---D--PITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALAS  419 (741)
T ss_dssp             ---C--THHHHHHHHHHTTCSSCTTCCCGGGEEEEEEECSSSCCHHHHHHHSC
T ss_pred             ---C--chHHHHHHHHHhhcccccccccccCeeEEEEeCCCcCCHHHHHHHhc
Confidence               1  2455555553          345678999999997 56677777654

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=96.90  E-value=0.00035  Score=58.14  Aligned_cols=41  Identities=24%  Similarity=0.532  Sum_probs=33.7

Q ss_pred             ccccccccccc--ccccCCCccchhhhhc-----CCCCCCccccccCc
Q 042398          377 ACPICLTNAKD--LAFGCGHMTCRECGSR-----VSNCPICRQRITNR  417 (422)
Q Consensus       377 ~CpIC~~~~~~--v~l~CGH~fC~~Ci~~-----~~~CP~CR~~i~~~  417 (422)
                      .|++|--..+.  -.+||.|.||.+|+..     ...||.|+.++...
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            58889877777  3569999999999964     36899999998754

>3zqk_A VON willebrand factor; blood clotting, adamts-13, force sensor, VON willebrand DISE domain, haemostasis; HET: NAG; 1.70A {Homo sapiens} PDB: 3ppv_A 3ppx_A 3ppw_A 3ppy_A 3gxb_A*

Probab=96.78  E-value=0.00091  Score=60.59  Aligned_cols=138  Identities=9%  Similarity=0.207  Sum_probs=91.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|.|.+.                  +.++++...+-.++..|+   ++-.|-+..|+....   ..|+|+. 
T Consensus        22 ~DivfvlD~S~Sm~~------------------~~~~~~k~~~~~~~~~l~~~~~~~rv~vv~fs~~~~---~~~~l~~-   79 (199)
T 3zqk_A           22 LDVAFVLEGSDKIGE------------------ADFNRSKEFMEEVIQRMDVGQDSIHVTVLQYSYMVT---VEYPFSE-   79 (199)
T ss_dssp             CEEEEEEECCTTTCH------------------HHHHHHHHHHHHHHHHSCBSTTSBEEEEEEESSSEE---EEECTTS-
T ss_pred             cCEEEEEECCCCCCH------------------HHHHHHHHHHHHHHHhcCCCCCceEEEEEEECCccc---EEEecCC-
Confidence            789999999999851                  345666666777777774   667899999997642   2455542 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCC-CChHHHHHHHHHHH-HH-c---CCceEEEEEEeCCcccccCCCCCCCCchhHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGP-TSYAPVVEAAMDIV-EK-S---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQ  249 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GP-T~fapiI~~a~~~~-~~-~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~  249 (422)
                         -...+.++++-.+. +.  ..|. |+...-|+.+.+.. .. .   .+.-.++++||||...|..           +
T Consensus        80 ---~~~~~~~~~~i~~l-~~--~gg~~T~~~~aL~~a~~~l~~~~~g~r~~~~~~iillTDG~~~d~v-----------~  142 (199)
T 3zqk_A           80 ---AQSKGDILQRLREI-RY--QGGNRTNTGLALRYLSDHSFLVSQGDREQAPNLVYMVTGNPASDEI-----------K  142 (199)
T ss_dssp             ---CCCHHHHHHHHHHC-CC--CCCSCCCHHHHHHHCCCCCTCGGGTCCTTSCEEEEEEECSCCSSCC-----------C
T ss_pred             ---cCCHHHHHHHHHhC-cC--CCCCcChHHHHHHHHHHHhhCcccCCCCCCCeEEEEEeCCCCchHH-----------H
Confidence               13456666654432 21  3454 99999888887632 11 1   1234789999999977622           0


Q ss_pred             HHHHHHHHhcCCCeeEEEEecC-CCCccccccccC
Q 042398          250 KTIKSIVAASSYPLSIVLVGVG-DGPWEDMQKFDD  283 (422)
Q Consensus       250 ~T~~aIv~AS~~PlSIiiVGVG-~~~f~~m~~LD~  283 (422)
                      +       + ...+.|.-|||| +.+.+.|+.+-.
T Consensus       143 ~-------~-~~~v~v~~iGiG~~~~~~~L~~iA~  169 (199)
T 3zqk_A          143 R-------L-PGDIQVVPIGVGPNANVQELERIGW  169 (199)
T ss_dssp             C-------C-CTTEEEEEEEESTTCCHHHHHHHHT
T ss_pred             H-------H-hCCCEEEEEEcCCCCCHHHHHHHhC
Confidence            0       1 156889999999 677888887754

>1jey_A KU70; double-strand DNA break repair, non-homologous END-joining, protein/nucleic acid complex, alpha/beta domain, beta barrel; HET: DNA; 2.50A {Homo sapiens} SCOP: b.131.1.1 c.62.1.3 PDB: 1jeq_A* 3rzx_B

Probab=96.75  E-value=0.008  Score=64.35  Aligned_cols=156  Identities=11%  Similarity=0.182  Sum_probs=100.7

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc---cCCCCCcceeeecCCCCCC----CCCccc
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP---FDEDNLIPCFGFGDATTHD----QEVFSF  172 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~---yD~D~~ip~~GFGa~~~~~----~~vf~~  172 (422)
                      .++++||.+.|+....           .+..++..+.|+..|..+++.   ....-.|-++.||...+..    .+++-+
T Consensus        37 ~ivf~IDvS~SM~~~d-----------~~~~~srl~~a~~~v~~~i~~kii~~~~D~vGlVlfgt~~t~n~l~~d~i~v~  105 (609)
T 1jey_A           37 SLIFLVDASKAMFESQ-----------SEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVL  105 (609)
T ss_dssp             EEEEEEECSGGGGCCC-----------SSSSCCHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESCSSCBSTTCCTTEEEE
T ss_pred             EEEEEEECCHHHcCCC-----------CCCCCChHHHHHHHHHHHHHHhhCCCCCCeEEEEEEccCCCCCcCCCCCeEEE
Confidence            4899999999986321           022479999999999999885   3344589999999876421    233322


Q ss_pred             CC-CCCCCCCHHHHHHHHHhhCC---------cccccCCCChHHHHHHHHHHHHHcCCc--eEEEEEEeCCcccccCCCC
Q 042398          173 HD-DHTPCHGFEEVLACYRNIVP---------NLRLAGPTSYAPVVEAAMDIVEKSGGQ--YHVLVIIADGQVTRSVNTG  240 (422)
Q Consensus       173 ~~-~~~~~~G~~gvl~~Y~~~l~---------~v~l~GPT~fapiI~~a~~~~~~~~~~--Y~VLlIiTDG~i~d~~~~~  240 (422)
                      .+ +.+   +.+ .+...+..+.         .+...+.|.+...|..|+++.+....+  =-++++||||.-.      
T Consensus       106 ~~L~~~---~~~-~ik~l~~l~~~~~~~~~~~~~g~~~~t~l~daL~~a~~~f~~~~~k~~~k~IiL~TDg~~p------  175 (609)
T 1jey_A          106 QELDNP---GAK-RILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNP------  175 (609)
T ss_dssp             EEEECC---CHH-HHHHHHTTSHHHHHHHHHHHHCCSCCCCHHHHHHHHHHHHHTCSSCEEEEEEEEEESCSCT------
T ss_pred             ecCCCC---CHH-HHHHHHHHhhcccchhhhhhcCCCCCCCHHHHHHHHHHHHHhhchhhcCCEEEEEcCCCCC------
Confidence            22 111   222 2222222221         011245799999999999888765333  3588899999643      


Q ss_pred             CCCCchhHHHHHHHHHHhcCCCeeEEEEecCCCC-cc
Q 042398          241 DGELSSQEQKTIKSIVAASSYPLSIVLVGVGDGP-WE  276 (422)
Q Consensus       241 ~~~~~~~~~~T~~aIv~AS~~PlSIiiVGVG~~~-f~  276 (422)
                      ++.-+........++..+..+-+.|.+||||..+ |+
T Consensus       176 ~~~~~~~~~~~~~~a~~l~~~gI~i~~igig~~~~fd  212 (609)
T 1jey_A          176 HGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFD  212 (609)
T ss_dssp             TTTCHHHHHHHHHHHHHHHHHTEEEEEEEBCCTTCCC
T ss_pred             CCCchHHHHHHHHHHHHHHhcCcEEEEEecCCCCccc
Confidence            2222233456677888889999999999999753 44

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.71  E-value=0.0016  Score=51.32  Aligned_cols=46  Identities=20%  Similarity=0.448  Sum_probs=37.0

Q ss_pred             CCcCCccccccccccc-c-cccCCCccchhhhhcC------CCCCCccccccCc
Q 042398          372 VAETQACPICLTNAKD-L-AFGCGHMTCRECGSRV------SNCPICRQRITNR  417 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v-~l~CGH~fC~~Ci~~~------~~CP~CR~~i~~~  417 (422)
                      .+....|.||++.+.. . -..|+|.|...|+.+|      ..||+||..+...
T Consensus        12 ~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             cCCCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            4556799999999886 2 2289999999999965      5799999987643

>1mjn_A Integrin alpha-L; rossmann fold, immune system; 1.30A {Homo sapiens} SCOP: c.62.1.1 PDB: 3hi6_A 1mq8_B* 3eoa_I 3eob_I 1rd4_A* 1lfa_A 1zon_A 1zoo_A 1zop_A 1dgq_A 1xdd_A* 1xdg_A* 1xuo_A* 3e2m_A* 3bqn_B* 1cqp_A* 3bqm_B* 2ica_A* 2o7n_A* 3m6f_A* ...

Probab=96.30  E-value=0.0084  Score=53.21  Aligned_cols=138  Identities=19%  Similarity=0.262  Sum_probs=85.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCC-CcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDN-LIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~-~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +++++.||-|.|.+.                  ..++++...+..++..++.++ .+-+..|+....   .+|+|+... 
T Consensus         3 ~divfvlD~S~Sm~~------------------~~~~~~k~~~~~~~~~l~~~~~rv~vv~fs~~~~---~~~~l~~~~-   60 (179)
T 1mjn_A            3 VDLVFLFDGSMSLQP------------------DEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYK---TEFDFSDYV-   60 (179)
T ss_dssp             EEEEEEEECBTTCCH------------------HHHHHHHHHHHHHHHHTTTSSEEEEEEEESSSEE---EEECHHHHH-
T ss_pred             ccEEEEEeCCCCCCH------------------HHHHHHHHHHHHHHHHhCCCCeEEEEEEECCcee---EEEcCcccC-
Confidence            678999999999851                  235666677777777775554 799999987642   234443100 


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHH-HHc----CCceEEEEEEeCCcccccCCCCCCCCchhHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIV-EKS----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTI  252 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~-~~~----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~  252 (422)
                      .-..++.++    ..++.  +.|-|+...-|+.|.+.. ...    .+.-.++++||||.-+|..+     .        
T Consensus        61 ~~~~~~~~~----~~i~~--~~g~T~~~~aL~~a~~~~~~~~~g~r~~~~~~iillTDG~~~~~~~-----~--------  121 (179)
T 1mjn_A           61 KRKDPDALL----KHVKH--MLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGN-----I--------  121 (179)
T ss_dssp             HHCCHHHHH----TTCCC--CCBCCCHHHHHHHHHHHTSSGGGTCCTTSEEEEEEEESSCCSSCSC-----C--------
T ss_pred             CHHHHHHHH----Hhccc--CCCCChHHHHHHHHHHHhcccccCCCCCCCeEEEEEcCCCCCCCcc-----h--------
Confidence            001222222    23333  458899999999988532 211    23468999999999887321     0        


Q ss_pred             HHHHHhcCCCeeEEEEecCCCCc-----ccccccc
Q 042398          253 KSIVAASSYPLSIVLVGVGDGPW-----EDMQKFD  282 (422)
Q Consensus       253 ~aIv~AS~~PlSIiiVGVG~~~f-----~~m~~LD  282 (422)
                           +...-+-|..||||+..-     ..|+.+=
T Consensus       122 -----~~~~~i~i~~igvG~~~~~~~~~~~L~~iA  151 (179)
T 1mjn_A          122 -----DAAKDIIRYIIGIGKHFQTKESQETLHKFA  151 (179)
T ss_dssp             -----GGGTTSEEEEEEESGGGCSHHHHHTTGGGS
T ss_pred             -----HHHCCCEEEEEEccccccccccHHHHHHHh
Confidence                 012357788899997532     4555553

>3k6s_A Integrin alpha-X; cell receptor, adhesion molecule, cell adhesion, pyrrolidone carboxylic acid; HET: NAG MAN; 3.50A {Homo sapiens} PDB: 3k71_A* 3k72_A*

Probab=96.17  E-value=0.0045  Score=70.60  Aligned_cols=142  Identities=15%  Similarity=0.296  Sum_probs=94.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCC-CCcceeeecCCCCCCCCCcccCC--C
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDED-NLIPCFGFGDATTHDQEVFSFHD--D  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D-~~ip~~GFGa~~~~~~~vf~~~~--~  175 (422)
                      +++++.||-|.|.+                  .+.++++...+-.+++.|+.+ -.|-+..|+....   .+|+|+.  +
T Consensus       131 ~DIvfvlD~SgSm~------------------~~~f~~~k~fv~~lv~~~~~~~~rVglV~Fs~~~~---~~~~lt~~~~  189 (1095)
T 3k6s_A          131 QDIVFLIDGSGSIS------------------SRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQ---THFTFEEFRR  189 (1095)
T ss_dssp             EEEEEEEECCTTSC------------------SHHHHHHHHHHHHHHHSSCSSSEEEEEEEESSSEE---EEECSHHHHS
T ss_pred             ccEEEEEcCCCCCC------------------hhHHHHHHHHHHHHHHhccccccEEEEEEECCeEE---EEecCcccCC
Confidence            78999999998874                  145777888888888888865 5788899987642   2354432  1


Q ss_pred             CCCCCCHHHHHHHHHhhCCcc-cccCCCChHHHHHHHHHHHH-H-c---CCceEEEEEEeCCccc-ccCCCCCCCCchhH
Q 042398          176 HTPCHGFEEVLACYRNIVPNL-RLAGPTSYAPVVEAAMDIVE-K-S---GGQYHVLVIIADGQVT-RSVNTGDGELSSQE  248 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v-~l~GPT~fapiI~~a~~~~~-~-~---~~~Y~VLlIiTDG~i~-d~~~~~~~~~~~~~  248 (422)
                      .   ..+       .+.+..+ .+.|-|+.+.-|++|.+..- . .   .+.-.|+++||||+.+ |.            
T Consensus       190 ~---~~l-------~~ai~~i~~~gG~T~~g~AL~~a~~~lf~~~~g~R~~~~kviIllTDG~~~~d~------------  247 (1095)
T 3k6s_A          190 S---SNP-------LSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITDGKKEGDS------------  247 (1095)
T ss_dssp             C---SCG-------GGGTTTCCCCCSCBCHHHHHHHHHTTTTSTTTTCCSSSEEEEEEEESSCCBSCS------------
T ss_pred             H---HHH-------HHHHhhhhcccCCChHHHHHHHHHHhhccccccCCCCCCeEEEEEeCCCcCCCc------------
Confidence            1   111       1223333 45789999999999876432 1 1   1235799999999985 42            


Q ss_pred             HHHHHHHHHhcCCCeeEEEEecCCC-----CccccccccC
Q 042398          249 QKTIKSIVAASSYPLSIVLVGVGDG-----PWEDMQKFDD  283 (422)
Q Consensus       249 ~~T~~aIv~AS~~PlSIiiVGVG~~-----~f~~m~~LD~  283 (422)
                      ....+++.+|...-+-|..||||++     +.+.|+++-+
T Consensus       248 ~~~~~~a~~~r~~GI~i~aIGVG~~~~~~~d~~eL~~IAs  287 (1095)
T 3k6s_A          248 LDYKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIAS  287 (1095)
T ss_dssp             SCHHHHHHHHHHHCEEECCEEBSSGGGSTTSSHHHHTTSC
T ss_pred             hhHHHHHHHHHHCCCEEEEEecccccccccCHHHHHHHHc
Confidence            1234444445555788999999987     6666766654

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=96.09  E-value=0.0018  Score=64.98  Aligned_cols=46  Identities=22%  Similarity=0.525  Sum_probs=36.3

Q ss_pred             CcCCccccccccccc-c--------cccCCCccchhhhhcC---------------CCCCCccccccCcc
Q 042398          373 AETQACPICLTNAKD-L--------AFGCGHMTCRECGSRV---------------SNCPICRQRITNRL  418 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v--------~l~CGH~fC~~Ci~~~---------------~~CP~CR~~i~~~i  418 (422)
                      .....|+||+....+ -        ...|||.|+..|+.+|               ..||.||.+++..+
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf  375 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSF  375 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccH
Confidence            456799999987765 1        2379999999999865               25999999997654

>1jey_B KU80; double-strand DNA break repair, non-homologous END-joining, protein/nucleic acid complex, alpha/beta domain, beta barrel; HET: DNA; 2.50A {Homo sapiens} SCOP: b.131.1.2 c.62.1.4 PDB: 1jeq_B*

Probab=95.96  E-value=0.021  Score=60.39  Aligned_cols=144  Identities=15%  Similarity=0.209  Sum_probs=96.1

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccc---cCCCCCcceeeecCCCCCC--------CC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAP---FDEDNLIPCFGFGDATTHD--------QE  168 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~---yD~D~~ip~~GFGa~~~~~--------~~  168 (422)
                      .++++||.+.|+....           .+ .++..+.|...+..+++.   ....-.+-++.||...+..        .+
T Consensus         9 ~iv~~iDvS~SM~~~d-----------~~-~~srl~~ak~~i~~~i~~ki~~~~~D~vGlv~f~~~~~~~plt~d~~y~~   76 (565)
T 1jey_B            9 AVVLCMDVGFTMSNSI-----------PG-IESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQN   76 (565)
T ss_dssp             EEEEEEECCGGGGCCB-----------TT-BCCHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESCSSCBSTTCTTTCSTT
T ss_pred             EEEEEEECChHhcccC-----------CC-CCCcHHHHHHHHHHHHHHHhcCCCCCEEEEEEEccCCCCCccccccCCCc
Confidence            6899999999986320           11 479999999999999983   5666789999999865311        12


Q ss_pred             CcccCC-CCCCCCCHHHHHHHHHhhCCccccc-CCCChHHHHHHHHHHHHHc--CCce--EEEEEEeCCcccccCCCCCC
Q 042398          169 VFSFHD-DHTPCHGFEEVLACYRNIVPNLRLA-GPTSYAPVVEAAMDIVEKS--GGQY--HVLVIIADGQVTRSVNTGDG  242 (422)
Q Consensus       169 vf~~~~-~~~~~~G~~gvl~~Y~~~l~~v~l~-GPT~fapiI~~a~~~~~~~--~~~Y--~VLlIiTDG~i~d~~~~~~~  242 (422)
                      ++-+.+ +.   .. ..+++....   .+..+ +.|.+...|..|++..+..  ..++  -++++||||+-.-      +
T Consensus        77 i~vl~~l~~---~~-~~~l~~l~~---~l~~~~~~t~i~~al~~A~~~l~~~~~~~k~~~krIiLlTDg~~~~------~  143 (565)
T 1jey_B           77 ITVHRHLML---PD-FDLLEDIES---KIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRF------S  143 (565)
T ss_dssp             EEEEEEEEC---CC-HHHHHHHHT---TCCCCSSCCCHHHHHHHHHHHHHHHSSSSCCSEEEEEEECCCCSCC------C
T ss_pred             eEEeecCCC---CC-HHHHHHHHh---hccCCCccccHHHHHHHHHHHHHHHhhcccccccEEEEEeCCCCCC------C
Confidence            221111 01   11 134444333   23333 6799999999999887665  3334  5789999997542      1


Q ss_pred             CCchhHHHHHHHHHHhcCCCeeEE-EEecCCC
Q 042398          243 ELSSQEQKTIKSIVAASSYPLSIV-LVGVGDG  273 (422)
Q Consensus       243 ~~~~~~~~T~~aIv~AS~~PlSIi-iVGVG~~  273 (422)
                           .....+++..+.+.-+.|. +||+|..
T Consensus       144 -----~~~~~~~a~~l~~~gI~i~~vig~g~~  170 (565)
T 1jey_B          144 -----KSQLDIIIHSLKKCDISLQFFLPFSLG  170 (565)
T ss_dssp             -----CTTHHHHHHHHHHTTEEEEEEESSCCC
T ss_pred             -----HHHHHHHHHHHHhcCcEEEEEeccCCC
Confidence                 1245566777888899999 8999864

>1yvr_A RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein, 60 kDa; heat repeat, VON willebrand factor A, rossmann fold, midas motif', RNA binding protein; 1.95A {Xenopus laevis} SCOP: a.118.25.1 c.62.1.5 PDB: 1yvp_A 2i91_A

Probab=95.59  E-value=0.081  Score=55.52  Aligned_cols=139  Identities=12%  Similarity=0.138  Sum_probs=83.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .++++.||-|+|+....    .+++       .. +.++.-.++-+.. - .+..+-++.|++...    .+++.++   
T Consensus       369 ~~v~lvvD~SgSM~~~~----~~~~-------l~-~~~~Aa~l~~~~~-~-~~d~vglv~Fs~~~~----~~~~t~~---  427 (538)
T 1yvr_A          369 KRFLLAIDVSASMNQRV----LGSI-------LN-ASVVAAAMCMLVA-R-TEKDSHMVAFSDEML----PCPITVN---  427 (538)
T ss_dssp             CCEEEEEECSGGGGSBS----TTSS-------CB-HHHHHHHHHHHHH-H-HCSSEEEEEESSSEE----CCSCCTT---
T ss_pred             ceEEEEEECccccCCCC----CCCc-------HH-HHHHHHHHHHHHh-c-cCCceEEEEECCCce----EcCCCCc---
Confidence            67999999999996421    0111       22 3333222221111 1 233588899986321    2233332   


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                       .++..+++.-.    .+ ..|-|+++..|..+.+.    ....-++++||||+.++.      ..+  ..+..+.+.+.
T Consensus       428 -~~l~~~l~~l~----~~-~~GgT~i~~aL~~a~~~----~~~~~~iIliTDg~~~~g------~~~--~~~~l~~~~~~  489 (538)
T 1yvr_A          428 -MLLHEVVEKMS----DI-TMGSTDCALPMLWAQKT----NTAADIFIVFTDCETNVE------DVH--PATALKQYREK  489 (538)
T ss_dssp             -SCHHHHHHHHT----TC-CCSCCCTTHHHHHHHHT----TCCCSEEEEEECCCCCSS------SCC--HHHHHHHHHHH
T ss_pred             -ccHHHHHHHHh----cC-CCCCCcHHHHHHHHHhc----cCCCCEEEEEcCCCCCCC------CCC--HHHHHHHHHHH
Confidence             34666665433    22 57889999999888754    234578899999987651      111  23555666666


Q ss_pred             cCCCeeEEEEecCCCCcc
Q 042398          259 SSYPLSIVLVGVGDGPWE  276 (422)
Q Consensus       259 S~~PlSIiiVGVG~~~f~  276 (422)
                      .+.++.+++||+|.....
T Consensus       490 ~~~~v~l~~igig~~~~~  507 (538)
T 1yvr_A          490 MGIPAKLIVCAMTSNGFS  507 (538)
T ss_dssp             HTCCCEEEEEECSSSSEE
T ss_pred             hCCCcEEEEEEecCCCCc
Confidence            678899999999986544

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=95.31  E-value=0.0082  Score=45.11  Aligned_cols=44  Identities=25%  Similarity=0.482  Sum_probs=33.2

Q ss_pred             CcCCccccccccccc-ccccCC--C---ccchhhhhcC------CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCG--H---MTCRECGSRV------SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CG--H---~fC~~Ci~~~------~~CP~CR~~i~~  416 (422)
                      ++...|.||++...+ ..+||.  |   .+...|+.+|      ..||+|+..+..
T Consensus         4 ~~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            355789999987554 445864  4   6899999976      579999998753

>2nvo_A RO sixty-related protein, RSR; alpha helical repeats, VON willebrand factor A domain, beta- RNA binding protein; 1.89A {Deinococcus radiodurans}

Probab=95.12  E-value=0.19  Score=52.88  Aligned_cols=140  Identities=13%  Similarity=0.131  Sum_probs=84.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTP  178 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~  178 (422)
                      .+++|+||-|+|+.+.+       ...  ....+..+-| ..++-++.. ..| .+-++.|++....    .++.++   
T Consensus       363 ~~~lv~vDvSgSM~~~~-------~~~--~~k~~~~e~A-a~la~~~~r-~~d-~v~lv~Fs~~~~~----~~~~~~---  423 (535)
T 2nvo_A          363 TRHLLALDVSGSMTCGD-------VAG--VPGLTPNMAA-AAMSLIALR-TEP-DALTMGFAEQFRP----LGITPR---  423 (535)
T ss_dssp             SEEEEEECCSGGGGSCC-------GGG--CTTCCHHHHH-HHHHHHHHH-HSS-EEEEEEEBSSEEE----CCCCTT---
T ss_pred             ceEEEEEECCccccCCC-------CCC--CCcccHHHHH-HHHHHHHcC-cCC-ceEEEEECCcceE----cCCCcc---
Confidence            67899999999996411       001  1124544444 455544333 222 5888999874311    122222   


Q ss_pred             CCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHh
Q 042398          179 CHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAA  258 (422)
Q Consensus       179 ~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~A  258 (422)
                       .++.++++.   +...  ..|.|+++..|+.+.+    ....+-+++|||||+..+      |..+|  .+.++...+.
T Consensus       424 -~~l~~~l~~---l~~~--~~ggTdi~~~l~~a~~----~~~~~~~vIliTD~~~~~------g~~~~--~~al~~~r~~  485 (535)
T 2nvo_A          424 -DTLESAMQK---AQSV--SFGGTDCAQPILWAAQ----ERLDVDTFVVYTDNETWA------GQVHP--TVALDQYAQK  485 (535)
T ss_dssp             -CCHHHHHHH---TCCS--SBCCCCTTHHHHHHHH----TTCCCSEEEEEESSCCCC------CSSCH--HHHHHHHHHH
T ss_pred             -hhHHHHHHH---HhhC--CCCCccHHHHHHHHHH----hcCCCCEEEEEeCCCccC------CCCCH--HHHHHHHHHh
Confidence             455555543   2222  3689999998877643    234567889999998765      22233  3455666666


Q ss_pred             cCCCeeEEEEecCCCCc
Q 042398          259 SSYPLSIVLVGVGDGPW  275 (422)
Q Consensus       259 S~~PlSIiiVGVG~~~f  275 (422)
                      .+.+.-+++||||....
T Consensus       486 ~~~~~klv~i~l~~~~~  502 (535)
T 2nvo_A          486 MGRAPKLIVVGLTATEF  502 (535)
T ss_dssp             HSCCCEEEEEETTCSCC
T ss_pred             hCCCCeEEEEeccCCCc
Confidence            67799999999998643

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=89.12  E-value=0.14  Score=41.43  Aligned_cols=30  Identities=30%  Similarity=0.654  Sum_probs=24.2

Q ss_pred             cCCcccccccc-ccc-cc--ccCCCccchhhhhc
Q 042398          374 ETQACPICLTN-AKD-LA--FGCGHMTCRECGSR  403 (422)
Q Consensus       374 e~~~CpIC~~~-~~~-v~--l~CGH~fC~~Ci~~  403 (422)
                      ++..|+||.+. ..+ +.  +.|+|.||..|+..
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~   35 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKA   35 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHH
Confidence            45789999975 445 44  69999999999985

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=88.08  E-value=0.3  Score=39.04  Aligned_cols=31  Identities=29%  Similarity=0.726  Sum_probs=25.6

Q ss_pred             CcCCcccccccccccccc-cC----CCccchhhhhc
Q 042398          373 AETQACPICLTNAKDLAF-GC----GHMTCRECGSR  403 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~v~l-~C----GH~fC~~Ci~~  403 (422)
                      ...+.|.+|.+.+.+..| .|    +|.||.-|...
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~   48 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRE   48 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHH
Confidence            345899999999999665 77    68899999873

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=82.44  E-value=0.54  Score=44.51  Aligned_cols=42  Identities=21%  Similarity=0.476  Sum_probs=33.5

Q ss_pred             CCccccccccccccc--ccCCCccchhhhhcC------CCCCCccccccC
Q 042398          375 TQACPICLTNAKDLA--FGCGHMTCRECGSRV------SNCPICRQRITN  416 (422)
Q Consensus       375 ~~~CpIC~~~~~~v~--l~CGH~fC~~Ci~~~------~~CP~CR~~i~~  416 (422)
                      ...|.+|.+....-.  -.|+|.|+..|+.++      ..||.|+.....
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            568999999887622  249999999999864      379999998754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	422
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	7e-09
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	8e-08
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-06
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-05
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-05
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-05
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-05
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	3e-04
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-04
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	5e-04

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 4e-10
 Identities = 18/54 (33%), Positives = 21/54 (38%), Gaps = 6/54 (11%)

Query: 374 ETQACPICLTNAKDLAF-GCGHMTCREC-----GSRVSNCPICRQRITNRLRLF 421
             Q C IC  N KD+    CGH+ C  C      S    CP CR  I     + 
Sbjct: 22  TFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV 75

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.5 bits (118), Expect = 7e-09
 Identities = 12/40 (30%), Positives = 14/40 (35%), Gaps = 2/40 (5%)

Query: 378 CPICLTNAKDLAF-GCGHMTCREC-GSRVSNCPICRQRIT 415
           C  C   AK      C H  C  C  +    CPIC+    
Sbjct: 9   CQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWP 48

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.6 bits (113), Expect = 8e-08
 Identities = 14/44 (31%), Positives = 15/44 (34%), Gaps = 6/44 (13%)

Query: 378 CPICLTNAKDLA-FGCGHMTCREC-----GSRVSNCPICRQRIT 415
           C IC     D     C H+ CR C         S CP CR    
Sbjct: 26  CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 46.1 bits (109), Expect = 1e-07
 Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 378 CPICLTNAKDLAF--GCGHMTCRECG----SRVSNCPICRQRIT 415
           CPICL +  + +    C H  C  C      +   CP+C+  + 
Sbjct: 8   CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 4e-06
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 8/48 (16%)

Query: 378 CPICLTNAKD-LAFGCGHMTCRECGSRVSN-------CPICRQRITNR 417
           CPICL   K+ ++  C H+ C+ C  ++ N       CP+C+  IT R
Sbjct: 24  CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.5 bits (94), Expect = 1e-05
 Identities = 5/45 (11%), Positives = 11/45 (24%), Gaps = 6/45 (13%)

Query: 378 CPICLTNAKDLAFG--CGHMTCREC----GSRVSNCPICRQRITN 416
           C I     +          +  +           N PI  + ++ 
Sbjct: 3   CAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSI 47

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 9/47 (19%)

Query: 378 CPICLTNAKD-----LAFGCGHMTCRECG----SRVSNCPICRQRIT 415
           C +CL   +D         CGH    EC        S CP+CR  + 
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 2e-05
 Identities = 14/55 (25%), Positives = 17/55 (30%), Gaps = 11/55 (20%)

Query: 374 ETQACPICLTNAKD------LAFGCGHMTCREC-----GSRVSNCPICRQRITNR 417
           + Q CP C T          +   CGH  C  C          NCP C   +   
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS 56

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 3e-05
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 10/49 (20%)

Query: 378 CPICLTNAKD-----LAFGCGHMTCRECGSRV-----SNCPICRQRITN 416
           CP+C+   +          CG+  CR C  R+       CP CR+    
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 13/44 (29%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 373 AETQACPICLTNAKDLAFGCGHMTCRECGSRVSNCPICRQRITN 416
           A T+ CP C     +   GC HM CR    +   C +C      
Sbjct: 4   ANTKECPKCHVTI-EKDGGCNHMVCRNQNCKAEFCWVCLGPWEP 46

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 4e-04
 Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 4/44 (9%)

Query: 378 CPICLTNAKDLAF--GCGHMTCRECGSRVSN--CPICRQRITNR 417
           C  C    ++     GC H+ C  C S      CP+C      +
Sbjct: 25  CSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQ 68

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 36.0 bits (82), Expect = 5e-04
 Identities = 12/52 (23%), Positives = 14/52 (26%), Gaps = 12/52 (23%)

Query: 378 CPICLTNAKDLAF------GCGHMTCRECGSR------VSNCPICRQRITNR 417
           C IC     +  F      G      R C S        + C IC      R
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	422
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.81
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.78
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	98.71
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	98.69
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.65
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.58
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.58
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.56
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.54
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.54
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.51
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.43
d1shux_	181	Capillary morphogenesis protein 2 domain {Human (H	98.22
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.15
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.0
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	97.87
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	97.72
d1jeya2	220	Ku70 subunit N-terminal domain {Human (Homo sapien	97.51
d1q0pa_	209	Complement factor B domain {Human (Homo sapiens) [	97.41
d1atza_	184	von Willebrand factor A3 domain, vWA3 {Human (Homo	97.34
d1v7pc_	193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	97.34
d1pt6a_	192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	97.23
d1mf7a_	194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	97.02
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.0
d1yvra2	174	60-kda SS-A/Ro ribonucleoprotein, RoRNP {African c	96.87
d1ijba_	202	von Willebrand factor A1 domain, vWA1 {Human (Homo	96.78
d1n3ya_	189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	96.46
d1jeyb2	236	Ku80 subunit N-terminal domain {Human (Homo sapien	96.35
d1mjna_	179	Integrin CD11a/CD18 (Leukocyte function associated	95.35
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	86.91

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=1.1e-09  Score=80.47  Aligned_cols=43  Identities=28%  Similarity=0.579  Sum_probs=37.7

Q ss_pred             cCCccccccccccc-ccccCCCccchhhhhcC-CCCCCccccccC
Q 042398          374 ETQACPICLTNAKD-LAFGCGHMTCRECGSRV-SNCPICRQRITN  416 (422)
Q Consensus       374 e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-~~CP~CR~~i~~  416 (422)
                      +.+.|+||++.+.+ +.++|||.||..|+.++ ..||+||.++..
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~~~~~CP~Cr~~~~~   49 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPL   49 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSSSSSCSSCCSSSSC
T ss_pred             CCCCCcccCcccCCCEEecCCCHHhHHHHHcCCCcCcCCCCcccC
Confidence            44699999999999 66799999999999977 589999999864

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=1.1e-09  Score=85.76  Aligned_cols=44  Identities=39%  Similarity=0.823  Sum_probs=37.5

Q ss_pred             Cccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccCccc
Q 042398          376 QACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITNRLR  419 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~~i~  419 (422)
                      ..|+||++.+.+ ++++|||.||..|+..|     ..||+||..+...-.
T Consensus        24 ~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          24 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TBCTTTSSSBCCEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCccCCCcCCCeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            579999999999 56699999999999854     569999999976543

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=98.71  E-value=1.7e-09  Score=82.03  Aligned_cols=43  Identities=33%  Similarity=0.868  Sum_probs=36.8

Q ss_pred             Cccccccccccc-c-cccCCCccchhhhhcC----CCCCCccccccCcc
Q 042398          376 QACPICLTNAKD-L-AFGCGHMTCRECGSRV----SNCPICRQRITNRL  418 (422)
Q Consensus       376 ~~CpIC~~~~~~-v-~l~CGH~fC~~Ci~~~----~~CP~CR~~i~~~i  418 (422)
                      ..|+||++.+.+ + .++|||.||..|+.+|    ..||+||.++....
T Consensus         6 d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~~~   54 (68)
T d1chca_           6 ERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVV   54 (68)
T ss_dssp             CCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCCEE
T ss_pred             CCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchHhhc
Confidence            479999999877 3 4699999999999976    78999999987644

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.69  E-value=1.4e-09  Score=86.76  Aligned_cols=44  Identities=34%  Similarity=0.709  Sum_probs=37.9

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      .+...|+||++.+.+ ++++|||.||..|+.++     ..||.||.++..
T Consensus        21 ~~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             ccCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            355799999999999 66799999999999965     579999998763

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=2e-09  Score=87.84  Aligned_cols=45  Identities=36%  Similarity=0.932  Sum_probs=37.7

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-------CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-------SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-------~~CP~CR~~i~~  416 (422)
                      +++.+.|+||++.+.+ +.++|||.||..|+..+       ..||+||.++..
T Consensus        18 l~~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          18 MQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HHHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cccCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            3456899999999999 56799999999998753       479999998853

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=6.3e-09  Score=83.94  Aligned_cols=45  Identities=24%  Similarity=0.719  Sum_probs=38.5

Q ss_pred             CCcCCccccccccccc-ccc-cCCCccchhhhhcC--CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAF-GCGHMTCRECGSRV--SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~--~~CP~CR~~i~~  416 (422)
                      +.+.+.|+||++.+.+ +++ +|||.||..|+.++  ..||.||.++..
T Consensus        19 l~~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~~   67 (97)
T d1jm7b_          19 LEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWI   67 (97)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCSC
T ss_pred             hhhcCCCccCCchhhcCceeCCCCCchhHHHHHHHHhccccccCCcCch
Confidence            4677899999999999 555 89999999999987  469999988754

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=5.6e-09  Score=78.56  Aligned_cols=43  Identities=33%  Similarity=0.813  Sum_probs=34.2

Q ss_pred             cCCccccccccccc------ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          374 ETQACPICLTNAKD------LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       374 e~~~CpIC~~~~~~------v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      |+..||||++....      ++.+|||.||..|+..|     ..||+||+++..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            56799999986422      23499999999999865     469999999854

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=98.56  E-value=1.3e-08  Score=74.19  Aligned_cols=43  Identities=33%  Similarity=0.791  Sum_probs=36.0

Q ss_pred             CCcCCccccccccccc---c-cc-cCCCccchhhhhcC----CCCCCccccc
Q 042398          372 VAETQACPICLTNAKD---L-AF-GCGHMTCRECGSRV----SNCPICRQRI  414 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~---v-~l-~CGH~fC~~Ci~~~----~~CP~CR~~i  414 (422)
                      +++...|+||++.+.+   + .+ .|||.||..|+.+|    ..||+||.++
T Consensus         2 ~ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i   53 (55)
T d1iyma_           2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEe
Confidence            4567789999999875   3 34 69999999999987    5799999976

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.54  E-value=1.2e-08  Score=79.58  Aligned_cols=44  Identities=14%  Similarity=0.076  Sum_probs=38.5

Q ss_pred             CcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      -+++.||||++.+.+ ++++|||.||..|+.++     ..||.||.++..
T Consensus         5 P~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            367899999999999 67799999999999864     579999998864

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.54  E-value=1.1e-08  Score=79.22  Aligned_cols=45  Identities=24%  Similarity=0.428  Sum_probs=38.9

Q ss_pred             CCcCCccccccccccc-ccccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          372 VAETQACPICLTNAKD-LAFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       372 ~~e~~~CpIC~~~~~~-v~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      ..+++.|+||++.+.+ ++++|||.||..|+.++     ..||.|+.++..
T Consensus         5 iP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CCccCCCcCcCchhhCceEccCCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            3467999999999999 66799999999999854     469999999865

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=1.4e-08  Score=73.11  Aligned_cols=41  Identities=32%  Similarity=0.852  Sum_probs=33.0

Q ss_pred             Cccccccccccc----c-cccCCCccchhhhhcC-----CCCCCccccccC
Q 042398          376 QACPICLTNAKD----L-AFGCGHMTCRECGSRV-----SNCPICRQRITN  416 (422)
Q Consensus       376 ~~CpIC~~~~~~----v-~l~CGH~fC~~Ci~~~-----~~CP~CR~~i~~  416 (422)
                      ..|+||++.+..    + .++|||.||..|+.+|     ..||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            379999998754    2 2389999999999965     369999998763

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.43  E-value=2e-08  Score=73.26  Aligned_cols=41  Identities=12%  Similarity=0.124  Sum_probs=36.0

Q ss_pred             Cccccccccccc-ccc-cCCCccchhhhhcC----CCCCCccccccC
Q 042398          376 QACPICLTNAKD-LAF-GCGHMTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       376 ~~CpIC~~~~~~-v~l-~CGH~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      +.|+||++.+.+ +.+ .|||.||.+|+.+|    ..||+||.++..
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~   47 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSI   47 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCG
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCH
Confidence            479999999999 555 69999999999976    789999999865

>d1shux_ c.62.1.1 (X:) Capillary morphogenesis protein 2 domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Capillary morphogenesis protein 2 domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.22  E-value=1.6e-06  Score=75.43  Aligned_cols=146  Identities=14%  Similarity=0.140  Sum_probs=97.7

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCC-CCcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDED-NLIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D-~~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +.+++.||-|+|.+                   +.+++....+..++..|... -.+-+.-|+...   ..+|+++.   
T Consensus         6 ~Div~llD~S~Sm~-------------------~~~~~~k~~~~~~~~~~~~~~~rvglv~fs~~~---~~~~~l~~---   60 (181)
T d1shux_           6 FDLYFVLDKSGSVA-------------------NNWIEIYNFVQQLAERFVSPEMRLSFIVFSSQA---TIILPLTG---   60 (181)
T ss_dssp             EEEEEEEECSGGGG-------------------GGHHHHHHHHHHHHHHCCCTTEEEEEEEESSSE---EEEEEEEC---
T ss_pred             eEEEEEEeCCCCcc-------------------cCHHHHHHHHHHHHHHhcCCCCEEEEEEeecce---EEEEEecC---
Confidence            78999999888773                   11334455555555666543 347777787753   23466643   


Q ss_pred             CCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--CCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSI  255 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aI  255 (422)
                         ..+.+.+. .+.++.+...|-|+++..++.+.+.....  .....++++||||..++.          +.....++.
T Consensus        61 ---~~~~~~~~-l~~l~~~~~~g~t~~~~al~~~~~~~~~~~~~~~~~~ivliTDG~~~~~----------~~~~~~~~~  126 (181)
T d1shux_          61 ---DRGKISKG-LEDLKRVSPVGETYIHEGLKLANEQIQKAGGLKTSSIIIALTDGKLDGL----------VPSYAEKEA  126 (181)
T ss_dssp             ---CHHHHHHH-HHHHHTCCCCSCCCHHHHHHHHHHHHHHHTGGGSCEEEEEEECCCCCTT----------HHHHHHHHH
T ss_pred             ---CHHHHHHH-hhhcccccCCCcchHHHHHHHHHHHhhhcccCCCceEEEEecCCCCCCC----------ccHHHHHHH
Confidence               22223222 23455677788999999999998876643  234688999999998762          134445566


Q ss_pred             HHhcCCCeeEEEEecCCCCccccccccC
Q 042398          256 VAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       256 v~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                      ..+...-+.|+.||||+.+...|+.+-+
T Consensus       127 ~~~k~~gv~v~~vgig~~~~~~L~~ia~  154 (181)
T d1shux_         127 KISRSLGASVYCVGVLDFEQAQLERIAD  154 (181)
T ss_dssp             HHHHHTTCEEEEEECSSCCHHHHHHHSS
T ss_pred             HHHHHCCCEEEEEEeCccCHHHHHHHhC
Confidence            6677788999999999888777777754

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.15  E-value=2.6e-07  Score=75.94  Aligned_cols=42  Identities=21%  Similarity=0.473  Sum_probs=32.6

Q ss_pred             CCccccccccccc-------------------ccccCCCccchhhhhcC---------CCCCCccccccC
Q 042398          375 TQACPICLTNAKD-------------------LAFGCGHMTCRECGSRV---------SNCPICRQRITN  416 (422)
Q Consensus       375 ~~~CpIC~~~~~~-------------------v~l~CGH~fC~~Ci~~~---------~~CP~CR~~i~~  416 (422)
                      +..|+||++.+.+                   ..++|||.||..|+..|         ..||+||..+..
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhcc
Confidence            3579999987632                   23599999999999866         269999998743

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.00  E-value=2.2e-06  Score=69.12  Aligned_cols=44  Identities=20%  Similarity=0.154  Sum_probs=37.3

Q ss_pred             CcCCccccccccccc-ccccCCC-ccchhhhhcC----CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGCGH-MTCRECGSRV----SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~CGH-~fC~~Ci~~~----~~CP~CR~~i~~  416 (422)
                      -+++.||||.+.+.+ |+++||| .||..|+.++    ..||+||.++..
T Consensus        20 P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            357999999999999 6667765 7999999976    679999999864

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.87  E-value=1.8e-06  Score=68.03  Aligned_cols=26  Identities=27%  Similarity=0.395  Sum_probs=23.0

Q ss_pred             ccCCCccchhhhhcC----CCCCCcccccc
Q 042398          390 FGCGHMTCRECGSRV----SNCPICRQRIT  415 (422)
Q Consensus       390 l~CGH~fC~~Ci~~~----~~CP~CR~~i~  415 (422)
                      ++|||.||..|+.++    ..||+||+++.
T Consensus        55 ~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          55 GVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             ETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             ccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            489999999999976    67999999864

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=97.72  E-value=5.1e-06  Score=60.71  Aligned_cols=44  Identities=23%  Similarity=0.413  Sum_probs=34.7

Q ss_pred             CcCCccccccccccc-ccccC-----CCccchhhhhcC------CCCCCccccccC
Q 042398          373 AETQACPICLTNAKD-LAFGC-----GHMTCRECGSRV------SNCPICRQRITN  416 (422)
Q Consensus       373 ~e~~~CpIC~~~~~~-v~l~C-----GH~fC~~Ci~~~------~~CP~CR~~i~~  416 (422)
                      ++...|+||++...+ ...+|     +|.||..|+.+|      ..||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            466799999998776 33344     599999999976      479999998754

>d1jeya2 c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Ku70 subunit N-terminal domain
domain: Ku70 subunit N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.51  E-value=0.00032  Score=61.72  Aligned_cols=162  Identities=10%  Similarity=0.139  Sum_probs=95.7

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCC----CCcccC
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQ----EVFSFH  173 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~----~vf~~~  173 (422)
                      +++.||-|.|+..+          . ..+....++.|+.++-.+++.+   -..-++-++.||...+...    +++-+.
T Consensus         5 ivf~ID~S~SM~~~----------d-~~~~~s~~~~~~~~~~~~~~~~i~~~~~d~vglv~f~t~~~~~~~~~~~~~~~~   73 (220)
T d1jeya2           5 LIFLVDASKAMFES----------Q-SEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQ   73 (220)
T ss_dssp             EEEEEECSGGGGCC----------C-SSSSCCHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESCSSCBSTTCCTTEEEEE
T ss_pred             EEEEEECCcccCcc----------c-cCCCCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEEeccccccCCCcccchhhhh
Confidence            89999999998521          1 1124578889998888888876   2344699999997653221    111111


Q ss_pred             C-CCCCCCCHHHHHHHHHhhCC---------cccccCCCChHHHHHHHHHHHHHcCCc--eEEEEEEeCCcccccCCCCC
Q 042398          174 D-DHTPCHGFEEVLACYRNIVP---------NLRLAGPTSYAPVVEAAMDIVEKSGGQ--YHVLVIIADGQVTRSVNTGD  241 (422)
Q Consensus       174 ~-~~~~~~G~~gvl~~Y~~~l~---------~v~l~GPT~fapiI~~a~~~~~~~~~~--Y~VLlIiTDG~i~d~~~~~~  241 (422)
                      + +.+.    ...+...+....         .....|.|++...|..+.+.......+  .-++++||||+-+.-     
T Consensus        74 ~l~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~l~~al~~a~~~~~~~~~~~~~k~IiliTDg~~~~~-----  144 (220)
T d1jeya2          74 ELDNPG----AKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHG-----  144 (220)
T ss_dssp             EEECCC----HHHHHHHHTTSHHHHHHHHHHHHCCSCCCCHHHHHHHHHHHHHTCSSCEEEEEEEEEESCSCTTT-----
T ss_pred             cccCch----HHHHHhhhhhhhhhhhhhhhhcccCCCCccHHHHHHHHHHHHHhcccccCCcEEEEEecCCCCCC-----
Confidence            1 1111    122222222111         122458899999999999887764322  358899999975431     


Q ss_pred             CCCchhHHHHHHHHHHhcCCCeeEEEEecCCCCccccccccC
Q 042398          242 GELSSQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQKFDD  283 (422)
Q Consensus       242 ~~~~~~~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~~LD~  283 (422)
                       .=+.+..+.++++.++...-+.|-.+|||..+--.++.|+.
T Consensus       145 -~~~~~~~~~~~~a~~~~~~gv~i~~i~ig~~~~~d~~~f~~  185 (220)
T d1jeya2         145 -NDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYR  185 (220)
T ss_dssp             -TCHHHHHHHHHHHHHHHHHTEEEEEEEBCCTTCCCTTTTGG
T ss_pred             -CcchhhHHHHHHHHHHhhhcceEEEEEeCCCCCcchhhhHH
Confidence             11233455566666666667777778887654233444443

>d1q0pa_ c.62.1.1 (A:) Complement factor B domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Complement factor B domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.41  E-value=0.00048  Score=59.98  Aligned_cols=152  Identities=14%  Similarity=0.121  Sum_probs=93.5

Q ss_pred             cccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCCCCcccCC
Q 042398           98 SSNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQEVFSFHD  174 (422)
Q Consensus        98 ~~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~~vf~~~~  174 (422)
                      ++++++.||.|+|.+.                  +.++++...+-.++..|   +..-.+-++.||....   .+++|+.
T Consensus         1 slDivfvlD~SgSm~~------------------~~~~~~k~~~~~li~~l~~~~~~~rv~lv~f~~~~~---~~~~l~~   59 (209)
T d1q0pa_           1 SMNIYLVLDGSDSIGA------------------SNFTGAKKSLVNLIEKVASYGVKPRYGLVTYATYPK---IWVKVSE   59 (209)
T ss_dssp             CEEEEEEEECSTTTCH------------------HHHHHHHHHHHHHHHHHHTTTCCCEEEEEEESSSEE---EEECTTS
T ss_pred             CcCEEEEEeCCCCCCh------------------HHHHHHHHHHHHHHHhcccCCCCcEEEEEEecCcee---EEecCcc
Confidence            4789999999999841                  34666666666666666   4455799999997532   1244432


Q ss_pred             CCCCCCCHHHHHHHHHhh-CCcccccCCCChHHHHHHHHHHHHHcC--------CceEEEEEEeCCcccccCCCCCCCCc
Q 042398          175 DHTPCHGFEEVLACYRNI-VPNLRLAGPTSYAPVVEAAMDIVEKSG--------GQYHVLVIIADGQVTRSVNTGDGELS  245 (422)
Q Consensus       175 ~~~~~~G~~gvl~~Y~~~-l~~v~l~GPT~fapiI~~a~~~~~~~~--------~~Y~VLlIiTDG~i~d~~~~~~~~~~  245 (422)
                      .  .......+.+.-.++ .......|-|+.+..|+.+.+......        ..-.|++++|||.-++..+       
T Consensus        60 ~--~~~~~~~l~~~i~~i~~~~~~~~g~t~~~~al~~a~~~~~~~~~~~~~~~~~~~kvvvl~TDG~~~~~~~-------  130 (209)
T d1q0pa_          60 A--DSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGD-------  130 (209)
T ss_dssp             G--GGGCHHHHHHHHHTCCTTSCSCTTCCCHHHHHHHHHHHHCCTTSSCCTTGGGCEEEEEEEECSCCCSSSC-------
T ss_pred             c--hhhHHHHHHHHHHHhhhccccCCCCchHHHHHHHHHHHHHhhhccCccccCCCceEEEEEcCCCccCCCC-------
Confidence            1  123344444333332 123356788999999999988764321        1246889999999877432       


Q ss_pred             hhHHHHHHHHHHhcC----------CCeeEEEEecCC-CCccccccc
Q 042398          246 SQEQKTIKSIVAASS----------YPLSIVLVGVGD-GPWEDMQKF  281 (422)
Q Consensus       246 ~~~~~T~~aIv~AS~----------~PlSIiiVGVG~-~~f~~m~~L  281 (422)
                        .....+.+.+...          ..+-|+.||||+ .+.+.|+.+
T Consensus       131 --~~~~~~~~~~~~~~~~~~~~~~~~gi~i~~vgvg~~~~~~~L~~i  175 (209)
T d1q0pa_         131 --PITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINAL  175 (209)
T ss_dssp             --THHHHHHHHHHTTCSCBTTBCCGGGEEEEEEECSSCCCHHHHHHH
T ss_pred             --hHHHHHHHHHhhhhHHHHHHHHhcCCceEEecCCccCCHHHHHHH
Confidence              2344455544322          236688889985 355556555

>d1atza_ c.62.1.1 (A:) von Willebrand factor A3 domain, vWA3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: von Willebrand factor A3 domain, vWA3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=0.00052  Score=59.59  Aligned_cols=142  Identities=13%  Similarity=0.189  Sum_probs=94.3

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC--CC-CCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD--ED-NLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD--~D-~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +.+++.||-|.|.++                  ..++++...+-+++..|+  .+ -.+-+..||....   ..|+|+. 
T Consensus         3 lDivfliD~S~s~~~------------------~~f~~~k~~v~~~i~~~~i~~~~~rv~vv~f~~~~~---~~~~l~~-   60 (184)
T d1atza_           3 LDVILLLDGSSSFPA------------------SYFDEMKSFAKAFISKANIGPRLTQVSVLQYGSITT---IDVPWNV-   60 (184)
T ss_dssp             EEEEEEEECSSSSCH------------------HHHHHHHHHHHHHHHHSCBSTTSEEEEEEEESSSEE---EEECTTC-
T ss_pred             eEEEEEEeCCCCCCH------------------HHHHHHHHHHHHHHHhcCCCCCCcEEEEEEEeccce---eeccccc-
Confidence            678999999988752                  236777777777888885  22 2688888987642   2355532 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc-----CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS-----GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~-----~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                         ....++++++-.+ ++.  ..|+|+....++.+.+..-..     .+.--|+++||||.-+|.           ..+
T Consensus        61 ---~~~~~~l~~~i~~-l~~--~gg~t~~~~al~~~~~~~~~~~~g~R~~~~kvvvlltdg~~~d~-----------~~~  123 (184)
T d1atza_          61 ---VPEKAHLLSLVDV-MQR--EGGPSQIGDALGFAVRYLTSEMHGARPGASKAVVILVTDVSVDS-----------VDA  123 (184)
T ss_dssp             ---CCCHHHHHHHHHT-CCC--CCCCCCHHHHHHHHHHHHHSCCTTCCTTSEEEEEEEECSCCSSC-----------CHH
T ss_pred             ---cccHHHHHHHHHh-hhh--cccccchhhhhhHHHHHhhhhhcCCCCCCceEEEEEEecCccch-----------hhH
Confidence               2346666554433 332  578999999999999876532     124678999999987762           234


Q ss_pred             HHHHHHHhcCCCeeEEEEecCCC-Ccccccccc
Q 042398          251 TIKSIVAASSYPLSIVLVGVGDG-PWEDMQKFD  282 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~~-~f~~m~~LD  282 (422)
                      ..+++.+   .-+-|+.||||+. +-..|+.+-
T Consensus       124 ~a~~lk~---~gi~v~~igiG~~~~~~~L~~ia  153 (184)
T d1atza_         124 AADAARS---NRVTVFPIGIGDRYDAAQLRILA  153 (184)
T ss_dssp             HHHHHHH---TTEEEEEEEESSSSCHHHHHHHT
T ss_pred             HHHHHHH---cCcEEEEEEeCCcCCHHHHHHHh
Confidence            4444443   4688999999974 555555553

>d1v7pc_ c.62.1.1 (C:) Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha2-beta1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=0.00083  Score=58.38  Aligned_cols=133  Identities=14%  Similarity=0.146  Sum_probs=87.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +.+++.||-|.|-+                    +++++...+-++++.|+   ++-.+-+.-||+...   .+|+|+. 
T Consensus         2 ~DivfvlD~S~Sv~--------------------~f~~~k~f~~~ii~~~~i~~~~~rv~vv~fs~~~~---~~~~l~~-   57 (193)
T d1v7pc_           2 IDVVVVCDESNSIY--------------------PWDAVKNFLEKFVQGLDIGPTKTQVGLIQYANNPR---VVFNLNT-   57 (193)
T ss_dssp             EEEEEEEECCTTCC--------------------CHHHHHHHHHHHHHTSCBSTTSEEEEEEEESSSEE---EEECTTT-
T ss_pred             EEEEEEEECCCCCc--------------------cHHHHHHHHHHHHHHcccCCCccEEEEEEeeccee---eeecccc-
Confidence            56889999876541                    15566666777788886   233689999988642   3466642 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHH--Hc---CCceEEEEEEeCCcccccCCCCCCCCchhHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVE--KS---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQK  250 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~--~~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~  250 (422)
                         -...++++++=.+..+.  -.|.|+....|+.|.+..-  ..   .+--.|+++||||..+|.            ..
T Consensus        58 ---~~~~~~~~~~i~~~~~~--~g~~t~~~~AL~~a~~~~f~~~~~~R~~~~kvvVllTDG~s~d~------------~~  120 (193)
T d1v7pc_          58 ---YKTKEEMIVATSQTSQY--GGDLTNTFGAIQYARKYAYSAASGGRRSATKVMVVVTDGESHDG------------SM  120 (193)
T ss_dssp             ---CSSHHHHHHHHHHCCCC--CCSCCCHHHHHHHHHHHTTSGGGTCCTTSEEEEEEEESSCCSCG------------GG
T ss_pred             ---hhhHHHHHHHHHhhhhh--ccCccchHHHHHHHHHhccccccCCCCCCceEEEEEecCCcCCC------------cc
Confidence               23566776654443221  2457999999999987642  11   123568899999998872            23


Q ss_pred             HHHHHHHhcCCCeeEEEEecCC
Q 042398          251 TIKSIVAASSYPLSIVLVGVGD  272 (422)
Q Consensus       251 T~~aIv~AS~~PlSIiiVGVG~  272 (422)
                      +.++..++...-+-++-||||+
T Consensus       121 ~~~~~~~~~~~gv~v~~Igvg~  142 (193)
T d1v7pc_         121 LKAVIDQCNHDNILRFGIAVLG  142 (193)
T ss_dssp             HHHHHHHHHHTTEEEEEEEECH
T ss_pred             HHHHHHHHHhCCCEEEEEEeCC
Confidence            4455666667778888888875

>d1pt6a_ c.62.1.1 (A:) Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha1-beta1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=0.0015  Score=56.51  Aligned_cols=133  Identities=20%  Similarity=0.291  Sum_probs=87.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +.+++.||-|.|-+                   | ++++...+-.++..|+   ++-.+-+.-||....   .+|+|+. 
T Consensus         2 ~DivfvlD~S~S~~-------------------~-~~~~k~f~~~~i~~~~i~~~~~rv~vv~fs~~~~---~~~~l~~-   57 (192)
T d1pt6a_           2 LDIVIVLDGSNSIY-------------------P-WDSVTAFLNDLLKRMDIGPKQTQVGIVQYGENVT---HEFNLNK-   57 (192)
T ss_dssp             EEEEEEEECCTTCC-------------------C-HHHHHHHHHHHHTTSCBSTTSBEEEEEEESSSEE---EEECTTT-
T ss_pred             eEEEEEEECCCCCC-------------------C-HHHHHHHHHHHHHHhccCCCCcEEEEEEEeccEE---EEEeCCc-
Confidence            68899999775541                   2 6677777778888885   233689999987642   2466642 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccC-CCChHHHHHHHHHHHH--HcC---CceEEEEEEeCCcccccCCCCCCCCchhHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAG-PTSYAPVVEAAMDIVE--KSG---GQYHVLVIIADGQVTRSVNTGDGELSSQEQ  249 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~G-PT~fapiI~~a~~~~~--~~~---~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~  249 (422)
                         ....+.++++-.+...   ..| .++-+-.++.+.+..-  ..+   +--.|+++||||..+|            ..
T Consensus        58 ---~~~~~~~~~~i~~~~~---~~g~~~~~~~al~~~~~~~~~~~~g~R~~~~kviillTDG~~~d------------~~  119 (192)
T d1pt6a_          58 ---YSSTEEVLVAAKKIVQ---RGGRQTMTALGTDTARKEAFTEARGARRGVKKVMVIVTDGESHD------------NH  119 (192)
T ss_dssp             ---CSSHHHHHHHHHTCCC---CCCSSCCHHHHHHHHHHTTTSGGGTCCTTCEEEEEEEESSCCSC------------SH
T ss_pred             ---chhhHHHHHHHhhhhh---hhhhccchHHHHHHHHHhhhccccCCCCCcceEEEEEecCCCCc------------ch
Confidence               1345677666544322   334 4666666776665421  111   2246889999999887            34


Q ss_pred             HHHHHHHHhcCCCeeEEEEecCCC
Q 042398          250 KTIKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       250 ~T~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      ...+++..+-+.-+-|+.||||..
T Consensus       120 ~~~~~a~~lk~~gi~v~~igvg~~  143 (192)
T d1pt6a_         120 RLKKVIQDCEDENIQRFSIAILGS  143 (192)
T ss_dssp             HHHHHHHHHHHTTEEEEEEEECHH
T ss_pred             hhHHHHHHHHHCCCeEEEEEEecc
Confidence            566677777788899999999953

>d1mf7a_ c.62.1.1 (A:) Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.02  E-value=6.7e-05  Score=65.70  Aligned_cols=144  Identities=18%  Similarity=0.278  Sum_probs=94.1

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCC-CcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDN-LIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~-~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +++++.||-|+|.+                  ...+++++..+..++..++.++ .+-+..|+....   ..|+|+..  
T Consensus         6 ~DivfvlD~S~s~~------------------~~~~~~~k~f~~~iv~~l~~~~~rv~vv~fs~~~~---~~~~l~~~--   62 (194)
T d1mf7a_           6 SDIAFLIDGSGSII------------------PHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFR---IHFTFKEF--   62 (194)
T ss_dssp             EEEEEEEECCTTSC------------------HHHHHHHHHHHHHHHHHHCCTTEEEEEEEESSSEE---EEECHHHH--
T ss_pred             eeEEEEEECCCCCC------------------HHHHHHHHHHHHHHHHHcCcCCceEEEEEEeccce---eEEecccc--
Confidence            68999999998874                  1346788888888888898776 788889987642   23444210  


Q ss_pred             CCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHHHH--c---CCceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIVEK--S---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~~~--~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                        ...+++    ++.+..+. .+|-|.....|+++.+..-.  .   .+.-.|+++||||..++..           ...
T Consensus        63 --~~~~~~----~~~i~~i~~~~~~t~~~~al~~~~~~~~~~~~~~~~~~~kvvvliTDG~~~~~~-----------~~~  125 (194)
T d1mf7a_          63 --QNNPNP----RSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDP-----------LGY  125 (194)
T ss_dssp             --HHSCCH----HHHHTTCCCCCSCBCHHHHHHHHHHTTTSGGGTCCTTSEEEEEEEESSCCBSCS-----------SCG
T ss_pred             --CCHHHH----HHHHhhhhhhhccchHHHHHHHHHHHHHhhhccCCCCCceEEEEEecCCCCCCc-----------hhH
Confidence              011122    22333443 46778888888888776421  1   1234688999999877621           123


Q ss_pred             HHHHHHhcCCCeeEEEEecCCC--Ccccccccc
Q 042398          252 IKSIVAASSYPLSIVLVGVGDG--PWEDMQKFD  282 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~--~f~~m~~LD  282 (422)
                      .+++..+...-+-|+.||||++  +...+++|.
T Consensus       126 ~~~~~~~~~~gv~i~~VGi~~~~~~~~~~~~L~  158 (194)
T d1mf7a_         126 EDVIPEADREGVIRYVIGVGDAFRSEKSRQELN  158 (194)
T ss_dssp             GGTHHHHHHTTEEEEEEEESGGGCSHHHHHHHH
T ss_pred             HHHHHHHHHcCCeeEEEecCCcccccccHHHHH
Confidence            4566667777899999999976  333455554

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.00  E-value=6.5e-05  Score=59.01  Aligned_cols=38  Identities=21%  Similarity=0.547  Sum_probs=28.9

Q ss_pred             CCccccccccccc---ccc-cCCCccchhhhhcC------------CCCCCccc
Q 042398          375 TQACPICLTNAKD---LAF-GCGHMTCRECGSRV------------SNCPICRQ  412 (422)
Q Consensus       375 ~~~CpIC~~~~~~---v~l-~CGH~fC~~Ci~~~------------~~CP~CR~  412 (422)
                      ...|+||++....   +.+ +|||.||..|+..+            ..||.|+-
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4589999998754   344 89999999998842            25998654

>d1yvra2 c.62.1.5 (A:364-537) 60-kda SS-A/Ro ribonucleoprotein, RoRNP {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: RoRNP C-terminal domain-like
domain: 60-kda SS-A/Ro ribonucleoprotein, RoRNP
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=96.87  E-value=0.0079  Score=50.97  Aligned_cols=139  Identities=13%  Similarity=0.160  Sum_probs=84.7

Q ss_pred             cceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCCCcceeeecCCCCCCCCCcccCCCCCCC
Q 042398          100 NLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDNLIPCFGFGDATTHDQEVFSFHDDHTPC  179 (422)
Q Consensus       100 nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~~ip~~GFGa~~~~~~~vf~~~~~~~~~  179 (422)
                      .++++||-|+|++++.           .++.....+.|+......+..   +..+-++.|+.....    .+..+    -
T Consensus         7 ~~vl~iD~SGSM~~~~-----------~~~~~~~~~~a~~~~~~~~~~---~~~~~vv~F~~~~~~----~~~~~----~   64 (174)
T d1yvra2           7 RFLLAIDVSASMNQRV-----------LGSILNASVVAAAMCMLVART---EKDSHMVAFSDEMLP----CPITV----N   64 (174)
T ss_dssp             CEEEEEECSGGGGSBS-----------TTSSCBHHHHHHHHHHHHHHH---CSSEEEEEESSSEEC----CSCCT----T
T ss_pred             eEEEEEECccccCCcc-----------cCccHHHHHHHHHHHHHhhcc---CCcEEEEEecCCccc----cccCc----c
Confidence            4899999999997531           112345566655444333333   235888999886421    12211    1


Q ss_pred             CCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHcCCceEEEEEEeCCcccccCCCCCCCCchhHHHHHHHHHHhc
Q 042398          180 HGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKSGGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTIKSIVAAS  259 (422)
Q Consensus       180 ~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~~aIv~AS  259 (422)
                      ..++++++.    +.... .|-|+++..|+++.+    ...++-++++||||+.+.      |.-+|  .+..+...+..
T Consensus        65 ~~~~~~~~~----~~~~~-~ggT~i~~al~~a~~----~~~~~~~ivllTDg~~~~------g~~~~--~~~l~~y~~~~  127 (174)
T d1yvra2          65 MLLHEVVEK----MSDIT-MGSTDCALPMLWAQK----TNTAADIFIVFTDCETNV------EDVHP--ATALKQYREKM  127 (174)
T ss_dssp             SCHHHHHHH----HTTCC-CSCCCTTHHHHHHHH----TTCCCSEEEEEECCCCCS------SSCCH--HHHHHHHHHHH
T ss_pred             chHHHHHHH----hhccc-cccccHHHHHHHHHh----hhccCCEEEEEeCCCccC------CCCCH--HHHHHHHHHHc
Confidence            346666543    22222 455998887776643    344567899999998764      22233  34556666777


Q ss_pred             CCCeeEEEEecCCCCccc
Q 042398          260 SYPLSIVLVGVGDGPWED  277 (422)
Q Consensus       260 ~~PlSIiiVGVG~~~f~~  277 (422)
                      +-|.-+++||++...+..
T Consensus       128 ~~~~~~~~i~l~~~g~~~  145 (174)
T d1yvra2         128 GIPAKLIVCAMTSNGFSI  145 (174)
T ss_dssp             TCCCEEEEEECSSSSEES
T ss_pred             CCCcEEEEEECcCCCCcc
Confidence            889999999987755553

>d1ijba_ c.62.1.1 (A:) von Willebrand factor A1 domain, vWA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: von Willebrand factor A1 domain, vWA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.78  E-value=0.0021  Score=56.33  Aligned_cols=146  Identities=9%  Similarity=0.119  Sum_probs=91.6

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccC---CCCCcceeeecCCCCCCCCCcccCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFD---EDNLIPCFGFGDATTHDQEVFSFHDD  175 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD---~D~~ip~~GFGa~~~~~~~vf~~~~~  175 (422)
                      +++++.||-|.|.+.                  ..++.+.+.+..++..|+   .+-.+-+.-||....   ..|+|+. 
T Consensus        14 ~Dl~fvlD~S~S~~~------------------~~f~~~k~fv~~~i~~l~~~~~~~rvavv~y~~~~~---~~~~l~~-   71 (202)
T d1ijba_          14 LDLVFLLDGSSRLSE------------------AEFEVLKAFVVDMMERLRVSQKWVRVAVVEYHDGSH---AYIGLKD-   71 (202)
T ss_dssp             EEEEEEEECBTTSCH------------------HHHHHHHHHHHHHHHTBCBSTTSEEEEEEEESSSEE---EEECTTC-
T ss_pred             eeEEEEEeCCCCCCH------------------HHHHHHHHHHHHHHHHhccCCCCcEEEEEEEeccee---eecCCcc-
Confidence            789999999988641                  224555566666777774   334788888988642   2355542 


Q ss_pred             CCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc---CCceEEEEEEeCCcccccCCCCCCCCchhHHHHH
Q 042398          176 HTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKTI  252 (422)
Q Consensus       176 ~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T~  252 (422)
                         -..-+++++..++. +. .-+|.|+-...|+.+.+.+-..   .+.--++++||||...+..       +   ....
T Consensus        72 ---~~~~~~l~~~i~~l-~~-~~g~~~~~~~al~~~~~~~~~~~~r~~~~k~vivitdg~~~~~~-------~---~~~~  136 (202)
T d1ijba_          72 ---RKRPSELRRIASQV-KY-AGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRM-------S---RNFV  136 (202)
T ss_dssp             ---CCCHHHHHHHHHTC-CC-CCBSCCCHHHHHHHHHHHTSSSCSCTTSEEEEEEEECCCCCGGG-------C---TTHH
T ss_pred             ---cchHHHHHHHHHhh-hh-hhhccccHHHHHHHHHHHhhhhccCCCCcceEEEecccCCCccc-------c---hHHH
Confidence               23456666655443 32 1234678888888887654322   1345788999999876521       1   2234


Q ss_pred             HHHHHhcCCCeeEEEEecCC-CCccccccc
Q 042398          253 KSIVAASSYPLSIVLVGVGD-GPWEDMQKF  281 (422)
Q Consensus       253 ~aIv~AS~~PlSIiiVGVG~-~~f~~m~~L  281 (422)
                      +++..+.+..+-|+.||||. .+-..|+.+
T Consensus       137 ~~~~~l~~~gv~i~~Vgig~~~~~~~L~~i  166 (202)
T d1ijba_         137 RYVQGLKKKKVIVIPVGIGPHANLKQIRLI  166 (202)
T ss_dssp             HHHHHHHHTTEEEEEEEESTTSCHHHHHHH
T ss_pred             HHHHHHHHcCCeEEEEEeCCcCCHHHHHHH
Confidence            45555556689999999984 444555555

>d1n3ya_ c.62.1.1 (A:) Integrin alpha-x beta2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha-x beta2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.46  E-value=0.00072  Score=58.50  Aligned_cols=135  Identities=15%  Similarity=0.234  Sum_probs=87.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCC-CcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDN-LIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~-~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      ..+++.||-|.|.+                  ...++++...+-.++..++.++ .+-+.-||....   ..|+|+... 
T Consensus         3 ~DivfvlD~S~Sm~------------------~~~~~~~k~~~~~~i~~l~~~~~rv~vv~fs~~~~---~~~~l~~~~-   60 (189)
T d1n3ya_           3 QDIVFLIDGSGSIS------------------SRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQ---THFTFEEFR-   60 (189)
T ss_dssp             EEEEEEEECCTTSC------------------HHHHHHHHHHHHHHHTTSCTTTEEEEEEEESSSEE---EEECHHHHH-
T ss_pred             ccEEEEEeCCCCCC------------------hHHHHHHHHHHHHHHHHhCCCCCEEEEEEeeccce---eeccccccc-
Confidence            57899999988874                  1347778888888899998776 588899987642   234442100 


Q ss_pred             CCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHHH--Hc---CCceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIVE--KS---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~~--~~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                         ..+.+    .+.+..+. +.|.|+....|+.+.+..-  ..   .+--.|+++||||..++..           ...
T Consensus        61 ---~~~~~----~~~i~~~~~~~g~t~~~~al~~a~~~~f~~~~~~r~~~~kvivllTDG~~~~~~-----------~~~  122 (189)
T d1n3ya_          61 ---RSSNP----LSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITDGKKEGDS-----------LDY  122 (189)
T ss_dssp             ---HCSSG----GGGGTTCCCCCSCBCHHHHHHHHHTTTTSGGGTCCTTSEEEEEEEESSCCBSCS-----------SCH
T ss_pred             ---cHHHH----HHHHHhhhhhhhhchHHHHHHHHHHHHhhhhcCCCCCCceEEEEEecCCCCCCc-----------ccH
Confidence               00011    22333332 5688998888888875431  11   1223688999999887621           234


Q ss_pred             HHHHHHhcCCCeeEEEEecCCC
Q 042398          252 IKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                      .+++..+-+.-+-|+.||+|+.
T Consensus       123 ~~~~~~~~~~gv~i~~Vgig~~  144 (189)
T d1n3ya_         123 KDVIPMADAAGIIRYAIGVGLA  144 (189)
T ss_dssp             HHHHHHHHHTTCEEEEEEESGG
T ss_pred             HHHHHHHHHCCCceEEEecccc
Confidence            5566666677889999999974

>d1jeyb2 c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Ku80 subunit N-terminal domain
domain: Ku80 subunit N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.35  E-value=0.027  Score=49.12  Aligned_cols=151  Identities=15%  Similarity=0.160  Sum_probs=86.6

Q ss_pred             ceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhcccccc---CCCCCcceeeecCCCCCCC----CCc---
Q 042398          101 LILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPF---DEDNLIPCFGFGDATTHDQ----EVF---  170 (422)
Q Consensus       101 l~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~y---D~D~~ip~~GFGa~~~~~~----~vf---  170 (422)
                      ++++||.++|+..+          |  ...++.++.|.+.+..+++..   ++.-++-+..||...+...    ..+   
T Consensus         5 iv~~lD~S~SM~~~----------~--~~~~srl~~ak~~~~~~v~~~~~~~~~d~vglV~f~~~~t~~~~~~~~~~~~i   72 (236)
T d1jeyb2           5 VVLCMDVGFTMSNS----------I--PGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNI   72 (236)
T ss_dssp             EEEEEECCGGGGCC----------B--TTBCCHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESCSSCBSTTCTTTCSTTE
T ss_pred             EEEEEECChhhccC----------C--CCCCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEcCCCcccccccccccceE
Confidence            78999999998631          1  113689999999999998876   5666899999998753221    100   


Q ss_pred             -ccCCCCCCCCCHHHHHHHHHhhCCcccccCCCChHHHHHHHHHHHHHc--CC--ceEEEEEEeCCcccccCCCCCCCCc
Q 042398          171 -SFHDDHTPCHGFEEVLACYRNIVPNLRLAGPTSYAPVVEAAMDIVEKS--GG--QYHVLVIIADGQVTRSVNTGDGELS  245 (422)
Q Consensus       171 -~~~~~~~~~~G~~gvl~~Y~~~l~~v~l~GPT~fapiI~~a~~~~~~~--~~--~Y~VLlIiTDG~i~d~~~~~~~~~~  245 (422)
                       -+.+  ...... +.+.........  -.+.|.+.-.|..|++.....  +.  .--++++||||+-+...+       
T Consensus        73 ~~~~~--~~~~~~-~~~~~~~~~~~~--~~~~~~~~~al~~a~~~~~~~~~~~~~~~r~IiL~TDG~~~~~~~-------  140 (236)
T d1jeyb2          73 TVHRH--LMLPDF-DLLEDIESKIQP--GSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKS-------  140 (236)
T ss_dssp             EEEEE--EECCCH-HHHHHHHTTCCC--CSSCCCHHHHHHHHHHHHHHHSSSSCCSEEEEEEECCCCSCCCCT-------
T ss_pred             EEEec--cccchh-hHHHHHhhhccc--cccccchhHHHHHHHHHHHHhhhcccccccEEEEEecCCCCcChH-------
Confidence             0000  011122 233322222222  245678888888888776542  11  124678889997432111       


Q ss_pred             hhHHHHHHHHHHhcCCCeeEEEEecCCCCccccc
Q 042398          246 SQEQKTIKSIVAASSYPLSIVLVGVGDGPWEDMQ  279 (422)
Q Consensus       246 ~~~~~T~~aIv~AS~~PlSIiiVGVG~~~f~~m~  279 (422)
                       +.+..   +..+.+.-+.|-+||+|..+.....
T Consensus       141 -~~~~~---a~~l~~~~I~i~~ig~g~~~~~~~~  170 (236)
T d1jeyb2         141 -QLDII---IHSLKKCDISLQFFLPFSLGKEDGS  170 (236)
T ss_dssp             -THHHH---HHHHHHTTEEEEEEESSCCC-----
T ss_pred             -HHHHH---HHHHHHcCCEEEEEecCCcCCCccc
Confidence             12233   3344456788888999876554433

>d1mjna_ c.62.1.1 (A:) Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.35  E-value=0.013  Score=49.99  Aligned_cols=128  Identities=16%  Similarity=0.233  Sum_probs=82.5

Q ss_pred             ccceeeeeccCCCCCCCCCCCCCCCcccCCCCCCHHHHHHHHHhccccccCCCC-CcceeeecCCCCCCCCCcccCCCCC
Q 042398           99 SNLILGIDFTKSNEWTGKVSFNNRSLHAIGDTPNPYEKAITIIGKTLAPFDEDN-LIPCFGFGDATTHDQEVFSFHDDHT  177 (422)
Q Consensus        99 ~nl~vaIDfT~SN~~~g~~~~~~~SLH~~~~~~N~Y~~AI~~ig~il~~yD~D~-~ip~~GFGa~~~~~~~vf~~~~~~~  177 (422)
                      +++++.||-|.|.+.                  ..++++..-+-.++..+..++ .+-+.-||....   ..|+|+..  
T Consensus         3 ~DivfllD~S~Si~~------------------~~f~~~k~f~~~~i~~i~~~~~rvgvv~fs~~~~---~~~~l~~~--   59 (179)
T d1mjna_           3 VDLVFLFDGSMSLQP------------------DEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYK---TEFDFSDY--   59 (179)
T ss_dssp             EEEEEEEECBTTCCH------------------HHHHHHHHHHHHHHHHTTTSSEEEEEEEESSSEE---EEECHHHH--
T ss_pred             eEEEEEEECCCCCCH------------------HHHHHHHHHHHHHHHHhCCCceEEEEEEEeeeee---EEechhhc--
Confidence            679999999988641                  347777777888888887666 688888987542   12444310  


Q ss_pred             CCCCHHHHHHHHHhhCCccc-ccCCCChHHHHHHHHHHH-H-Hc---CCceEEEEEEeCCcccccCCCCCCCCchhHHHH
Q 042398          178 PCHGFEEVLACYRNIVPNLR-LAGPTSYAPVVEAAMDIV-E-KS---GGQYHVLVIIADGQVTRSVNTGDGELSSQEQKT  251 (422)
Q Consensus       178 ~~~G~~gvl~~Y~~~l~~v~-l~GPT~fapiI~~a~~~~-~-~~---~~~Y~VLlIiTDG~i~d~~~~~~~~~~~~~~~T  251 (422)
                        ...+.++    +.+..++ ..|-|+....|+.+.+.. . ..   .+.-.|+++||||..+|...             
T Consensus        60 --~~~~~~~----~~i~~i~~~~g~t~~~~AL~~~~~~~f~~~~g~R~~~~kvvvllTDG~s~d~~~-------------  120 (179)
T d1mjna_          60 --VKRKDPD----ALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGN-------------  120 (179)
T ss_dssp             --HHHCCHH----HHHTTCCCCCBCCCHHHHHHHHHHHTSSGGGTCCTTSEEEEEEEESSCCSSCSC-------------
T ss_pred             --cchHHHH----HHHhhhhcccCcchHHHHHHHHHHHHhchhcCCCCCCCeEEEEEECCCCcccch-------------
Confidence              0111222    2333443 467899999999887643 1 11   12358899999999887321             


Q ss_pred             HHHHHHhcCCCeeEEEEecCCC
Q 042398          252 IKSIVAASSYPLSIVLVGVGDG  273 (422)
Q Consensus       252 ~~aIv~AS~~PlSIiiVGVG~~  273 (422)
                           .+...-+-+..||||..
T Consensus       121 -----~~~~~~i~~~~igvg~~  137 (179)
T d1mjna_         121 -----IDAAKDIIRYIIGIGKH  137 (179)
T ss_dssp             -----CGGGTTSEEEEEEESGG
T ss_pred             -----HHHHhcCccceEEeccc
Confidence                 12345677888888874

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.91  E-value=0.16  Score=37.66  Aligned_cols=29  Identities=31%  Similarity=0.772  Sum_probs=24.4

Q ss_pred             CCcccccccccccccc-cC----CCccchhhhhc
Q 042398          375 TQACPICLTNAKDLAF-GC----GHMTCRECGSR  403 (422)
Q Consensus       375 ~~~CpIC~~~~~~v~l-~C----GH~fC~~Ci~~  403 (422)
                      .+.|.+|.+.+.+..+ .|    +|.||..|...
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~   41 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRE   41 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccHH
Confidence            3799999999999665 77    68899999873