Citrus Sinensis ID: 013394

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440----
Protein Sequence
MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPASSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVASTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQSLPECECNI
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHccccEEEEEEcccEEEEEcccccccccccccccccEEEEEccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHccccEEEEEccccccHHHHHcccccccEEEEEEEcHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHcccEEEEEccccccccccccEEccccccccEEEEEccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHEEEEcccEEEEccccccccccccccccEEEEEccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHccccEEEEEEccccccEEEEcccccccEEEEEEEcccHHHHHHHHHccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHcccEEEEEccccccccccEEEEEEcccccccEEEEEccccHHHHHcccHHHHHccccccHcHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcc
Coil and Loop (DISEMBL)
MNLSVVYLLCVLLICRLASANVVlignnvtlsfddieanfapairgsgdcgvlyvaepldacsnLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLkqyagstdmeiwiipsfensawSIMAISFISLLAMSAVLATCFFVRrhrirreaprasrgrefhGMSRRLVKAMPSLIFTAVVednctsrtcaicledysvgeklrilpcrhkFHAFCVDSWLtswrtfcpvckrdartstgeppasestpllssspassSILSSIRSSlasssalhippsmshspsvshihsvastpyipqslrsycqsppisvsrssldlrhassqrshgsyimsshsigypsisplnsrymspylpspsnaspslvgssshqqhplhysesatsfspfasaqslpececni
Flexible Loop (DISEMBL)
MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFvrrhrirreaprasrgrefhgmsrrLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDartstgeppasestpllssspaSSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVASTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQSLPECECNI
Low Complexity Region (SEG)
MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVrrhrirreaprasrgrEFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEppasestpllssspasssilssirsslasssalhippsmshspsvshihsvasTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQSLPECECNI
Disordered region (IsUnstruct)
***SVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIR**************MSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK**************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*NLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGR***G***RLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD*****************************************************************************************************************************************************************PECECN*
Disordered Region (DISEMBL)
MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR*******************************************************IHSVASTPYIPQSLRSYCQ************************YIMSSHSIGYPSISPLNSRYMSPYLP***********************ESATSFSP**************
Disordered Region (DISPRO)
MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG*********************************************************************************************************P*******P*LPSPSNASP****************************QSLPECECNI
Transmembrane Helix (TMHMM)
iiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPASSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVASTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQSLPECECNI
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	444	2.2.26 [Sep-21-2011]
Q9H6Y7	350	E3 ubiquitin-protein liga	yes	no	0.594	0.754	0.323	1e-30
Q90972	381	E3 ubiquitin-protein liga	yes	no	0.569	0.664	0.325	2e-29
Q5XIL0	349	E3 ubiquitin-protein liga	yes	no	0.594	0.756	0.316	3e-29
Q91XF4	347	E3 ubiquitin-protein liga	yes	no	0.594	0.760	0.310	3e-29
Q0VD51	380	E3 ubiquitin-protein liga	no	no	0.605	0.707	0.312	4e-29
O54965	381	E3 ubiquitin-protein liga	no	no	0.619	0.721	0.307	1e-28
Q66HG0	380	E3 ubiquitin-protein liga	no	no	0.637	0.744	0.299	2e-28
Q5RCV8	381	E3 ubiquitin-protein liga	no	no	0.605	0.706	0.308	4e-28
O43567	381	E3 ubiquitin-protein liga	no	no	0.605	0.706	0.308	4e-28
Q8WWF5	429	Zinc/RING finger protein	no	no	0.583	0.603	0.312	3e-22

>sp|Q9H6Y7|RN167_HUMAN E3 ubiquitin-protein ligase RNF167 OS=Homo sapiens GN=RNF167 PE=1 SV=1

 Score =  134 bits (338), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 100/309 (32%), Positives = 140/309 (45%), Gaps = 45/309 (14%)

Query: 27  NNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGG 86
           +N ++ F D+ A F   +   G  G L  A P +ACS +        N S    L  R  
Sbjct: 32  HNASMDFADLPALFGATLSQEGLQGFLVEAHPDNACSPIAPPPPAPVNGSVFIALLRRFD 91

Query: 87  CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIK----IHAVFVSKASGEKLKQ 142
           C+F+ KV NAQKAG+ AA+V+ N +   L+ M  NS  I+    I +VF+ + S E L+ 
Sbjct: 92  CNFDLKVLNAQKAGYGAAVVH-NVNSNELLNMVWNSEEIQQQIWIPSVFIGERSSEYLRA 150

Query: 143 -YAGSTDMEIWIIP--SFENSAWSIMAISFISLL--AMSAVLATCFFVRRHRIRREAPRA 197
            +       + ++P  +F    + I     + LL  AM AV+       R R++R     
Sbjct: 151 LFVYEKGARVLLVPDNTFPLGYYLIPFTGIVGLLVLAMGAVMIARCIQHRKRLQRN---- 206

Query: 198 SRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAF 257
                      RL K     I T   +       CAICL++Y  G+KLR+LPC H +H+ 
Sbjct: 207 -----------RLTKEQLKQIPTHDYQKGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSR 255

Query: 258 CVDSWLTSWRTFCPVCKRDAR-----------------TSTGEP---PASESTPLLSSSP 297
           CVD WLT  R  CP+CK+                       GEP   PASE TPLL SSP
Sbjct: 256 CVDPWLTQTRKTCPICKQPVHRGPGDEDQEEETQGQEEGDEGEPRDHPASERTPLLGSSP 315

Query: 298 ASSSILSSI 306
              +   S+
Sbjct: 316 TLPTSFGSL 324

May act as an E3 ubiquitin-protein ligase, or as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2E1, and then transfers it to substrates, such as SLC22A18. May play a role in growth regulation involved in G1/S transition.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q90972|RNF13_CHICK E3 ubiquitin-protein ligase RNF13 OS=Gallus gallus GN=RNF13 PE=1 SV=1

 Score =  130 bits (328), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 92/283 (32%), Positives = 140/283 (49%), Gaps = 30/283 (10%)

Query: 28  NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRG-G 86
           N T +FDD+ A F   +   G  G L  ++P +AC  +     +  N S+AF++ IR   
Sbjct: 43  NGTQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLR-DNSSTAFIVLIRRLE 101

Query: 87  CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNS----AGIKIHAVFVSKASGEKLKQ 142
           C+F+ KV NAQ+AG++AAIV+ N D   L++M  N       I I +VF+ +AS   LK+
Sbjct: 102 CNFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKE 160

Query: 143 -YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGR 201
            +       + +IP F +       I F+ ++ +  +L   F + +        +     
Sbjct: 161 EFTYEKGGHVVLIPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFV------QDRHRA 213

Query: 202 EFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDS 261
             + + +  +K +P   F    E +     CAICL++Y  G+KLRILPC H +H  CVD 
Sbjct: 214 RRNRLRKDQLKKLPVHKFKKGDEYD----VCAICLDEYEDGDKLRILPCSHAYHCKCVDP 269

Query: 262 WLTSWRTFCPVCKRDARTSTG-----------EPPASESTPLL 293
           WLT  +  CPVCK+    S G           E   SE+TPLL
Sbjct: 270 WLTKTKKTCPVCKQKVVPSQGDSDSETDSSQEENEVSENTPLL 312

E3 ubiquitin-protein ligase. May play a role in controlling cell proliferation, including that of muscle cells.

Gallus gallus (taxid: 9031)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5XIL0|RN167_RAT E3 ubiquitin-protein ligase RNF167 OS=Rattus norvegicus GN=Rnf167 PE=2 SV=1

 Score =  130 bits (326), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 98/310 (31%), Positives = 146/310 (47%), Gaps = 46/310 (14%)

Query: 27  NNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGG 86
           +N ++ F D+ A F   +   G  G L  A P +ACS +        N S    L  R  
Sbjct: 32  HNASMDFADLPALFGATLSDEGLQGFLVEAHPENACSPIAPPPSAPVNGSVFIALLRRFD 91

Query: 87  CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIK----IHAVFVSKASGEKLKQ 142
           C+F+ KV NAQKAG+ AA+V+ N +   L+ M  NS  I+    I +VF+ + S E L+ 
Sbjct: 92  CNFDLKVLNAQKAGYGAAVVH-NVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRA 150

Query: 143 -YAGSTDMEIWIIP--SFENSAWSIMAISFISLLAMSAVLATCFFVR--RHRIRREAPRA 197
            +       + ++P  SF    + I     + LL ++  + T   VR  +HR R +  R 
Sbjct: 151 LFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLA--MGTVLIVRCIQHRKRLQRNR- 207

Query: 198 SRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAF 257
                   +++  +K +P+  +    E +     CAICL++Y  G+KLRILPC H +H+ 
Sbjct: 208 --------LTKEQLKQIPTHDYQKGDEYD----VCAICLDEYEDGDKLRILPCAHAYHSR 255

Query: 258 CVDSWLTSWRTFCPVCKRDARTSTG---------------------EPPASESTPLLSSS 296
           CVD WLT  R  CP+CK+      G                     + PASE TPLL SS
Sbjct: 256 CVDPWLTQTRKTCPICKQPVHRGPGDEEQEEETQGQEEEGDEGEPRDQPASEWTPLLGSS 315

Query: 297 PASSSILSSI 306
           P   +   S+
Sbjct: 316 PTLPTSFGSL 325

May act as an E3 ubiquitin-protein ligase, or as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2E1, and then transfers it to substrates, such as SLC22A18. May play a role in growth regulation involved in G1/S transition.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q91XF4|RN167_MOUSE E3 ubiquitin-protein ligase RNF167 OS=Mus musculus GN=Rnf167 PE=2 SV=1

 Score =  130 bits (326), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 96/309 (31%), Positives = 145/309 (46%), Gaps = 45/309 (14%)

Query: 27  NNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGG 86
           +N ++ F D+ A F   +   G  G L  A P +AC  +        N S    L  R  
Sbjct: 32  HNASMDFADLPALFGATLSDEGLQGFLVEAHPENACGPIAPPPSAPVNGSVFIALLRRFD 91

Query: 87  CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIK----IHAVFVSKASGEKLKQ 142
           C+F+ KV NAQKAG+ AA+V+ N +   L+ M  NS  I+    I +VF+ + S E L+ 
Sbjct: 92  CNFDLKVLNAQKAGYGAAVVH-NVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRA 150

Query: 143 -YAGSTDMEIWIIP--SFENSAWSIMAISFISLLAMSAVLATCFFVR--RHRIRREAPRA 197
            +       + ++P  SF    + I     + LL ++  + T   VR  +HR R +  R 
Sbjct: 151 LFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLA--MGTVLIVRCIQHRKRLQRNR- 207

Query: 198 SRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAF 257
                   +++  +K +P+  +    E +     CAICL++Y  G+KLR+LPC H +H+ 
Sbjct: 208 --------LTKEQLKQIPTHDYQKGDEYD----VCAICLDEYEDGDKLRVLPCAHAYHSR 255

Query: 258 CVDSWLTSWRTFCPVCKRDARTSTG--------------------EPPASESTPLLSSSP 297
           CVD WLT  R  CP+CK+      G                    + PASE TPLL SSP
Sbjct: 256 CVDPWLTQTRKTCPICKQPVHRGPGDEEQEEETQEQEEGDEGEPRDQPASEWTPLLGSSP 315

Query: 298 ASSSILSSI 306
              +   S+
Sbjct: 316 TLPTSFGSL 324

May act as an E3 ubiquitin-protein ligase, or as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2E1, and then transfers it to substrates, such as SLC22A18. May play a role in growth regulation involved in G1/S transition.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q0VD51|RNF13_BOVIN E3 ubiquitin-protein ligase RNF13 OS=Bos taurus GN=RNF13 PE=2 SV=1

 Score =  129 bits (325), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 94/301 (31%), Positives = 145/301 (48%), Gaps = 32/301 (10%)

Query: 28  NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC 87
           N + +FDD+ A F   +   G  G L  ++P +AC  +     + ++  +  VL  R  C
Sbjct: 43  NASQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPVRDNSSGTFIVLIRRLDC 102

Query: 88  SFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNS----AGIKIHAVFVSKASGEKLK-Q 142
           +F++KV NAQ+AG++AAIV+ N D   L++M  N       I I +VF+ ++S   LK +
Sbjct: 103 NFDEKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEVLKKIDIPSVFIGESSANSLKDE 161

Query: 143 YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGRE 202
           +       I ++P F +       I F+ ++ +  +L   F + +        +      
Sbjct: 162 FTYEKGGHIILVPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFV------QDRHRAR 214

Query: 203 FHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW 262
            + + +  +K +P   F    E +     CAICL++Y  G+KLRILPC H +H  CVD W
Sbjct: 215 RNRLRKDQLKKLPVHKFKKGDEYD----VCAICLDEYEDGDKLRILPCSHAYHCKCVDPW 270

Query: 263 LTSWRTFCPVCKRDARTSTG-----------EPPASESTPLL----SSSPASSSILSSIR 307
           LT  +  CPVCK+    S G           E   SE TPLL    S+S  S   LS  R
Sbjct: 271 LTKTKKTCPVCKQKVVPSQGDSDSDTDSSQEENEVSEHTPLLRPLASASTQSFGALSESR 330

Query: 308 S 308
           S
Sbjct: 331 S 331

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O54965|RNF13_MOUSE E3 ubiquitin-protein ligase RNF13 OS=Mus musculus GN=Rnf13 PE=1 SV=2

 Score =  127 bits (320), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 94/306 (30%), Positives = 145/306 (47%), Gaps = 31/306 (10%)

Query: 28  NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC 87
           N + +F+D+ A F   +   G  G L  ++P +AC  +     K ++  +  VL  R  C
Sbjct: 43  NASQTFEDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPLKDNSSGTFIVLIRRLDC 102

Query: 88  SFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNS----AGIKIHAVFVSKASGEKLK-Q 142
           +F+ KV NAQ+AG++AAIV+ N D   L++M  N       I I +VF+ ++S   LK +
Sbjct: 103 NFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIDTLKKIDIPSVFIGESSANSLKDE 161

Query: 143 YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGRE 202
           +       I ++P   +       I F+ ++ +  +L   F + +        +      
Sbjct: 162 FTYEKGGHIILVPEL-SLPLEYYLIPFLIIVGICLILIVIFMITKFV------QDRHRNR 214

Query: 203 FHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW 262
            + + +  +K +P   F    E       CAICLE+Y  G+KLRILPC H +H  CVD W
Sbjct: 215 RNRLRKDQLKKLPVHKFKKGDE----YDVCAICLEEYEDGDKLRILPCSHAYHCKCVDPW 270

Query: 263 LTSWRTFCPVCKRDARTSTG-----------EPPASESTPLLSSSPASSSILSSIRSSLA 311
           LT  +  CPVCK+    S G           E   SE TPLL   P S+S  +    SL+
Sbjct: 271 LTKTKKTCPVCKQKVVPSQGDSDSDTDSSQEENQVSEHTPLL---PPSASARTQSFGSLS 327

Query: 312 SSSALH 317
            S + H
Sbjct: 328 ESHSHH 333

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q66HG0|RNF13_RAT E3 ubiquitin-protein ligase RNF13 OS=Rattus norvegicus GN=Rnf13 PE=2 SV=1

 Score =  127 bits (319), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 94/314 (29%), Positives = 149/314 (47%), Gaps = 31/314 (9%)

Query: 28  NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC 87
           N + +F+D+ A F   +   G  G L  ++P +AC  +     K ++  +  VL  R  C
Sbjct: 43  NASQTFEDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPLKDNSSGTFIVLIRRLDC 102

Query: 88  SFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNS----AGIKIHAVFVSKASGEKLK-Q 142
           +F+ KV NAQ+AG++AAIV+ N D   L++M  N       I I +VF+ ++S   LK +
Sbjct: 103 NFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIDILKKIDIPSVFIGESSANSLKDE 161

Query: 143 YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGRE 202
           +       + ++P   +       I F+ ++ +  +L   F + +        +      
Sbjct: 162 FTYEKGGHVILVPEL-SLPLEYYLIPFLIIVGICLILIVIFMITKFV------QDRHRNR 214

Query: 203 FHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW 262
            + + +  +K +P   F    E +     CAICLE+Y  G+KLRILPC H +H  CVD W
Sbjct: 215 RNRLRKDQLKKLPVHKFKKGDEYD----VCAICLEEYEDGDKLRILPCSHAYHCKCVDPW 270

Query: 263 LTSWRTFCPVCKRDARTSTG-----------EPPASESTPLLSSSPASSSILSSIRSSLA 311
           LT  +  CPVCK+    S G           E   SE TPLL   P S+S  +    SL+
Sbjct: 271 LTKTKKTCPVCKQKVVPSQGDSDSDTDSSQEENQVSEHTPLL---PPSASARTQSFGSLS 327

Query: 312 SSSALHIPPSMSHS 325
            S + H+  S  + 
Sbjct: 328 ESHSHHMTESSDYE 341

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5RCV8|RNF13_PONAB E3 ubiquitin-protein ligase RNF13 OS=Pongo abelii GN=RNF13 PE=2 SV=1

 Score =  125 bits (315), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 93/301 (30%), Positives = 142/301 (47%), Gaps = 32/301 (10%)

Query: 28  NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC 87
           N + +FDD+ A F   +   G  G L  ++P +AC  +     K ++  +  VL  R  C
Sbjct: 43  NASQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPVKDNSSGTFIVLIRRLDC 102

Query: 88  SFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNS----AGIKIHAVFVSKASGEKLK-Q 142
           +F+ KV NAQ+AG++AAIV+ N D   L++M  N       I I +VF+ ++S   LK +
Sbjct: 103 NFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEVLKKIDIPSVFIGESSANSLKDE 161

Query: 143 YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGRE 202
           +       + ++P F +       I F+ ++ +  +L   F + +        +      
Sbjct: 162 FTYEKGGHLILVPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFV------QDRHRAR 214

Query: 203 FHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW 262
            + + +  +K +P   F    E       CAICL++Y  G+KLRILPC H +H  CVD W
Sbjct: 215 RNRLRKDQLKKLPVHKFKKGDE----YDVCAICLDEYEDGDKLRILPCSHAYHCKCVDPW 270

Query: 263 LTSWRTFCPVCKRDARTSTG-----------EPPASESTPLL----SSSPASSSILSSIR 307
           LT  +  CPVCK+    S G           E   +E TPLL    S S  S   LS  R
Sbjct: 271 LTKTKKTCPVCKQKVVPSQGDSDSDTDSSQEENEVTEHTPLLRPLASVSAQSFGALSESR 330

Query: 308 S 308
           S
Sbjct: 331 S 331

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O43567|RNF13_HUMAN E3 ubiquitin-protein ligase RNF13 OS=Homo sapiens GN=RNF13 PE=1 SV=1

 Score =  125 bits (315), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 93/301 (30%), Positives = 142/301 (47%), Gaps = 32/301 (10%)

Query: 28  NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC 87
           N + +FDD+ A F   +   G  G L  ++P +AC  +     K ++  +  VL  R  C
Sbjct: 43  NASQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPVKDNSSGTFIVLIRRLDC 102

Query: 88  SFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNS----AGIKIHAVFVSKASGEKLK-Q 142
           +F+ KV NAQ+AG++AAIV+ N D   L++M  N       I I +VF+ ++S   LK +
Sbjct: 103 NFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEVLKKIDIPSVFIGESSANSLKDE 161

Query: 143 YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRASRGRE 202
           +       + ++P F +       I F+ ++ +  +L   F + +        +      
Sbjct: 162 FTYEKGGHLILVPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFV------QDRHRAR 214

Query: 203 FHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW 262
            + + +  +K +P   F    E       CAICL++Y  G+KLRILPC H +H  CVD W
Sbjct: 215 RNRLRKDQLKKLPVHKFKKGDE----YDVCAICLDEYEDGDKLRILPCSHAYHCKCVDPW 270

Query: 263 LTSWRTFCPVCKRDARTSTG-----------EPPASESTPLL----SSSPASSSILSSIR 307
           LT  +  CPVCK+    S G           E   +E TPLL    S S  S   LS  R
Sbjct: 271 LTKTKKTCPVCKQKVVPSQGDSDSDTDSSQEENEVTEHTPLLRPLASVSAQSFGALSESR 330

Query: 308 S 308
           S
Sbjct: 331 S 331

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8WWF5|ZNRF4_HUMAN Zinc/RING finger protein 4 OS=Homo sapiens GN=ZNRF4 PE=2 SV=3

 Score =  107 bits (266), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 137/285 (48%), Gaps = 26/285 (9%)

Query: 3   LSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDAC 62
           +  + +L +L +   A    VL  N+ ++ F D+ A F   +   G  G L   +P +AC
Sbjct: 83  VKALLVLSLLQVPAQAVVRAVLEDNSSSVDFADLPALFGVPLAPEGIRGYLMEVKPANAC 142

Query: 63  SNLTSKVEKVSNMS-SAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMA-- 119
             +  +  ++ N S  A VL  R  C+F+ KV NAQ+AGFEAAIV++   D  LV+M   
Sbjct: 143 HPI--EAPRLGNRSLGAIVLIRRYDCTFDLKVLNAQRAGFEAAIVHNVHSDD-LVSMTHV 199

Query: 120 --GNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWII-----PSFENSAWSIMAISFISL 172
                  I I +VFVS+A+ + L+   G       ++     P  +     ++ +S++ L
Sbjct: 200 YEDLRGQIAIPSVFVSEAASQDLRVILGCNKSAHALLLPDDPPCHDLGCHPVLTVSWV-L 258

Query: 173 LAMSAVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVED-NCTSRT 231
               A++ + FFV  H         S         RR VK   S    A V      +  
Sbjct: 259 GCTLALVVSAFFVLNHLWLWAQACCSH--------RRPVKT--STCQKAQVRTFTWHNDL 308

Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-RTFCPVCKR 275
           CAICL++Y  G++L+ILPC H +H  C+D W +   R  CPVCK+
Sbjct: 309 CAICLDEYEEGDQLKILPCSHTYHCKCIDPWFSQAPRRSCPVCKQ 353

Homo sapiens (taxid: 9606)

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	444
225470792	446	PREDICTED: E3 ubiquitin-protein ligase R	0.986	0.982	0.793	1e-173
356576139	495	PREDICTED: E3 ubiquitin-protein ligase R	0.957	0.858	0.675	1e-171
224146378	437	predicted protein [Populus trichocarpa]	0.943	0.958	0.75	1e-171
296081075	424	unnamed protein product [Vitis vinifera]	0.903	0.945	0.775	1e-166
356535715	469	PREDICTED: E3 ubiquitin-protein ligase R	0.957	0.906	0.709	1e-165
22330577	448	protease-associated and C3HC4-type RING	0.986	0.977	0.68	1e-156
297839045	448	predicted protein [Arabidopsis lyrata su	0.986	0.977	0.675	1e-154
6942149	444	ReMembR-H2 protein JR702 [Arabidopsis th	0.977	0.977	0.677	1e-153
449528049	463	PREDICTED: E3 ubiquitin-protein ligase R	0.945	0.907	0.716	1e-152
449441754	451	PREDICTED: E3 ubiquitin-protein ligase R	0.945	0.931	0.716	1e-152

>gi|225470792|ref|XP_002269731.1| PREDICTED: E3 ubiquitin-protein ligase RNF167-like [Vitis vinifera]

 Score =  613 bits (1581), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 353/445 (79%), Positives = 391/445 (87%), Gaps = 7/445 (1%)

Query: 1   MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLD 60
           MNL +++   + L+  +A ANVVLIGNNVTLSFDDI+ANFA  ++GSG+CG+LYVAEPLD
Sbjct: 4   MNLVLLFCAFLNLMASVAFANVVLIGNNVTLSFDDIQANFAKPVKGSGECGILYVAEPLD 63

Query: 61  ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAG 120
           ACS LT+ VEKV   SS FVL +RGGC FEDKVRNAQKAGF AAIVYDNED GVLVAMAG
Sbjct: 64  ACSPLTNAVEKVEGASSPFVLIVRGGCGFEDKVRNAQKAGFAAAIVYDNEDGGVLVAMAG 123

Query: 121 NSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLA 180
           NSAGIKIHAVFVSKASG  L+ YAGS DME+WIIPSFENSAWSIMAISFISLLAMSAVLA
Sbjct: 124 NSAGIKIHAVFVSKASGMVLQTYAGSPDMELWIIPSFENSAWSIMAISFISLLAMSAVLA 183

Query: 181 TCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYS 240
           TCFFVRRHRIRR+ PR SR REFHGMS RLVKAMPSLIFT V+EDNCTSRTCAICLEDY+
Sbjct: 184 TCFFVRRHRIRRQRPRVSRVREFHGMSSRLVKAMPSLIFTTVLEDNCTSRTCAICLEDYN 243

Query: 241 VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPAS- 299
           VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG+PP SESTPLLSSSP S 
Sbjct: 244 VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGDPP-SESTPLLSSSPGSL 302

Query: 300 --SSILSSIRSSLASSSALHIPPSMSHSPSVSHI--HSVASTPYIPQSLRSYCQSPPISV 355
             SS++SS+RSSLASSSA+HI PS S S S+S    +S+++TPYI QSL+SY QS  +SV
Sbjct: 303 APSSLVSSVRSSLASSSAIHIAPSPSPSHSLSVSRNNSLSATPYIQQSLQSYRQS-SLSV 361

Query: 356 SRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQ 415
           SRSSLDLR+ASSQRSH SY++S HS+GYPS+SPLNSRY+SPY+PSPSNAS S VGSSS  
Sbjct: 362 SRSSLDLRNASSQRSHASYLVSPHSMGYPSLSPLNSRYLSPYIPSPSNASLSYVGSSSRP 421

Query: 416 QHPLHYSESATSFSPFASAQSLPEC 440
            HPLHYSESATSFSP+ SAQSLPEC
Sbjct: 422 PHPLHYSESATSFSPYTSAQSLPEC 446

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576139|ref|XP_003556191.1| PREDICTED: E3 ubiquitin-protein ligase RNF167-like [Glycine max]

 Score =  608 bits (1567), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 325/481 (67%), Positives = 373/481 (77%), Gaps = 56/481 (11%)

Query: 15  CRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSN 74
           C +A++ VVLIGNN+TLSFDDIEANFAPA++GSG  GVLY+AEPLDAC+ LT+KVE++ N
Sbjct: 16  CAMAASKVVLIGNNITLSFDDIEANFAPAVKGSGKYGVLYLAEPLDACAELTNKVEQLPN 75

Query: 75  MSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSK 134
            SS F L +RGGCSFE+KVR AQKAGF+A IVYDNE+ G+LVAMAGNSAGI+IHAVFVSK
Sbjct: 76  ASSPFALVVRGGCSFEEKVRIAQKAGFKAVIVYDNEEGGILVAMAGNSAGIRIHAVFVSK 135

Query: 135 ASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREA 194
           ASGE LK+YAG T++EIW+IP+FENSAWSIMAISFISLLAMSAVLATCFFVR+HRIRRE 
Sbjct: 136 ASGEILKKYAGLTNVEIWLIPTFENSAWSIMAISFISLLAMSAVLATCFFVRKHRIRRER 195

Query: 195 PRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKF 254
           PRAS  REFHGMS RLVKAMPSL+FT+V+EDNCTSRTCAICLEDY VGEKLRILPC HKF
Sbjct: 196 PRASLVREFHGMSSRLVKAMPSLVFTSVLEDNCTSRTCAICLEDYCVGEKLRILPCCHKF 255

Query: 255 HAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPAS--------------- 299
           HA CVDSWLTSWRTFCPVCKRDART   +PP SESTPLLSS+PAS               
Sbjct: 256 HAACVDSWLTSWRTFCPVCKRDARTGLTDPPPSESTPLLSSTPASMASSVLSSARSSLAS 315

Query: 300 ---------SSILSS-----------------IRSSLASSSALH-------------IPP 320
                    +S+ SS                  R++  +SSALH             I  
Sbjct: 316 SSAIQIARTASMASSALPSARSSLASSSAIQIARTASMASSALHSARSSLASSSAIQISR 375

Query: 321 SMSHSPSVSHIHSVASTPYIPQSLR-SYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSH 379
           + S +PSVS  HS+ASTPY+  SLR SY QSP +S+SRSS+DLR+A SQRS  S++ S  
Sbjct: 376 AASQTPSVSRNHSIASTPYVQPSLRSSYHQSPSLSISRSSVDLRNA-SQRSLASHLNSPC 434

Query: 380 SIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQSLPE 439
           S+GYPS+S LNSRYMSP++PSPSNAS S +GSSSHQQHPL YSESA SFSPFAS  SLPE
Sbjct: 435 SMGYPSLSSLNSRYMSPHIPSPSNASVSYMGSSSHQQHPLRYSESAASFSPFASTHSLPE 494

Query: 440 C 440
           C
Sbjct: 495 C 495

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146378|ref|XP_002325986.1| predicted protein [Populus trichocarpa] gi|222862861|gb|EEF00368.1| predicted protein [Populus trichocarpa]

 Score =  606 bits (1563), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 318/424 (75%), Positives = 364/424 (85%), Gaps = 5/424 (1%)

Query: 18  ASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSS 77
           AS NV+LIGNNVT++FDDIEANFAPAI+GSG+CGVLY+AEP+DACS+LT++ EK SN SS
Sbjct: 18  ASGNVLLIGNNVTMAFDDIEANFAPAIKGSGECGVLYLAEPIDACSDLTNQAEKGSNCSS 77

Query: 78  AFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASG 137
            FVL IR GCSFEDKVR AQKAG++AAI+YDNE+ G+LVAMAGNSAG+ I AVFVSK SG
Sbjct: 78  PFVLIIREGCSFEDKVRRAQKAGYKAAIIYDNEE-GILVAMAGNSAGVTIPAVFVSKTSG 136

Query: 138 EKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRA 197
           E LK+YAG TD+E+WIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRE PR+
Sbjct: 137 ETLKKYAGLTDLELWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRERPRS 196

Query: 198 SRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAF 257
           SR REFHGMS RLVKAMPSL FT+ +EDNCTS TCAICLEDY+VGEKLRILPCRHKFHAF
Sbjct: 197 SRVREFHGMSSRLVKAMPSLTFTSALEDNCTSTTCAICLEDYTVGEKLRILPCRHKFHAF 256

Query: 258 CVDSWLTSWRTFCPVCKRDARTSTGEPPASESTP-LLSSSPASSSILSSIRSSLASSSAL 316
           CVDSWLT+WRTFCPVCKRDARTSTGEPPA+ESTP L S+  + +S          +S+A+
Sbjct: 257 CVDSWLTTWRTFCPVCKRDARTSTGEPPATESTPLLSSNPSSLASSSMLSSFRSGTSTAI 316

Query: 317 HIPPSMSHSPSVSHIHSVASTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIM 376
            I P  S +PSVS+I S++STPY  QSLRSY  SP I++S+SS DLR+ SS RS  S+++
Sbjct: 317 QITP--SRTPSVSYIPSLSSTPYAQQSLRSYRHSPSITLSQSSADLRNMSSLRSRASFLV 374

Query: 377 SSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQS 436
           S HS+GYPSISPLN+RYMS Y+PSPSNASPSLV SSS Q  PLH SESA SFSPFASA S
Sbjct: 375 SPHSLGYPSISPLNTRYMSAYIPSPSNASPSLV-SSSRQPRPLHCSESAASFSPFASAHS 433

Query: 437 LPEC 440
           LP+C
Sbjct: 434 LPDC 437

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081075|emb|CBI18269.3| unnamed protein product [Vitis vinifera]

 Score =  590 bits (1522), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 332/428 (77%), Positives = 363/428 (84%), Gaps = 27/428 (6%)

Query: 17  LASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMS 76
           +A ANVVLIGNNVTLSFDDI+ANFA  ++GSG+CG+LYVAEPLDACS LT+ VEKV   S
Sbjct: 4   VAFANVVLIGNNVTLSFDDIQANFAKPVKGSGECGILYVAEPLDACSPLTNAVEKVEGAS 63

Query: 77  SAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKAS 136
           S FVL +RGGC FEDKVRNAQKAGF AAIVYDNED GVLVAMAGNSAGIKIHAVFVSKAS
Sbjct: 64  SPFVLIVRGGCGFEDKVRNAQKAGFAAAIVYDNEDGGVLVAMAGNSAGIKIHAVFVSKAS 123

Query: 137 GEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPR 196
           G  L+ YAGS DME+WIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRR+ PR
Sbjct: 124 GMVLQTYAGSPDMELWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRQRPR 183

Query: 197 ASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHA 256
            SR REFHGMS RLVKAMPSLIFT V+EDNCTSRTCAICLEDY+VGEKLRILPCRHKFHA
Sbjct: 184 VSRVREFHGMSSRLVKAMPSLIFTTVLEDNCTSRTCAICLEDYNVGEKLRILPCRHKFHA 243

Query: 257 FCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPAS---SSILSSIRSSLASS 313
           FCVDSWLTSWRTFCPVCKRDARTSTG+PP SESTPLLSSSP S   SS++SS+RSSLASS
Sbjct: 244 FCVDSWLTSWRTFCPVCKRDARTSTGDPP-SESTPLLSSSPGSLAPSSLVSSVRSSLASS 302

Query: 314 SALHIPPSMSHSPSVSHI--HSVASTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSH 371
           SA+HI PS S S S+S    +S+++TPYI Q                     +ASSQRSH
Sbjct: 303 SAIHIAPSPSPSHSLSVSRNNSLSATPYIQQ---------------------NASSQRSH 341

Query: 372 GSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPF 431
            SY++S HS+GYPS+SPLNSRY+SPY+PSPSNAS S VGSSS   HPLHYSESATSFSP+
Sbjct: 342 ASYLVSPHSMGYPSLSPLNSRYLSPYIPSPSNASLSYVGSSSRPPHPLHYSESATSFSPY 401

Query: 432 ASAQSLPE 439
            SAQSLPE
Sbjct: 402 TSAQSLPE 409

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535715|ref|XP_003536389.1| PREDICTED: E3 ubiquitin-protein ligase RNF167-like [Glycine max]

 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 323/455 (70%), Positives = 368/455 (80%), Gaps = 30/455 (6%)

Query: 15  CRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSN 74
           C +A++ VVLIGNN+TLSFDDIEANFAP ++GSG+ G+LY+AEPLDAC+ LT+KVE++ N
Sbjct: 16  CAMAASKVVLIGNNITLSFDDIEANFAPTVKGSGEYGILYLAEPLDACTELTNKVEQLPN 75

Query: 75  MSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSK 134
            SS F L +RGGCSFE+KVR AQKAGF+A IVYDNED G+LVAMAGNSAGIKIHAVFVSK
Sbjct: 76  ASSPFALVVRGGCSFEEKVRRAQKAGFKAVIVYDNEDGGILVAMAGNSAGIKIHAVFVSK 135

Query: 135 ASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREA 194
           ASGE L +YAG T++EIW+IP+FENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRE 
Sbjct: 136 ASGEILSKYAGLTNVEIWLIPTFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRER 195

Query: 195 PRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKF 254
           PRA   REFHGMS RLVKAMPSLIFTAV+EDNCTSRTCAICLEDY VGEKLRILPC HKF
Sbjct: 196 PRAPLVREFHGMSSRLVKAMPSLIFTAVLEDNCTSRTCAICLEDYCVGEKLRILPCCHKF 255

Query: 255 HAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPAS--------------- 299
           HA CVDSWLTSWRTFCPVCKRDAR+   +PP SESTPLLSS+PAS               
Sbjct: 256 HAACVDSWLTSWRTFCPVCKRDARSGLTDPPPSESTPLLSSTPASMASSVLSSARSSLAS 315

Query: 300 SSILSSIRSSLASSSAL-------------HIPPSMSHSPSVSHIHSVASTPYIPQSLR- 345
           SS +   R++  +SSAL              I  + S +PSVS  HS+ASTPY+  SLR 
Sbjct: 316 SSAIQIARTASMASSALPSARSSLASSSAIQIARAASQTPSVSRNHSIASTPYVQPSLRS 375

Query: 346 SYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNAS 405
           SY QSP +S+SRSS+DLR+A SQRS  S++ S  S+GYPS+S LNSRYMSP++PSPSNAS
Sbjct: 376 SYHQSPSLSISRSSVDLRNA-SQRSLASHLNSPRSMGYPSLSSLNSRYMSPHIPSPSNAS 434

Query: 406 PSLVGSSSHQQHPLHYSESATSFSPFASAQSLPEC 440
            S +GSSSHQQHPL YSESA SFSPFAS  SLPEC
Sbjct: 435 VSYMGSSSHQQHPLRYSESAASFSPFASTHSLPEC 469

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330577|ref|NP_177343.2| protease-associated and C3HC4-type RING finger domain-containing protein [Arabidopsis thaliana] gi|17529200|gb|AAL38826.1| unknown protein [Arabidopsis thaliana] gi|22136866|gb|AAM91777.1| unknown protein [Arabidopsis thaliana] gi|332197139|gb|AEE35260.1| protease-associated and C3HC4-type RING finger domain-containing protein [Arabidopsis thaliana]

 Score =  556 bits (1433), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 306/450 (68%), Positives = 366/450 (81%), Gaps = 12/450 (2%)

Query: 1   MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLD 60
           MN ++V LL V  +  LAS+ V+L+ NN+TLSFDDIEANFAP+++G+G+ GV+YVAEPLD
Sbjct: 1   MNRALVLLLYVCTVSCLASSKVILMRNNITLSFDDIEANFAPSVKGTGEIGVVYVAEPLD 60

Query: 61  ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAG 120
           AC NL +K E+ SN +S FVL +RGGCSFE+KVR AQ+AGF+AAI+YDNED G L+AMAG
Sbjct: 61  ACQNLMNKPEQSSNETSPFVLIVRGGCSFEEKVRKAQRAGFKAAIIYDNEDRGTLIAMAG 120

Query: 121 NSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLA 180
           NS GI+IHAVFV+K +GE LK+YAG  D ++W+IPSFENSAWSIMA+SFISLLAMSAVLA
Sbjct: 121 NSGGIRIHAVFVTKETGEVLKEYAGFPDTKVWLIPSFENSAWSIMAVSFISLLAMSAVLA 180

Query: 181 TCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYS 240
           TCFFVRRHRIRR   R+SR REFHGMSRRLVKAMPSLIF++  EDN T+ TCAICLEDY+
Sbjct: 181 TCFFVRRHRIRRRTSRSSRVREFHGMSRRLVKAMPSLIFSSFHEDNTTAFTCAICLEDYT 240

Query: 241 VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPASS 300
           VG+KLR+LPC HKFHA CVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSS  A+S
Sbjct: 241 VGDKLRLLPCCHKFHAACVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSS--AAS 298

Query: 301 SILSSIRSSLASSSALHIPPSMSHSP-SVSHIHSVASTPYIPQSLRSYC--QSPPISVSR 357
           S  SS   S   SSAL I PS+   P S+S   + AS+ YI QS +S    +SPPISVSR
Sbjct: 299 SFTSSSLHSSVRSSALLIGPSLGSLPTSISFSPAYASSSYIRQSFQSSSNRRSPPISVSR 358

Query: 358 SSLDLR-------HASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVG 410
           SS+DLR        + SQRS+ S++ S  S+GYP+ISP N+RYMSPY PSPSNASP++ G
Sbjct: 359 SSVDLRQQAASPSPSPSQRSYISHMASPQSLGYPTISPFNTRYMSPYRPSPSNASPAMAG 418

Query: 411 SSSHQQHPLHYSESATSFSPFASAQSLPEC 440
           SS++  +PL YSESA +FSP+ASA SLP+C
Sbjct: 419 SSNYPLNPLRYSESAGTFSPYASANSLPDC 448

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839045|ref|XP_002887404.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297333245|gb|EFH63663.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  550 bits (1417), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 304/450 (67%), Positives = 363/450 (80%), Gaps = 12/450 (2%)

Query: 1   MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLD 60
           MN ++V LL V  +  LAS+ V+L+ NN+TLSFDDIEANFAP+++G+G+ G++YVAEPLD
Sbjct: 1   MNRALVLLLYVYTVSCLASSKVILMRNNITLSFDDIEANFAPSVKGTGEIGLVYVAEPLD 60

Query: 61  ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAG 120
           AC NL +K E+ SN +S FVL +RGGCSFE+KVR AQ+AGF+AAI++DNED G L+AMAG
Sbjct: 61  ACQNLMNKPEQSSNETSPFVLIVRGGCSFEEKVRKAQRAGFKAAIIFDNEDRGTLIAMAG 120

Query: 121 NSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLA 180
           NS GIKIHAVFV+K +GE LK YAG  D ++W+IPSFENSAWSIMA+SFISLLAMSAVLA
Sbjct: 121 NSGGIKIHAVFVTKETGEVLKDYAGFPDTKVWLIPSFENSAWSIMAVSFISLLAMSAVLA 180

Query: 181 TCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYS 240
           TCFFVRRHRIRR   R+SR REFHGMSRRLVKAMPSLIF++  EDN T+ TCAICLEDY 
Sbjct: 181 TCFFVRRHRIRRRTSRSSRVREFHGMSRRLVKAMPSLIFSSFHEDNTTAFTCAICLEDYI 240

Query: 241 VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPASS 300
           VG+KLR+LPC HKFHA CVDSWLTSWRTFCPVCKRDART+TGEPPASESTPLLSS  A+S
Sbjct: 241 VGDKLRLLPCCHKFHAACVDSWLTSWRTFCPVCKRDARTNTGEPPASESTPLLSS--AAS 298

Query: 301 SILSSIRSSLASSSALHIPPSMSHSP-SVSHIHSVASTPYIPQSLRSYC--QSPPISVSR 357
           S  SS   S   SSAL I PSM   P SVS   +  S+ YI QS +S    +SPPISVSR
Sbjct: 299 SFTSSSLHSSVRSSALLIGPSMGSLPSSVSFSPAYVSSSYIRQSFQSSSNRRSPPISVSR 358

Query: 358 SSLDLR-------HASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVG 410
           SS+DLR        + SQRS+ S++ S  S+GYP+ISP N+RYMSPY PSPS+ASP++ G
Sbjct: 359 SSVDLRQQAASPSPSPSQRSYISHMASPQSLGYPTISPFNTRYMSPYRPSPSDASPAVAG 418

Query: 411 SSSHQQHPLHYSESATSFSPFASAQSLPEC 440
           SS++  +PL YSESA +FSP+ASA SLP+C
Sbjct: 419 SSNYPFNPLRYSESAGTFSPYASANSLPDC 448

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6942149|gb|AAF32326.1|AF218808_1 ReMembR-H2 protein JR702 [Arabidopsis thaliana]

 Score =  547 bits (1409), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 302/446 (67%), Positives = 361/446 (80%), Gaps = 12/446 (2%)

Query: 5   VVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSN 64
           +V LL V  +  LAS+ V+L+ NN+TLSFDDIEAN AP+++G+G+ GV+YVAE LDAC N
Sbjct: 1   LVLLLYVCTVSCLASSKVILMRNNITLSFDDIEANIAPSVKGTGEIGVVYVAEXLDACQN 60

Query: 65  LTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAG 124
           L +K E+ SN +S FVL +RGGCSFE+KVR AQ+AGF+AAI+YDNED G L+AMAGNS G
Sbjct: 61  LMNKXEQSSNETSPFVLIVRGGCSFEEKVRKAQRAGFKAAIIYDNEDRGTLIAMAGNSGG 120

Query: 125 IKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFF 184
           I+IHAVFV+K +GE LK+YAG  D ++W+IPSFENSAWSIMA+SFISLLAMSAVLATCFF
Sbjct: 121 IRIHAVFVTKETGEVLKEYAGFPDTKVWLIPSFENSAWSIMAVSFISLLAMSAVLATCFF 180

Query: 185 VRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEK 244
           VRRHRIRR   R+SR REFHGMSRRLVKAMPSLIF++  EDN T+ TCAICLEDY+VG+K
Sbjct: 181 VRRHRIRRRTSRSSRVREFHGMSRRLVKAMPSLIFSSFHEDNTTAFTCAICLEDYTVGDK 240

Query: 245 LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPASSSILS 304
           LR+LPC HKFHA CVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSS  A+SS  S
Sbjct: 241 LRLLPCCHKFHAACVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSS--AASSFTS 298

Query: 305 SIRSSLASSSALHIPPSMSHSP-SVSHIHSVASTPYIPQSLRSYC--QSPPISVSRSSLD 361
           S   S   SSAL I PS+   P S+S   + AS+ YI QS +S    +SPPISVSRSS+D
Sbjct: 299 SSLHSSVRSSALLIGPSLGSLPTSISFSPAYASSSYIRQSFQSSSNRRSPPISVSRSSVD 358

Query: 362 LR-------HASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSH 414
           LR        + SQRS+ S++ S  S+GYP+ISP N+RYMSPY PSPSNASP++ GSS++
Sbjct: 359 LRQQAASPSPSPSQRSYISHMASPQSLGYPTISPFNTRYMSPYRPSPSNASPAMAGSSNY 418

Query: 415 QQHPLHYSESATSFSPFASAQSLPEC 440
             +PL YSESA +FSP+ASA SLP+C
Sbjct: 419 PLNPLRYSESAGTFSPYASANSLPDC 444

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449528049|ref|XP_004171019.1| PREDICTED: E3 ubiquitin-protein ligase RNF167-like [Cucumis sativus]

 Score =  543 bits (1400), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 311/434 (71%), Positives = 358/434 (82%), Gaps = 14/434 (3%)

Query: 19  SANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSA 78
           +ANVVLIG NVTLSFD IEANFAP+I  SG+ GVLY+A+PLDACS L +KV    N SS 
Sbjct: 32  AANVVLIGANVTLSFDSIEANFAPSIESSGEPGVLYLAKPLDACSTLENKVVVPVNTSSP 91

Query: 79  FVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGE 138
           F L +RGGCSFEDKVR AQ AGF+AAI+YDNED G L+AMAG+SAGI+IHAVFV+K SGE
Sbjct: 92  FALIVRGGCSFEDKVRRAQVAGFKAAIIYDNEDGG-LIAMAGSSAGIRIHAVFVTKTSGE 150

Query: 139 KLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRAS 198
            LK+YAG  ++EIWI+PSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRR  PR+S
Sbjct: 151 TLKKYAGLANVEIWIVPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRGRPRSS 210

Query: 199 RGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFC 258
             +EF GMSRR+VKAMPSLIFT  +EDNCTS TCAICLEDY+ GEKLRILPCRHKFHA C
Sbjct: 211 HTQEFRGMSRRVVKAMPSLIFTTALEDNCTSMTCAICLEDYTPGEKLRILPCRHKFHALC 270

Query: 259 VDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLL---SSSPASSSILSSIRSSLASSSA 315
           VDSWLT+WRTFCPVCKRDARTSTG+PP S STPLL    SS ASSSILSS RSSL  SSA
Sbjct: 271 VDSWLTAWRTFCPVCKRDARTSTGDPPPSASTPLLSSAPSSVASSSILSSSRSSLPPSSA 330

Query: 316 LHIPPSMSHSPSVSHIHSVASTPYIPQSL-RSYCQSPPISVSR--------SSLDLRHAS 366
           + I P++  SPSVS  HS++STPY+ QSL  SY QSP  S  +        SS++LR+AS
Sbjct: 331 IQISPAL-RSPSVSRNHSLSSTPYLHQSLISSYHQSPRSSYHQSPSLSVSRSSVELRNAS 389

Query: 367 SQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESAT 426
           SQRS+ S+++S +S  YPS+SPL+SRYM P++PSPSNASPS++GSSSHQ +PLH S SA 
Sbjct: 390 SQRSYTSHLISPYSSCYPSVSPLHSRYMIPHIPSPSNASPSIIGSSSHQHNPLHCSGSAA 449

Query: 427 SFSPFASAQSLPEC 440
           S SPFAS +SLPEC
Sbjct: 450 SLSPFASTRSLPEC 463

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441754|ref|XP_004138647.1| PREDICTED: E3 ubiquitin-protein ligase RNF167-like [Cucumis sativus]

 Score =  543 bits (1398), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 311/434 (71%), Positives = 358/434 (82%), Gaps = 14/434 (3%)

Query: 19  SANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSA 78
           +ANVVLIG NVTLSFD IEANFAP+I  SG+ GVLY+A+PLDACS L +KV    N SS 
Sbjct: 20  AANVVLIGANVTLSFDSIEANFAPSIESSGEPGVLYLAKPLDACSTLENKVVVPVNTSSP 79

Query: 79  FVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGE 138
           F L +RGGCSFEDKVR AQ AGF+AAI+YDNED G L+AMAG+SAGI+IHAVFV+K SGE
Sbjct: 80  FALIVRGGCSFEDKVRRAQVAGFKAAIIYDNEDGG-LIAMAGSSAGIRIHAVFVTKTSGE 138

Query: 139 KLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREAPRAS 198
            LK+YAG  ++EIWI+PSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRR  PR+S
Sbjct: 139 TLKKYAGLANVEIWIVPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRGRPRSS 198

Query: 199 RGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFC 258
             +EF GMSRR+VKAMPSLIFT  +EDNCTS TCAICLEDY+ GEKLRILPCRHKFHA C
Sbjct: 199 HTQEFRGMSRRVVKAMPSLIFTTALEDNCTSMTCAICLEDYTPGEKLRILPCRHKFHALC 258

Query: 259 VDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLL---SSSPASSSILSSIRSSLASSSA 315
           VDSWLT+WRTFCPVCKRDARTSTG+PP S STPLL    SS ASSSILSS RSSL  SSA
Sbjct: 259 VDSWLTAWRTFCPVCKRDARTSTGDPPPSASTPLLSSAPSSVASSSILSSSRSSLPPSSA 318

Query: 316 LHIPPSMSHSPSVSHIHSVASTPYIPQSL-RSYCQSPPISVSR--------SSLDLRHAS 366
           + I P++  SPSVS  HS++STPY+ QSL  SY QSP  S  +        SS++LR+AS
Sbjct: 319 IQISPAL-RSPSVSRNHSLSSTPYLHQSLISSYHQSPRSSYHQSPSLSVSRSSVELRNAS 377

Query: 367 SQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESAT 426
           SQRS+ S+++S +S  YPS+SPL+SRYM P++PSPSNASPS++GSSSHQ +PLH S SA 
Sbjct: 378 SQRSYTSHLISPYSSCYPSVSPLHSRYMIPHIPSPSNASPSIIGSSSHQHNPLHCSGSAA 437

Query: 427 SFSPFASAQSLPEC 440
           S SPFAS +SLPEC
Sbjct: 438 SLSPFASTRSLPEC 451

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	444
TAIR|locus:2016044	448	AT1G71980 [Arabidopsis thalian	0.988	0.979	0.594	3.2e-136
TAIR|locus:2133697	448	AT4G09560 [Arabidopsis thalian	0.621	0.616	0.593	1.8e-99
TAIR|locus:2199665	422	AT1G22670 [Arabidopsis thalian	0.626	0.658	0.541	3e-93
TAIR|locus:2014726	318	AT1G35630 [Arabidopsis thalian	0.628	0.877	0.557	2.4e-83
TAIR|locus:2156872	310	RMR1 "receptor homology region	0.587	0.841	0.437	1.5e-53
TAIR|locus:2824666	201	AT1G35625 "AT1G35625" [Arabido	0.364	0.805	0.509	1.7e-41
FB|FBgn0037442	536	CG10277 [Drosophila melanogast	0.603	0.5	0.321	1.6e-30
UNIPROTKB|F1NA38	380	RNF13 "E3 ubiquitin-protein li	0.547	0.639	0.324	1.5e-28
UNIPROTKB|F1NUJ3	272	RNF13 "E3 ubiquitin-protein li	0.547	0.893	0.324	1.5e-28
UNIPROTKB|Q90972	381	RNF13 "E3 ubiquitin-protein li	0.547	0.637	0.324	1.5e-28

TAIR|locus:2016044 AT1G71980 [Arabidopsis thaliana (taxid:3702)]

 Score = 1334 (474.7 bits), Expect = 3.2e-136, P = 3.2e-136
 Identities = 267/449 (59%), Positives = 321/449 (71%)

Query:     1 MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLD 60
             MN ++V LL V  +  LAS+ V+L+ NN+TLSFDDIEANFAP+++G+G+ GV+YVAEPLD
Sbjct:     1 MNRALVLLLYVCTVSCLASSKVILMRNNITLSFDDIEANFAPSVKGTGEIGVVYVAEPLD 60

Query:    61 ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAG 120
             AC NL +K E+ SN +S FVL +RGGCSFE+KVR AQ+AGF+AAI+YDNED G L+AMAG
Sbjct:    61 ACQNLMNKPEQSSNETSPFVLIVRGGCSFEEKVRKAQRAGFKAAIIYDNEDRGTLIAMAG 120

Query:   121 NSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLA 180
             NS GI+IHAVFV+K +GE LK+YAG  D ++W+IPSFENSAWSIMA+SFISLLAMSAVLA
Sbjct:   121 NSGGIRIHAVFVTKETGEVLKEYAGFPDTKVWLIPSFENSAWSIMAVSFISLLAMSAVLA 180

Query:   181 TCFFVXXXXXXXXXXXXXXXXEFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYS 240
             TCFFV                EFHGMSRRLVKAMPSLIF++  EDN T+ TCAICLEDY+
Sbjct:   181 TCFFVRRHRIRRRTSRSSRVREFHGMSRRLVKAMPSLIFSSFHEDNTTAFTCAICLEDYT 240

Query:   241 VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEXXXXXXXXXXXXXXXXX 300
             VG+KLR+LPC HKFHA CVDSWLTSWRTFCPVCKRDARTSTGE                 
Sbjct:   241 VGDKLRLLPCCHKFHAACVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSAASSF 300

Query:   301 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTPYIPQSLRSYC--QSPPISVSRS 358
                                                 + YI QS +S    +SPPISVSRS
Sbjct:   301 TSSSLHSSVRSSALLIGPSLGSLPTSISFSPAYASSS-YIRQSFQSSSNRRSPPISVSRS 359

Query:   359 SLDLRH--AS-----SQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLPSPSNASPSLVGS 411
             S+DLR   AS     SQRS+ S++ S  S+GYP+ISP N+RYMSPY PSPSNASP++ GS
Sbjct:   360 SVDLRQQAASPSPSPSQRSYISHMASPQSLGYPTISPFNTRYMSPYRPSPSNASPAMAGS 419

Query:   412 SSHQQHPLHYSESATSFSPFASAQSLPEC 440
             S++  +PL YSESA +FSP+ASA SLP+C
Sbjct:   420 SNYPLNPLRYSESAGTFSPYASANSLPDC 448

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:2133697 AT4G09560 [Arabidopsis thaliana (taxid:3702)]

 Score = 850 (304.3 bits), Expect = 1.8e-99, Sum P(2) = 1.8e-99
 Identities = 165/278 (59%), Positives = 203/278 (73%)

Query:     4 SVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACS 63
             S + +L +LLI  L SA V+LIGN+ +LSFDD+EA F P I+ S   GVLYVAEPLDACS
Sbjct:     4 SSIVILSLLLISHLVSAKVLLIGNSTSLSFDDVEATFTPMIKRSDQGGVLYVAEPLDACS 63

Query:    64 NL--TSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGN 121
             +L  T  V+  + +S  +VL IRGGCSFEDK+RNAQKAG++AAIVYD ED G LV+MAGN
Sbjct:    64 DLVNTVNVKNGTTVSPPYVLIIRGGCSFEDKIRNAQKAGYKAAIVYDYEDFGFLVSMAGN 123

Query:   122 SAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLAT 181
              +G+ I+  FVSKA+GE LK+YAG TD E+W++PSFE SAWSIMAISFISLLAMSAVLAT
Sbjct:   124 PSGVLIYGTFVSKATGEVLKEYAGRTDFEVWLMPSFETSAWSIMAISFISLLAMSAVLAT 183

Query:   182 CFFVXXXXXXXXXXXXXXXXEFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSV 241
             CFFV                +FH M + ++  MP+ IF  + ++  TS  C ICLE+Y  
Sbjct:   184 CFFVRRHRVRRRRILALNGNDFHRMPKSMIIRMPTTIFNGICDEATTSILCCICLENYEK 243

Query:   242 GEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART 279
             G+KLRILPC HKFH  CVD WL   ++FCPVCKRDAR+
Sbjct:   244 GDKLRILPCHHKFHVACVDLWLGQRKSFCPVCKRDARS 281

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:2199665 AT1G22670 [Arabidopsis thaliana (taxid:3702)]

 Score = 752 (269.8 bits), Expect = 3.0e-93, Sum P(2) = 3.0e-93
 Identities = 156/288 (54%), Positives = 200/288 (69%)

Query:     1 MNLSVVYLLCVLL--ICRLASAN-VVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAE 57
             MNL V+ +L +LL  +  +  A  V+L+ +N+T SF D+EA+F+P++  + + GV+YVAE
Sbjct:     1 MNLVVLLILTLLLFIVSYVVDAGQVILVDSNITRSFVDMEADFSPSVT-TVETGVVYVAE 59

Query:    58 PLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVA 117
             PL+AC NL +K E+    +S  VL IRGGCSFE KVRNAQ++GF+AAIVYDN D   L A
Sbjct:    60 PLNACRNLRNKPEQSPYGTSPLVLIIRGGCSFEYKVRNAQRSGFKAAIVYDNVDRNFLSA 119

Query:   118 MAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIP-SFENSAWSIMA-ISFISLLAM 175
             M G+S GIKI AVFV K +GE LK+YAGS +ME+ ++P + E+S WS+ A I+ I  LA+
Sbjct:   120 MGGDSDGIKIQAVFVMKRAGEMLKKYAGSEEMEVMLVPPNTEDSVWSLYASIALILSLAI 179

Query:   176 SAVLATCFFVXXXXXXXXXXXXXXXXEFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAIC 235
               V+ TC F                 +F+GM RR VKAMPS+ FT    DN T  +CAIC
Sbjct:   180 FCVMVTCVFFYRYCSTIRNSTS----QFNGMCRRTVKAMPSVTFTCAKIDNTTGFSCAIC 235

Query:   236 LEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE 283
             LEDY VG+KLR+LPC HKFH  CVDSWL SWRTFCPVCKRDART+  E
Sbjct:   236 LEDYIVGDKLRVLPCSHKFHVACVDSWLISWRTFCPVCKRDARTTADE 283

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:2014726 AT1G35630 [Arabidopsis thaliana (taxid:3702)]

 Score = 835 (299.0 bits), Expect = 2.4e-83, P = 2.4e-83
 Identities = 156/280 (55%), Positives = 210/280 (75%)

Query:     1 MNLSVVYLLCVLLICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLD 60
             MN S + ++ +L+IC+LASA VVLIG N  LSFDD+EA F P +R SG+CG+LYVAEPL+
Sbjct:     1 MNYSWITIMSLLVICKLASAKVVLIGKNTILSFDDVEATFTPIVRNSGECGILYVAEPLE 60

Query:    61 ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAG 120
             ACS++T+  EK S   S++VL + GGCSFE+KVR AQKAG++AAIVY++  D +LV MAG
Sbjct:    61 ACSDITNMAEKRSKYRSSYVLIVLGGCSFEEKVRKAQKAGYKAAIVYNDGYDELLVPMAG 120

Query:   121 NSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLA 180
             NS+G+ IH + V++ASGE LK YA   +M++W+IP F  S+WSIM I+FISLLAMSA+LA
Sbjct:   121 NSSGVDIHGLLVTRASGEVLKGYADQDEMKLWLIPGFGISSWSIMGITFISLLAMSAILA 180

Query:   181 TCFFVXXXXXXXXXXXXXXXXE-FHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDY 239
             TCF V                +    M R L+++MP+ +++ V+E++ TS TCAIC++DY
Sbjct:   181 TCFVVRRHQIRQSVRDLPHGGQGLSCMPRDLLQSMPTEVYSGVLEESSTSVTCAICIDDY 240

Query:   240 SVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART 279
              VGEKLRILPC+HK+HA C+DSWL   R+FCPVCK++ RT
Sbjct:   241 CVGEKLRILPCKHKYHAVCIDSWLGRCRSFCPVCKQNPRT 280

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:2156872 RMR1 "receptor homology region transmembrane domain ring H2 motif protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 554 (200.1 bits), Expect = 1.5e-53, P = 1.5e-53
 Identities = 118/270 (43%), Positives = 152/270 (56%)

Query:    14 ICRLASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEK-- 71
             + R++ A VVL  N+++ SF D+ A F  ++  +G CG LYVA+PLD CS L        
Sbjct:    19 LLRVSLATVVL--NSISASFADLPAKFDGSVTKNGICGALYVADPLDGCSPLLHAAASNW 76

Query:    72 VSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVF 131
               + ++ F L IRG CSFEDK+ NAQ +GF+A IVYDN D+  L+ M  N   I + AVF
Sbjct:    77 TQHRTTKFALIIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVF 136

Query:   132 VSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVXXXXXX 191
             VS  +GE L++YA   D E  + P    SAW+++AISF SLL +   L   FF       
Sbjct:   137 VSNVAGEILRKYARGRDGECCLNPPDRGSAWTVLAISFFSLLLIVTFLLIAFFAPRHWTQ 196

Query:   192 XXXXXXXXXXEFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCR 251
                           +  +LV  +P   FT          TCAICLEDY  GE LR+LPC+
Sbjct:   197 WRGRHTRTIR----LDAKLVHTLPCFTFTDSAHHKA-GETCAICLEDYRFGESLRLLPCQ 251

Query:   252 HKFHAFCVDSWLTSWRTFCPVCKRDARTST 281
             H FH  C+DSWLT W T CPVCK D RT T
Sbjct:   252 HAFHLNCIDSWLTKWGTSCPVCKHDIRTET 281

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0000306 "extrinsic to vacuolar membrane" evidence=IDA

GO:0006886 "intracellular protein transport" evidence=IDA

GO:0006869 "lipid transport" evidence=RCA

GO:0006891 "intra-Golgi vesicle-mediated transport" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0010351 "lithium ion transport" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2824666 AT1G35625 "AT1G35625" [Arabidopsis thaliana (taxid:3702)]

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 83/163 (50%), Positives = 114/163 (69%)

Query:   118 MAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSA 177
             MAGNS+G+ IH V V++ SGE LK+Y    +ME+ +IP F  S+WSIMAI+F+SLL +SA
Sbjct:     1 MAGNSSGVYIHGVLVTRTSGEVLKEYTSRAEMELLLIPGFGISSWSIMAITFVSLLVISA 60

Query:   178 VLATCFFVXXXXXXXXXXXXXXXXEFHG-MSRRLVKAMPSLIFTAVVEDNCTSRTCAICL 236
             VLA+ F V                + H  M + L+++MP+ ++T V+E+  TS TCAIC+
Sbjct:    61 VLASYFSVRRHRIRQHVRDLHHGGQGHSRMPKDLLQSMPTEVYTGVLEEGSTSVTCAICI 120

Query:   237 EDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART 279
             +DY VGE LRILPC+HK+HA C+DSWL   R+FCPVCK++ RT
Sbjct:   121 DDYRVGEILRILPCKHKYHAVCIDSWLGRCRSFCPVCKQNPRT 163

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008233 "peptidase activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

FB|FBgn0037442 CG10277 [Drosophila melanogaster (taxid:7227)]

 Score = 340 (124.7 bits), Expect = 1.6e-30, P = 1.6e-30
 Identities = 93/289 (32%), Positives = 139/289 (48%)

Query:     5 VVYLLCVLLICRLAS--ANVVLIGNNVTLS----FDDIEANFAPAIRGSG-DCGVLYVAE 57
             ++ LL + L+C  A+     VL+    T      F+D+ A F P +  +G    V+    
Sbjct:     8 ILTLLGLCLVCHEATLVGGHVLVYRKATSQLIEEFNDLPAQFGPNLPSNGLKVYVVPARR 67

Query:    58 PLDACSNLTSKVEKVSNMSSAFV-LTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLV 116
             P   C +L          S+ FV L  RG C FE K+R AQ A + A IVY+NE D +  
Sbjct:    68 PYYGCDSLDRPPHLKYPPSAKFVALVARGECVFERKIRVAQNASYSAVIVYNNEGDDLEQ 127

Query:   117 AMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSAWSIMAISFISLLAMS 176
               A N  GI+I +VFV   +G+ L  Y  +   E+ +I + E        I+   +L  S
Sbjct:   128 MSAENITGIRIPSVFVGHTTGKALATYFTT---EVVLIINDELP----FNINTQLILPFS 180

Query:   177 AVLATCFFVXXXXXXXXXXXXXXXXEFHGMSRRLVKAMPSLIFTAVVEDNCTSR--TCAI 234
              ++  CF +                  H + + ++K +P L +T   ++N  ++  TC I
Sbjct:   181 ILIGMCFIIMVIYMIYKCIREQRRLRRHRLPKSMLKKLPVLRYT---KNNANNKYDTCVI 237

Query:   235 CLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE 283
             CLED+   +KLR+LPC H +H  C+D WLT  R  CP+CKR   T  GE
Sbjct:   238 CLEDFIEDDKLRVLPCSHPYHTHCIDPWLTENRRVCPICKRKVFTK-GE 285

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1NA38 RNF13 "E3 ubiquitin-protein ligase RNF13" [Gallus gallus (taxid:9031)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 85/262 (32%), Positives = 131/262 (50%)

Query:    28 NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRG-G 86
             N T +FDD+ A F   +   G  G L  ++P +AC  +     +  N S+AF++ IR   
Sbjct:    42 NGTQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLR-DNSSTAFIVLIRRLE 100

Query:    87 CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGI----KIHAVFVSKASGEKLKQ 142
             C+F+ KV NAQ+AG++AAIV+ N D   L++M  N   I     I +VF+ +AS   LK+
Sbjct:   101 CNFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKE 159

Query:   143 -YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVXXXXXXXXXXXXXXXX 201
              +       + +IP F +       I F+ ++ +  +L   F +                
Sbjct:   160 EFTYEKGGHVVLIPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRARR---- 214

Query:   202 EFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDS 261
               + + +  +K +P   F    E +     CAICL++Y  G+KLRILPC H +H  CVD 
Sbjct:   215 --NRLRKDQLKKLPVHKFKKGDEYD----VCAICLDEYEDGDKLRILPCSHAYHCKCVDP 268

Query:   262 WLTSWRTFCPVCKRDARTSTGE 283
             WLT  +  CPVCK+    S G+
Sbjct:   269 WLTKTKKTCPVCKQKVVPSQGD 290

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005765 "lysosomal membrane" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=IEA

UNIPROTKB|F1NUJ3 RNF13 "E3 ubiquitin-protein ligase RNF13" [Gallus gallus (taxid:9031)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 85/262 (32%), Positives = 131/262 (50%)

Query:    28 NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRG-G 86
             N T +FDD+ A F   +   G  G L  ++P +AC  +     +  N S+AF++ IR   
Sbjct:     1 NGTQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLR-DNSSTAFIVLIRRLE 59

Query:    87 CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGI----KIHAVFVSKASGEKLKQ 142
             C+F+ KV NAQ+AG++AAIV+ N D   L++M  N   I     I +VF+ +AS   LK+
Sbjct:    60 CNFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKE 118

Query:   143 -YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVXXXXXXXXXXXXXXXX 201
              +       + +IP F +       I F+ ++ +  +L   F +                
Sbjct:   119 EFTYEKGGHVVLIPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRARR---- 173

Query:   202 EFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDS 261
               + + +  +K +P   F    E +     CAICL++Y  G+KLRILPC H +H  CVD 
Sbjct:   174 --NRLRKDQLKKLPVHKFKKGDEYD----VCAICLDEYEDGDKLRILPCSHAYHCKCVDP 227

Query:   262 WLTSWRTFCPVCKRDARTSTGE 283
             WLT  +  CPVCK+    S G+
Sbjct:   228 WLTKTKKTCPVCKQKVVPSQGD 249

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005765 "lysosomal membrane" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=IEA

UNIPROTKB|Q90972 RNF13 "E3 ubiquitin-protein ligase RNF13" [Gallus gallus (taxid:9031)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 85/262 (32%), Positives = 131/262 (50%)

Query:    28 NVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRG-G 86
             N T +FDD+ A F   +   G  G L  ++P +AC  +     +  N S+AF++ IR   
Sbjct:    43 NGTQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLR-DNSSTAFIVLIRRLE 101

Query:    87 CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGI----KIHAVFVSKASGEKLKQ 142
             C+F+ KV NAQ+AG++AAIV+ N D   L++M  N   I     I +VF+ +AS   LK+
Sbjct:   102 CNFDIKVLNAQRAGYKAAIVH-NVDSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKE 160

Query:   143 -YAGSTDMEIWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVXXXXXXXXXXXXXXXX 201
              +       + +IP F +       I F+ ++ +  +L   F +                
Sbjct:   161 EFTYEKGGHVVLIPEF-SLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRARR---- 215

Query:   202 EFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDS 261
               + + +  +K +P   F    E +     CAICL++Y  G+KLRILPC H +H  CVD 
Sbjct:   216 --NRLRKDQLKKLPVHKFKKGDEYD----VCAICLDEYEDGDKLRILPCSHAYHCKCVDP 269

Query:   262 WLTSWRTFCPVCKRDARTSTGE 283
             WLT  +  CPVCK+    S G+
Sbjct:   270 WLTKTKKTCPVCKQKVVPSQGD 291

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0051865 "protein autoubiquitination" evidence=ISS

---

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	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	444
cd02123	153	cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-a	1e-51
cd00538	126	cd00538, PA, PA: Protease-associated (PA) domain	3e-18
pfam02225	96	pfam02225, PA, PA domain	1e-15
cd04818	118	cd04818, PA_subtilisin_1, PA_subtilisin_1: Proteas	2e-15
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	6e-14
cd02133	143	cd02133, PA_C5a_like, PA_C5a_like: Protease-associ	3e-13
cd02132	139	cd02132, PA_GO-like, PA_GO-like: Protease-associat	1e-12
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-12
cd02126	126	cd02126, PA_EDEM3_like, PA_EDEM3_like: protease as	6e-12
cd02125	127	cd02125, PA_VSR, PA_VSR: Protease-associated (PA)	4e-11
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	6e-11
cd02130	122	cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-as	5e-10
cd02127	118	cd02127, PA_hPAP21_like, PA_hPAP21_like: Protease-	6e-10
cd04813	117	cd04813, PA_1, PA_1: Protease-associated (PA) doma	8e-10
smart00184	40	smart00184, RING, Ring finger	2e-09
cd04816	122	cd04816, PA_SaNapH_like, PA_SaNapH_like: Protease-	1e-08
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-07
cd02124	129	cd02124, PA_PoS1_like, PA_PoS1_like: Protease-asso	9e-07
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	3e-06
cd02122	138	cd02122, PA_GRAIL_like, PA _GRAIL_like: Protease-a	9e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-04
cd02120	126	cd02120, PA_subtilisin_like, PA_subtilisin_like: P	2e-04
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	3e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	3e-04

>gnl|CDD|239038 cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like

 Score =  170 bits (434), Expect = 1e-51
 Identities = 70/155 (45%), Positives = 97/155 (62%), Gaps = 6/155 (3%)

Query: 11  VLLICRLASA-NVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKV 69
           +L++  LA+A  + L  +N+T  FDD+ ANF P   GSG  GVL VAEPL+ACS + +  
Sbjct: 1   LLVVSPLATADKLALADSNLTDEFDDLPANFGPIPPGSGLKGVLVVAEPLNACSPIENPP 60

Query: 70  EKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSA---GIK 126
              +   S  VL  RG CSFE KVRNAQ+AG++AAIVY++E +  L++M+GN     GI 
Sbjct: 61  LNSNASGSFIVLIRRGNCSFETKVRNAQRAGYKAAIVYNDESN-DLISMSGNDQEIKGID 119

Query: 127 IHAVFVSKASGEKLKQYAGSTDMEIWIIPSFENSA 161
           I +VFV K++GE LK+YA      + +IP      
Sbjct: 120 IPSVFVGKSTGEILKKYASYEKG-VILIPDLPLKI 153

This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 153

>gnl|CDD|238300 cd00538, PA, PA: Protease-associated (PA) domain

 Score = 80.3 bits (198), Expect = 3e-18
 Identities = 37/99 (37%), Positives = 49/99 (49%), Gaps = 3/99 (3%)

Query: 52  VLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNED 111
           V  VA PL  C   T+      ++    VL  RGGCSF +KV+NAQKAG +A I+Y+N D
Sbjct: 23  VGVVAGPLVGCGYGTTDDSGA-DVKGKIVLVRRGGCSFSEKVKNAQKAGAKAVIIYNNGD 81

Query: 112 DGVL--VAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTD 148
           D      ++   S    I  V +S A GE L     +  
Sbjct: 82  DPGPQMGSVGLESTDPSIPTVGISYADGEALLSLLEAGK 120

The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2. Length = 126

>gnl|CDD|216938 pfam02225, PA, PA domain

 Score = 71.8 bits (176), Expect = 1e-15
 Identities = 29/88 (32%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 53  LYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD 112
           L      D       +    S++    VL  RGGCSF +K  NAQ+AG    I+Y+N+  
Sbjct: 10  LVYVGNGDDAGGCCPEDLADSDVKGKIVLVRRGGCSFVEKAENAQRAGAAGVIIYNNDTG 69

Query: 113 GVLVAMAGNSAGIKIHAVFVSKASGEKL 140
           G+     G+ + + I  VF+S   GE L
Sbjct: 70  GLGG-TVGDPSDVTIPVVFISYEDGEAL 96

The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors. Length = 96

>gnl|CDD|240122 cd04818, PA_subtilisin_1, PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1

 Score = 72.0 bits (177), Expect = 2e-15
 Identities = 39/121 (32%), Positives = 53/121 (43%), Gaps = 8/121 (6%)

Query: 37  EANFAPAIRGSGDCGVL---YVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKV 93
            A F PA+       VL     A   D C+  T+        +    L  RG C+F  KV
Sbjct: 2   SAGFGPALTNVTADVVLAGAAPASNTDGCTAFTNAAA----FAGKIALIDRGTCNFTVKV 57

Query: 94  RNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLK-QYAGSTDMEIW 152
            NAQ AG  A IV +N   G  + M G+   I I AV +S+A G+ LK   A    + + 
Sbjct: 58  LNAQNAGAIAVIVANNVAGGAPITMGGDDPDITIPAVMISQADGDALKAALAAGGTVTVT 117

Query: 153 I 153
           +
Sbjct: 118 L 118

A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following subtilisin-like proteases: i) melon cucumisin, ii) Arabidopsis thaliana Ara12, iii) Alnus glutinosa ag12, iv) members of the tomato P69 family, and v) tomato LeSBT2. However, these proteins belong to other subtilisin-like subgroups. Relatively little is known about proteins in this subgroup. Length = 118

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

 Score = 65.5 bits (160), Expect = 6e-14
 Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
             C ICL+++  GE++ +LPC H FH  C+D WL S  T CP+C+  
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNT-CPLCRAP 46

Length = 46

>gnl|CDD|239048 cd02133, PA_C5a_like, PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase

 Score = 66.5 bits (163), Expect = 3e-13
 Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 80  VLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEK 139
            L  RG  +F +K+ NA+ AG    I+Y+N  DG L+      A + I  VF+SK  GE 
Sbjct: 51  ALIQRGEITFVEKIANAKAAGAVGVIIYNN-VDG-LIPGTLGEA-VFIPVVFISKEDGEA 107

Query: 140 LKQ 142
           LK 
Sbjct: 108 LKA 110

This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from Bacillus subtilis, ii) a large molecular mass collagenolytic protease from Geobacillus collagenovorans MO-1, and iii) PrtS, a cell envelope protease from Streptococcus thermophilus CNRZ 385. Proteins in this group belong to the peptidase S8 family. C5a peptidase is a cell surface serine protease which specifically inactivates C5a [a chemotactic peptide, which attracts polymorphonuclear leukocytes (PMNs)], by cleaving it to release a 7-residue carboxy-terminal fragment which contains the PMN binding site. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 143

>gnl|CDD|239047 cd02132, PA_GO-like, PA_GO-like: Protease-associated domain containing proteins like Arabidopsis thaliana growth-on protein GRO10

 Score = 64.8 bits (158), Expect = 1e-12
 Identities = 30/117 (25%), Positives = 52/117 (44%), Gaps = 15/117 (12%)

Query: 32  SFDDIEANFAPAIRGSGDCGV---LYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCS 88
               + A F  ++    D        +A PLD CS  TSK+      S +  L  RG C+
Sbjct: 18  ELVGVTARFGASLPSKEDNANKTRAVLANPLDCCSPSTSKL------SGSIALVERGECA 71

Query: 89  FEDKVRNAQKAGFEAAIVYDNEDDGVLVAMA----GNSAGIKIHAVFVSKASGEKLK 141
           F +K + A+  G  A ++ +++++  L  M       S  I I  V + +++G+ L 
Sbjct: 72  FTEKAKIAEAGGASALLIINDQEE--LYKMVCEDNDTSLNISIPVVMIPQSAGDALN 126

This group contains various PA domain-containing proteins similar to the functionally uncharacterized Arabidopsis GRO10. The PA domain may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 139

>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 = 60.5 bits (147), Expect = 3e-12
 Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 2/46 (4%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            C ICLE++   E + +LPC H F   C+D WL S +  CP+C+  
Sbjct: 1   ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44

Length = 45

>gnl|CDD|239041 cd02126, PA_EDEM3_like, PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins

 Score = 62.4 bits (152), Expect = 6e-12
 Identities = 33/101 (32%), Positives = 45/101 (44%), Gaps = 18/101 (17%)

Query: 51  GVLYVAEPLDACSNLTSK---VEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVY 107
           G +  A+P  ACS +T+      K++ M        RG C F +K R  QKAG    IV 
Sbjct: 19  GRVVKAKPYRACSEITNAEEVKGKIAIME-------RGDCMFVEKARRVQKAGAIGGIVI 71

Query: 108 DNE-----DDGVLVAMAGNSAG---IKIHAVFVSKASGEKL 140
           DN      D   + AM+G+      + I  VF+    G KL
Sbjct: 72  DNNEGSSSDTAPMFAMSGDGDSTDDVTIPVVFLFSKEGSKL 112

This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I alpha-mannosidases (gylcosyl hydrolase family 47), N-terminal to the PA domain. EDEM3 accelerates glycoprotein ERAD (ER-associated degradation). In transfected mammalian cells, overexpression of EDEM3 enhances the mannose trimming from the N-glycans, of a model misfolded protein [alpha1-antitrypsin null (Hong Kong)] as well as, from total glycoproteins. Mannose trimming appears to be involved in the selection of ERAD substrates. EDEM3 has a different specificity of trimming than ER alpha-mannosidase 1. The significance of the PA domain to EDEM3 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 126

>gnl|CDD|239040 cd02125, PA_VSR, PA_VSR: Protease-associated (PA) domain-containing plant vacuolar sorting receptor (VSR)

 Score = 59.8 bits (145), Expect = 4e-11
 Identities = 33/108 (30%), Positives = 48/108 (44%), Gaps = 10/108 (9%)

Query: 52  VLYVAEPLDACSNLTSKVEKVSNMSSA---FVLTIRGGCSFEDKVRNAQKAGFEAAIVYD 108
           V+Y  E    C       +   +        +L  RGGC F  K  NAQ+AG  A +V D
Sbjct: 15  VVYPKENRTGCKEFDVFFKPKKSEPGRRPVILLLDRGGCFFTLKAWNAQQAGAAAVLVAD 74

Query: 109 NEDDGVLVAMAGNSAG-------IKIHAVFVSKASGEKLKQYAGSTDM 149
           N D+ +L       +G       I I +  ++KA GEKLK+   + +M
Sbjct: 75  NVDEPLLTMDTPEESGSADYIEKITIPSALITKAFGEKLKKAISNGEM 122

This group includes various PA domain-containing VSRs such as garden pea BP-80, pumpkin PV72, and various Arabidopsis VSRs including AtVSR1. In contrast to most eukaryotes, which only have one or two VSRs, plants have several. This may in part be a reflection of having a more complex vacuolar system with both lytic vacuoles and storage vacuoles. The lytic vacuole is thought to be equivalent to the mammalian lysosome and the yeast vacuole. Pea BP-80 is a type 1 transmembrane protein, involved in the targeting of proteins to the lytic vacuole; it has been suggested that this protein also mediates targeting to the storage vacuole. PV72 and AtVSR1 may mediate transport of seed storage proteins to protein storage vacuoles. The significance of the PA domain to VSRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 127

>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 63.5 bits (154), Expect = 6e-11
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK 274
           CAIC+ ++   ++LR+LPC H+FH  CVD WL  +   CPVC+
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

>gnl|CDD|239045 cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY)

 Score = 56.5 bits (137), Expect = 5e-10
 Identities = 23/70 (32%), Positives = 34/70 (48%)

Query: 73  SNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFV 132
           ++++    L  RG C F DK   A  AG  AAI+Y+N   G L    G  +G  +  V +
Sbjct: 41  ASVAGNIALIERGECPFGDKSALAGAAGAAAAIIYNNVPAGGLSGTLGEPSGPYVPTVGI 100

Query: 133 SKASGEKLKQ 142
           S+  G+ L  
Sbjct: 101 SQEDGKALVA 110

This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 122

>gnl|CDD|239042 cd02127, PA_hPAP21_like, PA_hPAP21_like: Protease-associated domain containing proteins like the human secreted glycoprotein hPAP21 (human protease-associated domain-containing protein, 21kDa)

 Score = 56.2 bits (136), Expect = 6e-10
 Identities = 26/60 (43%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 53  LYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD 112
           L  A+PL+AC  L +  +   N+     L  RGGCSF  K  NAQKAG  A I+ D  +D
Sbjct: 15  LVPADPLEACEELRNIHDINGNI----ALIERGGCSFLTKAINAQKAGALAVIITDVNND 70

This group contains various PA domain-containing proteins similar to hPAP21. Complex N-glycosylation may be required for the secretion of hPAP21. The significance of the PA domain to hPAP21 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 118

>gnl|CDD|240117 cd04813, PA_1, PA_1: Protease-associated (PA) domain subgroup 1

 Score = 55.9 bits (135), Expect = 8e-10
 Identities = 31/86 (36%), Positives = 41/86 (47%), Gaps = 7/86 (8%)

Query: 58  PLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVA 117
           P DACS                 L +RGGC F DKV  AQ+ G +A IV D+E    L+ 
Sbjct: 26  PTDACSLQEHAEIDGK-----VALVLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRGLIT 80

Query: 118 M--AGNSAGIKIHAVFVSKASGEKLK 141
           M   G++  + I A+F S+ S   L 
Sbjct: 81  MFSNGDTDNVTIPAMFTSRTSYHLLS 106

A subgroup of PA-domain containing proteins. Proteins in this subgroup contain a RING-finger (Really Interesting New Gene) domain C-terminal to this PA domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuolar sorting receptors such as Pisum sativum BP-80, vi) prostate-specific membrane antigen (PSMA), vii) yeast aminopeptidase Y viii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, ix) various subtilisin-like proteases such as Cucumisin from the juice of melon fruits, and x) human TfR (transferrin receptor) 1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup. Length = 117

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

 Score = 52.5 bits (126), Expect = 2e-09
 Identities = 19/42 (45%), Positives = 23/42 (54%), Gaps = 2/42 (4%)

Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVC 273
           C ICLE+Y   +   ILPC H F   C+  WL S    CP+C
Sbjct: 1   CPICLEEYL--KDPVILPCGHTFCRSCIRKWLESGNNTCPIC 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|240120 cd04816, PA_SaNapH_like, PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH)

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 74  NMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVA-MAGNSAGIKIHAVFV 132
           ++  A VL  RGGC F DK + A   G  A IV +N D G     +   +  +K+    +
Sbjct: 41  DVKGAIVLVDRGGCPFADKQKVAAARGAVAVIVVNNSDGGGTAGTLGAPNIDLKVPVGVI 100

Query: 133 SKASGEKLKQYAGS 146
           +KA+G  L++  G+
Sbjct: 101 TKAAGAALRRRLGA 114

This group contains various PA domain-containing proteins similar SaNapH. Proteins in this group belong to the peptidase M28 family. NapH is a terminal enzyme in the puromycin biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin to the active antibiotic. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 122

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

 Score = 47.5 bits (113), Expect = 1e-07
 Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVC 273
           C ICLE+    + + ILPC H F + C+ SWL S    CP+C
Sbjct: 1   CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 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|239039 cd02124, PA_PoS1_like, PA_PoS1_like: Protease-associated (PA) domain PoS1-like

 Score = 47.7 bits (114), Expect = 9e-07
 Identities = 27/92 (29%), Positives = 37/92 (40%), Gaps = 9/92 (9%)

Query: 58  PLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVA 117
             DAC  L    +   ++S   VL  RG C+F  K  NA   G +  ++Y+N        
Sbjct: 40  ADDACQPLP---DDTPDLSGYIVLVRRGTCTFATKAANAAAKGAKYVLIYNNGSG--PTD 94

Query: 118 MAGNSAGIKIHAVFVSKASGEKLKQ--YAGST 147
             G+ A   I A  V+   GE       AGS 
Sbjct: 95  QVGSDAD-SIIAA-VTPEDGEAWIDALAAGSN 124

This group includes various PA domain-containing proteins similar to Pleurotus ostreatus (Po)S1. PoSl, the main extracellular protease in P. ostreatus is a subtilisin-like serine protease belonging to the peptidase S8 family. Ca2+ and Mn2+ both stimulate the protease activity of (Po)S1. Ca2+ protects PoS1 from autolysis. PoS1 is a monomeric glycoprotein, which may play a role in the regulation of laccases in lignin formation. (Po)S1 participates in the degradation of POXA1b, and in the activation of POXA3, (POXA1b and POXA3 are laccase isoenzymes), but its effect may be indirect. The significance of the PA domain to PoS1 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 129

>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 48.8 bits (116), Expect = 3e-06
 Identities = 40/166 (24%), Positives = 67/166 (40%), Gaps = 32/166 (19%)

Query: 198 SRGREFHGMSRRLVKAMPSLIFTAVVEDNCTS-RTCAICLEDY----------SVGEKLR 246
            R RE     RR  K + ++  TA  E    S RTC IC+++            +    +
Sbjct: 256 RRIREHARF-RRATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPK 314

Query: 247 ILPCRHKFHAFCVDSWLTSWRTFCPVCKR----DARTS------------TGEPPASEST 290
            LPC H  H  C+ +WL   +T CP+C+R    D  +               + P  ++T
Sbjct: 315 RLPCGHILHLHCLKNWLERQQT-CPICRRPVIFDQSSPTPASPNVRNTQIATQVPNPDNT 373

Query: 291 PLLSSSPASSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVAS 336
           P  ++ P    I +S       +S  +  P+ + S   +H   ++S
Sbjct: 374 PTTTAVPG---ITNSSNQGDPQASTFNGVPNANSSGFAAHTQDLSS 416

Length = 491

>gnl|CDD|239037 cd02122, PA_GRAIL_like, PA _GRAIL_like: Protease-associated (PA) domain GRAIL-like

 Score = 45.0 bits (107), Expect = 9e-06
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 13/57 (22%)

Query: 84  RGGCSFEDKVRNAQKAGFEAAIVYDNEDDG-------------VLVAMAGNSAGIKI 127
           RG C+FE+K++ A +    A ++Y+N   G             ++  M  N  G++I
Sbjct: 68  RGNCTFEEKIKLAAERNASAVVIYNNPGTGNETVKMSHPGTGDIVAIMITNPKGMEI 124

This group includes PA domain containing E3 (ubiquitin ligases) similar to human GRAIL (gene related to anergy in lymphocytes) protein. Proteins in this group contain a C3H2C3 RING finger. E3 ubiquitin ligase is part of an enzymic cascade, the end result of which is the ubiquitination of proteins. In this cascade, E1 activates the ubiquitin, the activated ubiquitin is carried by E2, and E3 recognizes the acceptor protein as well as catalyzes the transfer of the activated ubiquitin from E2 to this acceptor. GRAIL, a transmembrane protein localized in the endosomes, controls the development of T cell clonal anergy, and may ubiquitinate membrane-associated targets for T cell activation. GRAIL1 is associated with, and regulated by, two isoforms of otubain 1 (the ubiquitin-specific protease). Additional E3s belonging to this group include human (h)Goliath and Xenopus GREUL1 (Goliath Related E3 Ubiquitin Ligase 1). hGoliath and GRAIL both have the property of self-ubiquitination. hGoliath is expressed in leukocytes; its expression and localization is not modified in leukemia. GREUL1 may play a role in the generation of anterior ectoderm. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 138

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR 275
               C ICL+     + + + PC H F   C+  +L   ++ CP+C+ 
Sbjct: 1   EELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKK-KSKCPICRT 45

Length = 45

>gnl|CDD|239035 cd02120, PA_subtilisin_like, PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 32/130 (24%), Positives = 46/130 (35%), Gaps = 15/130 (11%)

Query: 22  VVLIGNNVTL---SFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSA 78
           VV +GN  T+   S         P +  S + G +        C   +    KV      
Sbjct: 1   VVTLGNGKTIVGQSLYPGNLKTYPLVYKSANSGDVD----ASLCLPGSLDPSKVKGK--- 53

Query: 79  FVLTIRGG-CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASG 137
            VL  RGG  S   K    + AG    I+ ++  DG+ V    +     + AV V    G
Sbjct: 54  IVLCDRGGNTSRVAKGDAVKAAGGAGMILANDPTDGLDVVADAHV----LPAVHVDYEDG 109

Query: 138 EKLKQYAGST 147
             +  Y  ST
Sbjct: 110 TAILSYINST 119

This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from Alnus glutinosa ag12, members of the tomato P69 family, and tomato LeSBT2. These proteins belong to the peptidase S8 family. Cucumisin from the juice of melon fruits is a thermostable serine peptidase, with a broad substrate specificity for oligopeptides and proteins. A. thaliana Ara12 is a thermostable, extracellular serine protease, found chiefly in silique tissue and stem tissue. Ara12 is stimulated by Ca2+ ions. A. glutinosa ag12 is expressed at high levels in the nodules, and at low levels in the shoot tips; it is implicated in both symbiotic and non-symbiotic processes in plant development. The tomato P69 protease family is comprised of various protein isoforms of approximately 69KDa. These isoforms accumulate extracellularly. Some of the P69 genes are tightly regulated in a tissue specific fashion, and by environmental and developmental signals. For example: infection with avirulent bacteria activates transcription of the genes for the P69 B and C isoforms, the P69 E transcript was detected only in roots, and the P69F transcript only in hydathodes. The Tomato LeSBT2 subtilase transcript was not detected in flowers and roots, but was present in cotyledons and leaves. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Length = 126

>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 11/54 (20%)

Query: 231 TCAICLEDY--------SVGE--KLRILPCRHKFHAFCVDSWLTSWRTFCPVCK 274
            CAIC   +        S G+   +    C H FH  C+  WL + R  CP+C+
Sbjct: 21  VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKT-RNTCPLCR 73

There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control. Length = 73

>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 11/53 (20%)

Query: 230  RTCAICLEDYSVGEKL-RILP------CRHKFHAFCVDSWL-TSWRTFCPVCK 274
              CAIC   YSV + + R LP      C++KFH  C+  W  +S R+ CP+C+
Sbjct: 1470 EECAIC---YSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519

Length = 1525

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	444
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
cd02123	153	PA_C_RZF_like PA_C-RZF_ like: Protease-associated	99.87
cd02127	118	PA_hPAP21_like PA_hPAP21_like: Protease-associated	99.83
cd02126	126	PA_EDEM3_like PA_EDEM3_like: protease associated d	99.83
cd02125	127	PA_VSR PA_VSR: Protease-associated (PA) domain-con	99.83
cd02122	138	PA_GRAIL_like PA _GRAIL_like: Protease-associated	99.8
cd04813	117	PA_1 PA_1: Protease-associated (PA) domain subgrou	99.8
cd02132	139	PA_GO-like PA_GO-like: Protease-associated domain	99.8
cd02129	120	PA_hSPPL_like PA_hSPPL_like: Protease-associated d	99.76
cd04818	118	PA_subtilisin_1 PA_subtilisin_1: Protease-associat	99.72
cd04816	122	PA_SaNapH_like PA_SaNapH_like: Protease-associated	99.69
cd02130	122	PA_ScAPY_like PA_ScAPY_like: Protease-associated d	99.65
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.58
cd04817	139	PA_VapT_like PA_VapT_like: Protease-associated dom	99.58
KOG3920	193	consensus Uncharacterized conserved protein, conta	99.55
PF02225	101	PA: PA domain; InterPro: IPR003137 The PA (Proteas	99.52
cd02124	129	PA_PoS1_like PA_PoS1_like: Protease-associated (PA	99.5
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.48
KOG2442	541	consensus Uncharacterized conserved protein, conta	99.42
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.39
cd00538	126	PA PA: Protease-associated (PA) domain. The PA dom	99.31
cd02133	143	PA_C5a_like PA_C5a_like: Protease-associated domai	99.26
PHA02929	238	N1R/p28-like protein; Provisional	99.19
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.18
cd04819	127	PA_2 PA_2: Protease-associated (PA) domain subgrou	99.09
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.97
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.97
cd04815	134	PA_M28_2 PA_M28_2: Protease-associated (PA) domain	98.94
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.93
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.92
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.87
cd02120	126	PA_subtilisin_like PA_subtilisin_like: Protease-as	98.85
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.82
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.82
cd02128	183	PA_TfR PA_TfR: Protease-associated domain containi	98.8
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.75
PF14634	44	zf-RING_5: zinc-RING finger domain	98.7
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.68
PHA02926	242	zinc finger-like protein; Provisional	98.66
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.66
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.65
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.61
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.55
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.39
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.37
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.35
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.34
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.3
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.29
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.23
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.2
cd02121	220	PA_GCPII_like PA_GCPII_like: Protease-associated d	98.13
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.12
cd04822	151	PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) do	98.12
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.1
cd04820	137	PA_M28_1_1 PA_M28_1_1: Protease-associated (PA) do	98.1
cd04814	142	PA_M28_1 PA_M28_1: Protease-associated (PA) domain	98.08
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.04
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.01
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.98
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.93
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.85
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.78
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	97.73
cd02131	153	PA_hNAALADL2_like PA_hNAALADL2_like: Protease-asso	97.72
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.71
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.69
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.69
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.6
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.6
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.3
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.27
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.25
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.25
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.21
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	96.9
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.9
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.9
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	96.89
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.87
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.85
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.67
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.49
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.43
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.2
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.97
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.83
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.78
PHA02862	156	5L protein; Provisional	95.77
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.69
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.66
PHA02825	162	LAP/PHD finger-like protein; Provisional	95.54
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.42
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.3
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.17
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.07
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.89
COG5152	259	Uncharacterized conserved protein, contains RING a	94.79
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.77
KOG4739	233	consensus Uncharacterized protein involved in syna	94.7
COG5236	493	Uncharacterized conserved protein, contains RING Z	94.64
cd04821	157	PA_M28_1_2 PA_M28_1_2: Protease-associated (PA) do	94.31
PHA03096	284	p28-like protein; Provisional	94.25
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	93.87
KOG2660	331	consensus Locus-specific chromosome binding protei	93.82
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	93.8
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	93.53
PF04641	260	Rtf2: Rtf2 RING-finger	93.47
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	93.23
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	93.19
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.87
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	92.77
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.5
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	92.45
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	91.88
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	91.45
KOG1940	276	consensus Zn-finger protein [General function pred	90.93
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	90.6
KOG1001	674	consensus Helicase-like transcription factor HLTF/	90.45
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	90.0
KOG3002	299	consensus Zn finger protein [General function pred	88.95
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	87.7
KOG0298	1394	consensus DEAD box-containing helicase-like transc	86.77
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	84.97
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	84.43
KOG0260	1605	consensus RNA polymerase II, large subunit [Transc	84.21
KOG3053	293	consensus Uncharacterized conserved protein [Funct	83.95
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	83.87
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	82.51
KOG0825	1134	consensus PHD Zn-finger protein [General function	81.41
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	80.97
KOG1609	323	consensus Protein involved in mRNA turnover and st	80.89

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

Probab=100.00  E-value=8.9e-56  Score=438.02  Aligned_cols=279  Identities=53%  Similarity=0.881  Sum_probs=251.4

Q ss_pred             ccceEEEEEeCceeeEeeccccccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHH
Q 013394           17 LASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNA   96 (444)
Q Consensus        17 ~~~a~v~~~~~~~~~~f~~~~A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~A   96 (444)
                      ..++.+.+...|++++|.+.+|.||+....++..|.+|.++|.|||+++.+.+...+....++|||+||+|+|++|+++|
T Consensus        20 ~~a~~v~~~~~n~S~sf~d~~a~f~~s~~~e~~~G~l~~~ep~~aC~~i~~~p~~~~~~~~~laLI~Rg~CsFe~Kv~~A   99 (348)
T KOG4628|consen   20 LRAVAVALVDRNTSLSFADLPALFGPSLPSEGNLGVLVVAEPLNACNPITNFPEHSTRSTSFLALIRRGGCSFEDKVLNA   99 (348)
T ss_pred             ccceEEEEccccccccccCCccccCCccccccceeeeecCCCccccCccccCccCCCCCcceEEEEEccCCchHHHHhhc
Confidence            66778888899999999999999999999999999999999999999999876666666789999999999999999999


Q ss_pred             HHcCCeEEEEeccCCCcceeeecCCCCCceEEEEEEeccccchhhhhcCcccceeeeec-cccccchhhHHHHHHHHHHH
Q 013394           97 QKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGSTDMEIWIIP-SFENSAWSIMAISFISLLAM  175 (444)
Q Consensus        97 q~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~v~Is~~~G~~L~~~l~~~~v~v~I~P-~~~~s~~~i~~IsfI~ll~l  175 (444)
                      |++|++|+|||||.+.+.++.|.++..++.|+++||+...|+.|+++.+.....+|..+ .++...|.++.+.++.++++
T Consensus       100 Q~aGfkaaIVynn~~~~~lv~~~~~~~~v~i~~~~vs~~~ge~l~~~~~~~~~~~~~~~~~~~~~~ws~~~~~~i~~l~v  179 (348)
T KOG4628|consen  100 QRAGFKAAIVYNNVGSEDLVAMASNPSKVDIHIVFVSVFSGELLSSYAGRTEFECLLIPLGFDTSPWSILAISLISLLTV  179 (348)
T ss_pred             ccccCceEEEecCCCCchheeeccCCccceeEEEEEeeehHHHHHHhhcccceeeeeccccccCCcchhhhhhhhhHHHH
Confidence            99999999999998888888999999999999999999999999999888889999888 78889999999889999999


Q ss_pred             HHHHHhhhhccccccccccccccccccccCCcHHHHhhcccceeeccccccCCCccccccccccccCceeEEeccCCeec
Q 013394          176 SAVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFH  255 (444)
Q Consensus       176 ~~vl~~~~~~~~~r~rr~~~~~~~~r~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH  255 (444)
                      ..++.+++++++++.+.+.+..   .+.+++.++.++++|..+|++..+++.. +.|+||||+|+.||++|+|||+|.||
T Consensus       180 ~~il~~~f~i~~~~~~~~~r~~---~~~~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLPC~H~FH  255 (348)
T KOG4628|consen  180 VAILVTCFFIYRIRRLIRARNR---LRRNRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILPCSHKFH  255 (348)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhH---hhhhhhHHHHHhhCCcEEeccccccCCC-ceEEEeecccccCCeeeEecCCCchh
Confidence            9999988888776654433322   4567899999999999999988877655 89999999999999999999999999


Q ss_pred             HhHHHHHHhcCCCCCCccccCCcCCCCCCCCCCCCCCCCCCCCC
Q 013394          256 AFCVDSWLTSWRTFCPVCKRDARTSTGEPPASESTPLLSSSPAS  299 (444)
Q Consensus       256 ~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~~~~~~~~~~~~~~~~~  299 (444)
                      ..|||+||.++++.||+||+++....+.+...|.+|..+..+++
T Consensus       256 ~~CIDpWL~~~r~~CPvCK~di~~~~~~~~~~e~tp~~~~~~~~  299 (348)
T KOG4628|consen  256 VNCIDPWLTQTRTFCPVCKRDIRTDSGSEPVSEDTPLLSQGPSS  299 (348)
T ss_pred             hccchhhHhhcCccCCCCCCcCCCCCCCCCccCCCccccCCCCc
Confidence            99999999999888999999999999999999988877766644

>cd02123 PA_C_RZF_like PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like

Probab=99.87  E-value=1.6e-21  Score=176.18  Aligned_cols=120  Identities=52%  Similarity=0.786  Sum_probs=103.2

Q ss_pred             eeeEeeccccccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEec
Q 013394           29 VTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYD  108 (444)
Q Consensus        29 ~~~~f~~~~A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n  108 (444)
                      ....|+..+|.||+..++.++.|.|+.++|.+||+++++.+.+..+..++||||+||+|+|.+|+++||++||+||||||
T Consensus        20 ~~~~~~~~~A~FG~~~~~~~~~g~lv~~~p~~gC~~~~~~~~~~~~~~g~IvLV~RG~CtF~~Kv~nAq~aGA~avII~n   99 (153)
T cd02123          20 LTDEFDDLPANFGPIPPGSGLKGVLVVAEPLNACSPIENPPLNSNASGSFIVLIRRGNCSFETKVRNAQRAGYKAAIVYN   99 (153)
T ss_pred             ccceEeeecccCCCCCCCCceEEEEEeCCccccCCCCcccccccccCCCeEEEEECCCCCHHHHHHHHHHCCCCEEEEEE
Confidence            44568889999999998888999999999999999998754344566899999999999999999999999999999999


Q ss_pred             cCCCcceeeecCCCC---CceEEEEEEeccccchhhhhcCcccc
Q 013394          109 NEDDGVLVAMAGNSA---GIKIHAVFVSKASGEKLKQYAGSTDM  149 (444)
Q Consensus       109 ~~~~~~~~~~~g~~~---~i~Ip~v~Is~~~G~~L~~~l~~~~v  149 (444)
                      ++++ .+..|.++..   .++||+++|++++|+.|++.++....
T Consensus       100 ~~~~-~~~~m~~~~~~~~~v~IP~v~Is~~dg~~L~~~l~~~~~  142 (153)
T cd02123         100 DESN-DLISMSGNDQEIKGIDIPSVFVGKSTGEILKKYASYEKG  142 (153)
T ss_pred             CCCC-cceeccCCCCCCcCCEEEEEEeeHHHHHHHHHHHhcCCc
Confidence            8775 4556666554   78999999999999999998877655

This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and acce

>cd02127 PA_hPAP21_like PA_hPAP21_like: Protease-associated domain containing proteins like the human secreted glycoprotein hPAP21 (human protease-associated domain-containing protein, 21kDa)

Probab=99.83  E-value=2.5e-20  Score=161.19  Aligned_cols=107  Identities=31%  Similarity=0.438  Sum_probs=90.8

Q ss_pred             ccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCC--ccee
Q 013394           39 NFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD--GVLV  116 (444)
Q Consensus        39 ~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~--~~~~  116 (444)
                      .||..++.+...|.|+.++|.+||++.++.    .+++++||||+||+|+|.+|+++||++||+||||||+.++  ....
T Consensus         1 ~~~~~~~~~~~~~~lv~~~p~~gC~~~~~~----~~~~g~I~Lv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~~~   76 (118)
T cd02127           1 DFGTIFNTRYKHVPLVPADPLEACEELRNI----HDINGNIALIERGGCSFLTKAINAQKAGALAVIITDVNNDSDEYYV   76 (118)
T ss_pred             CCCccccccccceEEEECCccccCCCCCCc----cccCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccce
Confidence            489999999999999999999999986542    3467999999999999999999999999999999998654  2344


Q ss_pred             eecCC--CCCceEEEEEEeccccchhhhhcCcccc
Q 013394          117 AMAGN--SAGIKIHAVFVSKASGEKLKQYAGSTDM  149 (444)
Q Consensus       117 ~~~g~--~~~i~Ip~v~Is~~~G~~L~~~l~~~~v  149 (444)
                      .|.++  ...++||+++|++++|+.|++.+..+..
T Consensus        77 ~m~~~~~~~~i~IP~v~Is~~dG~~L~~~l~~g~~  111 (118)
T cd02127          77 EMIQDDSSRRADIPAAFLLGKNGYMIRKTLERLGL  111 (118)
T ss_pred             EecCCCCCCCceEEEEEecHHHHHHHHHHHHcCCc
Confidence            56555  4568999999999999999998876654

This group contains various PA domain-containing proteins similar to hPAP21. Complex N-glycosylation may be required for the secretion of hPAP21. The significance of the PA domain to hPAP21 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>cd02126 PA_EDEM3_like PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins

Probab=99.83  E-value=2.4e-20  Score=163.34  Aligned_cols=109  Identities=30%  Similarity=0.491  Sum_probs=91.1

Q ss_pred             ccccccCCCCCCC-CceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCc
Q 013394           35 DIEANFAPAIRGS-GDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDG  113 (444)
Q Consensus        35 ~~~A~Fg~~~~~~-~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~  113 (444)
                      ..+|.||..++.. .+.|.|+.++|.+||+++++..    ++.++||||+||+|+|.+|+++||++||+||||||+.++.
T Consensus         2 ~~pa~FG~~~~~~~~~~g~l~~~~p~~gC~~~~~~~----~~~gkIaLv~RG~C~f~~K~~~Aq~aGA~avII~n~~~~~   77 (126)
T cd02126           2 AGPAQFGMDLTGDKAGVGRVVKAKPYRACSEITNAE----EVKGKIAIMERGDCMFVEKARRVQKAGAIGGIVIDNNEGS   77 (126)
T ss_pred             CCCcccCCcCCCCCCceEEEEeCCchhcccCCCCcc----ccCceEEEEECCCCcHHHHHHHHHHCCCcEEEEEECCCCc
Confidence            3589999988864 6899999999999999886522    3579999999999999999999999999999999876652


Q ss_pred             -----ceeeecCCC---CCceEEEEEEeccccchhhhhcCcc
Q 013394          114 -----VLVAMAGNS---AGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       114 -----~~~~~~g~~---~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                           ....|.++.   ..+.||+++|++.+|+.|++.+..+
T Consensus        78 ~~~~~~~~~m~~~~~~~~~~~IP~v~I~~~dG~~L~~~l~~~  119 (126)
T cd02126          78 SSDTAPMFAMSGDGDSTDDVTIPVVFLFSKEGSKLLAAIKEH  119 (126)
T ss_pred             cccccceeEeecCCCCCCCCeEEEEEEEHHHHHHHHHHHHhC
Confidence                 345566654   3679999999999999999987654

This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I alpha-mannosidases (gylcosyl hydrolase family 47), N-terminal to the PA domain. EDEM3 accelerates glycoprotein ERAD (ER-associated degradation). In transfected mammalian cells, overexpression of EDEM3 enhances the mannose trimming from the N-glycans, of a model misfolded protein [alpha1-antitrypsin null (Hong Kong)] as well as, from total glycoproteins. Mannose trimming appears to be involved in the selection of ERAD substrates. EDEM3 has a different specificity of trimming than ER alpha-mannosidase 1. The significance of the PA domain to EDEM3 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or pr

>cd02125 PA_VSR PA_VSR: Protease-associated (PA) domain-containing plant vacuolar sorting receptor (VSR)

Probab=99.83  E-value=2.8e-20  Score=162.93  Aligned_cols=108  Identities=33%  Similarity=0.440  Sum_probs=88.0

Q ss_pred             ccCCCCCCCCceEEEEec-CCcCCCCCCCCCC--cc-cCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcc
Q 013394           39 NFAPAIRGSGDCGVLYVA-EPLDACSNLTSKV--EK-VSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGV  114 (444)
Q Consensus        39 ~Fg~~~~~~~~~G~L~~~-~p~~aC~~l~~~~--~~-~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~  114 (444)
                      +||...+++.+.|.|+.+ ++.+||+++....  .+ .+...++||||+||+|+|.+|+++||++||+||||||+.++. 
T Consensus         1 ~FG~~~yg~~~~G~l~~~~~~~~gC~~~~~~~~~~~~~~~~~~~IvLv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~-   79 (127)
T cd02125           1 NFGLPQYGGTLTGVVVYPKENRTGCKEFDVFFKPKKSEPGRRPVILLLDRGGCFFTLKAWNAQQAGAAAVLVADNVDEP-   79 (127)
T ss_pred             CCCCCCcCCeeEEEEEecCCccccCCCCcccccccccccCCCceEEEEECCCcCHHHHHHHHHHCCCcEEEEEECCCCc-
Confidence            699999999999999776 7899999986632  11 113578999999999999999999999999999999987763 


Q ss_pred             eeeec--------CCCCCceEEEEEEeccccchhhhhcCcc
Q 013394          115 LVAMA--------GNSAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       115 ~~~~~--------g~~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      +..|.        +....++||++||++.+|+.|++.+..+
T Consensus        80 ~~~m~~~~~~~~~~~~~~i~IP~v~Is~~~G~~L~~~l~~g  120 (127)
T cd02125          80 LLTMDTPEESGSADYIEKITIPSALITKAFGEKLKKAISNG  120 (127)
T ss_pred             cccccCcccccccccCCCceEeEEEECHHHHHHHHHHHhcC
Confidence            33342        2234678999999999999999987665

This group includes various PA domain-containing VSRs such as garden pea BP-80, pumpkin PV72, and various Arabidopsis VSRs including AtVSR1. In contrast to most eukaryotes, which only have one or two VSRs, plants have several. This may in part be a reflection of having a more complex vacuolar system with both lytic vacuoles and storage vacuoles. The lytic vacuole is thought to be equivalent to the mammalian lysosome and the yeast vacuole. Pea BP-80 is a type 1 transmembrane protein, involved in the targeting of proteins to the lytic vacuole; it has been suggested that this protein also mediates targeting to the storage vacuole. PV72 and AtVSR1 may mediate transport of seed storage proteins to protein storage vacuoles. The significance of the PA domain to VSRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may partic

>cd02122 PA_GRAIL_like PA _GRAIL_like: Protease-associated (PA) domain GRAIL-like

Probab=99.80  E-value=2e-19  Score=159.66  Aligned_cols=111  Identities=19%  Similarity=0.277  Sum_probs=90.3

Q ss_pred             ccccccCCCCCCCCceEEEEec---CCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCC
Q 013394           35 DIEANFAPAIRGSGDCGVLYVA---EPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNED  111 (444)
Q Consensus        35 ~~~A~Fg~~~~~~~~~G~L~~~---~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~  111 (444)
                      ..+|.||...++.++.|.|+.+   .+.+||.++.+. ....+..++||||+||+|+|.+|+++||++||+||||||+++
T Consensus        17 ~~~a~fg~~~~~~~~~G~l~~~~~~~~~~gC~~~~~~-~~~~~~~g~IaLV~RG~C~F~~K~~nA~~aGA~aVIIyn~~~   95 (138)
T cd02122          17 TESGRYGEHSPKEEAKGLVVVPDPPNDHYGCDPDTRF-PIPPNGEPWIALIQRGNCTFEEKIKLAAERNASAVVIYNNPG   95 (138)
T ss_pred             ccccccCCCCCCCccEEEEecCCCCCCcCCCCCCccc-cCCccCCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCC
Confidence            3479999999999999998554   458999998752 112345799999999999999999999999999999999987


Q ss_pred             -CcceeeecCCCCCceEEEEEEeccccchhhhhcCcc
Q 013394          112 -DGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       112 -~~~~~~~~g~~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                       ......|..+. ...||+++|++.+|+.|++.+..+
T Consensus        96 ~~~~~~~m~~~~-~~~ip~v~Is~~~G~~l~~~l~~G  131 (138)
T cd02122          96 TGNETVKMSHPG-TGDIVAIMITNPKGMEILELLERG  131 (138)
T ss_pred             CCCceeeccCCC-CCcceEEEEcHHHHHHHHHHHHcC
Confidence             33455554443 347999999999999999988664

This group includes PA domain containing E3 (ubiquitin ligases) similar to human GRAIL (gene related to anergy in lymphocytes) protein. Proteins in this group contain a C3H2C3 RING finger. E3 ubiquitin ligase is part of an enzymic cascade, the end result of which is the ubiquitination of proteins. In this cascade, E1 activates the ubiquitin, the activated ubiquitin is carried by E2, and E3 recognizes the acceptor protein as well as catalyzes the transfer of the activated ubiquitin from E2 to this acceptor. GRAIL, a transmembrane protein localized in the endosomes, controls the development of T cell clonal anergy, and may ubiquitinate membrane-associated targets for T cell activation. GRAIL1 is associated with, and regulated by, two isoforms of otubain 1 (the ubiquitin-specific protease). Additional E3s belonging to this group include human (h)Goliath and Xenopus GREUL1 (Goliath Related E3 Ubiquitin Ligase

>cd04813 PA_1 PA_1: Protease-associated (PA) domain subgroup 1

Probab=99.80  E-value=1.9e-19  Score=155.53  Aligned_cols=106  Identities=34%  Similarity=0.507  Sum_probs=86.3

Q ss_pred             ccccccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcc
Q 013394           35 DIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGV  114 (444)
Q Consensus        35 ~~~A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~  114 (444)
                      +..|.|||..... +.+. +.++|.+||++.+.     .++.++||||+||+|+|.+|+++||++||+||||||+.++..
T Consensus         5 ~~~~~~~~~~~~~-~~~~-~~~~p~~gC~~~~~-----~~l~gkIvLV~RG~CsF~~K~~nAq~aGA~avII~n~~~~~~   77 (117)
T cd04813           5 GRYASFSPILNPH-LRGS-YKVSPTDACSLQEH-----AEIDGKVALVLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRG   77 (117)
T ss_pred             ccccccCCccCcc-cccc-ccCCCCCCCCCCCc-----CCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCccc
Confidence            3678999988765 4443 44899999998732     456899999999999999999999999999999999877644


Q ss_pred             eeeec--CCCCCceEEEEEEeccccchhhhhcCcc
Q 013394          115 LVAMA--GNSAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       115 ~~~~~--g~~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      +..|.  ++...++||+++|++++|+.|+.++++.
T Consensus        78 ~~~m~~~~~~~~v~IPav~Is~~~g~~L~~l~~~~  112 (117)
T cd04813          78 LITMFSNGDTDNVTIPAMFTSRTSYHLLSSLLPKS  112 (117)
T ss_pred             ceecccCCCCCCcEEEEEEEcHHHHHHHHHhcccc
Confidence            44454  3445789999999999999999987753

A subgroup of PA-domain containing proteins. Proteins in this subgroup contain a RING-finger (Really Interesting New Gene) domain C-terminal to this PA domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabid

>cd02132 PA_GO-like PA_GO-like: Protease-associated domain containing proteins like Arabidopsis thaliana growth-on protein GRO10

Probab=99.80  E-value=2.7e-19  Score=159.31  Aligned_cols=112  Identities=25%  Similarity=0.460  Sum_probs=92.9

Q ss_pred             ceeeEeeccccccCCCCCC---CCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEE
Q 013394           28 NVTLSFDDIEANFAPAIRG---SGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAA  104 (444)
Q Consensus        28 ~~~~~f~~~~A~Fg~~~~~---~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~av  104 (444)
                      ...-+|.+.+|.||+.++.   .++.+.|+.++|.+||+++.+      +++++||||+||+|+|.+|+++||++||+||
T Consensus        14 ~~~~~~~~~~a~FG~~~p~~~~~~~~~~lv~~~~~~gC~~~~~------~~~g~IvLV~RG~C~F~~K~~nA~~aGA~av   87 (139)
T cd02132          14 DEGDELVGVTARFGASLPSKEDNANKTRAVLANPLDCCSPSTS------KLSGSIALVERGECAFTEKAKIAEAGGASAL   87 (139)
T ss_pred             ccccEEEeeccccCCCCCCcccCccEEEEEECCcccccCCCCc------ccCCeEEEEECCCCCHHHHHHHHHHcCCcEE
Confidence            3445789999999988865   357889999999999999853      3579999999999999999999999999999


Q ss_pred             EEeccCCCcceeeecCC----CCCceEEEEEEeccccchhhhhcCcc
Q 013394          105 IVYDNEDDGVLVAMAGN----SAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       105 II~n~~~~~~~~~~~g~----~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      ||||+.++  +..|.+.    ...+.||+++|++.+|+.|++.++++
T Consensus        88 Iv~n~~~~--~~~~~~~~~~~~~~~~IP~v~Is~~~G~~L~~~l~~g  132 (139)
T cd02132          88 LIINDQEE--LYKMVCEDNDTSLNISIPVVMIPQSAGDALNKSLDQG  132 (139)
T ss_pred             EEEECCCc--ccccccCCCCCCCCCcEeEEEecHHHHHHHHHHHHcC
Confidence            99998764  3344322    12578999999999999999988664

This group contains various PA domain-containing proteins similar to the functionally uncharacterized Arabidopsis GRO10. The PA domain may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>cd02129 PA_hSPPL_like PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like

Probab=99.76  E-value=1.7e-18  Score=149.45  Aligned_cols=94  Identities=21%  Similarity=0.209  Sum_probs=77.2

Q ss_pred             eEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceEEE
Q 013394           50 CGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHA  129 (444)
Q Consensus        50 ~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~  129 (444)
                      .-.|+.++|..||++.+..+   .++.++|+||+||+|+|.+|+++||++||+|||||||++........++...++||+
T Consensus        21 ~~~~~~~~~~~gC~~~~~~~---~~l~gkIaLV~RG~CsF~~K~~~Aq~aGA~aVII~nn~~~~~~~~~~~~~~~v~IP~   97 (120)
T cd02129          21 LLPLRNLTSSVLCSASDVPP---GGLKGKAVVVMRGNCTFYEKARLAQSLGAEGLLIVSRERLVPPSGNRSEYEKIDIPV   97 (120)
T ss_pred             ceeeecCCCcCCCCccccCc---cccCCeEEEEECCCcCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCcCCcccE
Confidence            44688999999999886543   245799999999999999999999999999999999876422222233346789999


Q ss_pred             EEEeccccchhhhhcCc
Q 013394          130 VFVSKASGEKLKQYAGS  146 (444)
Q Consensus       130 v~Is~~~G~~L~~~l~~  146 (444)
                      +||++++|+.|++.+++
T Consensus        98 v~Is~~dG~~i~~~l~~  114 (120)
T cd02129          98 ALLSYKDMLDIQQTFGD  114 (120)
T ss_pred             EEEeHHHHHHHHHHhcc
Confidence            99999999999998874

This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha triggering IL-12 production. hSPPL2a and 2b may have a broad substrate spectrum. The significance of the PA domain to these SPPLs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>cd04818 PA_subtilisin_1 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1

Probab=99.72  E-value=3.4e-17  Score=141.55  Aligned_cols=113  Identities=32%  Similarity=0.461  Sum_probs=93.1

Q ss_pred             cccccCCCCCC---CCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCC
Q 013394           36 IEANFAPAIRG---SGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD  112 (444)
Q Consensus        36 ~~A~Fg~~~~~---~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~  112 (444)
                      .+|.||+.+..   ..+.|.|+.++|.++|++....    .+..+||||++||+|+|.+|+++|+++||+|+||||+.++
T Consensus         1 ~~a~fg~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~----~~v~GkIvL~~rg~c~f~~k~~~a~~aGA~gvIi~~~~~~   76 (118)
T cd04818           1 VSAGFGPALTNVTADVVLAGAAPASNTDGCTAFTNA----AAFAGKIALIDRGTCNFTVKVLNAQNAGAIAVIVANNVAG   76 (118)
T ss_pred             CCcccCCcCccccccceeEEEecCCcccccCCCCcC----CCCCCEEEEEECCCCCHHHHHHHHHHCCCeEEEEEECCCC
Confidence            37899988885   5688999999999999988652    2467999999999999999999999999999999998776


Q ss_pred             cceeeecCCCCCceEEEEEEeccccchhhhhcCc-ccceee
Q 013394          113 GVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGS-TDMEIW  152 (444)
Q Consensus       113 ~~~~~~~g~~~~i~Ip~v~Is~~~G~~L~~~l~~-~~v~v~  152 (444)
                      .....|.++.....||+++|++++|+.|++++.. ..+.++
T Consensus        77 ~~~~~~~~~~~~~~iP~v~V~~~~g~~l~~~l~~g~~v~v~  117 (118)
T cd04818          77 GAPITMGGDDPDITIPAVMISQADGDALKAALAAGGTVTVT  117 (118)
T ss_pred             CcceeccCCCCCCEEeEEEecHHHHHHHHHHHhcCCcEEEe
Confidence            4344455544456899999999999999998874 345443

A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following subtilisin-like proteases: i) melon cucumisin, ii) Arabidopsis thaliana Ara12, iii) Alnus glutinosa ag12, iv) members of the tomato P69 family, and v) tomato LeSBT2. However, these proteins belong to other subtilisin-like subgroups. Relatively little is known about proteins in this subgroup.

>cd04816 PA_SaNapH_like PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH)

Probab=99.69  E-value=1.1e-16  Score=139.41  Aligned_cols=109  Identities=28%  Similarity=0.452  Sum_probs=87.2

Q ss_pred             ccccCCCCCCCCceEEEEecCC--cCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcc
Q 013394           37 EANFAPAIRGSGDCGVLYVAEP--LDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGV  114 (444)
Q Consensus        37 ~A~Fg~~~~~~~~~G~L~~~~p--~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~  114 (444)
                      +..|++..+..+++|.|+..++  .++|++.+...   .++++|||||+||+|+|.+|+++||++||+|+||||+.++..
T Consensus         5 ~~~~~~~~~~~gi~~~lv~~~~~~~~gC~~~~~~~---~~~~GkIvLv~rg~c~f~~K~~~A~~aGA~avIi~n~~~~~~   81 (122)
T cd04816           5 SLSYSPSTPPGGVTAPLVPLDPERPAGCDASDYDG---LDVKGAIVLVDRGGCPFADKQKVAAARGAVAVIVVNNSDGGG   81 (122)
T ss_pred             EEeccCCCCCCCcEEEEEEcCCCCccCCCccccCC---CCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEeCCCCcc
Confidence            4568888888899999988765  58999875432   356899999999999999999999999999999999877432


Q ss_pred             eeeecCC-CCCceEEEEEEeccccchhhhhcCccc
Q 013394          115 LVAMAGN-SAGIKIHAVFVSKASGEKLKQYAGSTD  148 (444)
Q Consensus       115 ~~~~~g~-~~~i~Ip~v~Is~~~G~~L~~~l~~~~  148 (444)
                      ...+..+ .....||+++|++++|+.|+++++.+.
T Consensus        82 ~~~~~~~~~~~~~iP~~~Is~~~G~~l~~~l~~g~  116 (122)
T cd04816          82 TAGTLGAPNIDLKVPVGVITKAAGAALRRRLGAGE  116 (122)
T ss_pred             ccccccCCCCCCeeeEEEEcHHHHHHHHHHHcCCC
Confidence            2222222 246689999999999999999887653

This group contains various PA domain-containing proteins similar SaNapH. Proteins in this group belong to the peptidase M28 family. NapH is a terminal enzyme in the puromycin biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin to the active antibiotic. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>cd02130 PA_ScAPY_like PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY)

Probab=99.65  E-value=8.2e-16  Score=133.79  Aligned_cols=107  Identities=28%  Similarity=0.406  Sum_probs=81.8

Q ss_pred             eeccccccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCC
Q 013394           33 FDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD  112 (444)
Q Consensus        33 f~~~~A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~  112 (444)
                      |+..+..|.+.   .+.+|.|+.. +.++|.+.+..    .++.++||||+||+|+|.+|+++|+++||++|||||+.+.
T Consensus         9 ~~~~~~~~~~~---~~~~g~lv~~-~~~gC~~~~~~----~~~~gkIvlv~rg~c~f~~K~~~A~~aGA~~vIv~n~~~~   80 (122)
T cd02130           9 IPTTAFTYSPA---GEVTGPLVVV-PNLGCDAADYP----ASVAGNIALIERGECPFGDKSALAGAAGAAAAIIYNNVPA   80 (122)
T ss_pred             EeeeecccCCC---CCcEEEEEEe-CCCCCCcccCC----cCCCCEEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCC
Confidence            44444334442   3468988886 46899986543    2468999999999999999999999999999999998743


Q ss_pred             cceeeecCCCCCceEEEEEEeccccchhhhhcCcc
Q 013394          113 GVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       113 ~~~~~~~g~~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      .....+.++.....||+++|++++|+.|++.++.+
T Consensus        81 ~~~~~~~~~~~~~~Ip~v~Is~~~G~~L~~~l~~g  115 (122)
T cd02130          81 GGLSGTLGEPSGPYVPTVGISQEDGKALVAALANG  115 (122)
T ss_pred             cccccccCCCCCCEeeEEEecHHHHHHHHHHHhcC
Confidence            33333344445678999999999999999987665

This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stab

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

Probab=99.58  E-value=2.5e-16  Score=151.58  Aligned_cols=52  Identities=40%  Similarity=1.052  Sum_probs=47.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ..-+|+||+++|..+|++++|||.|.||..|+++|+.-++..||+||.++++
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            3579999999999999999999999999999999999766669999998875

>cd04817 PA_VapT_like PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530

Probab=99.58  E-value=1.3e-14  Score=128.59  Aligned_cols=102  Identities=29%  Similarity=0.361  Sum_probs=77.1

Q ss_pred             ccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCC-----HHHHHHHHHHcCCeEEEEeccCCCc
Q 013394           39 NFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCS-----FEDKVRNAQKAGFEAAIVYDNEDDG  113 (444)
Q Consensus        39 ~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~Cs-----F~~Kv~~Aq~aGA~avII~n~~~~~  113 (444)
                      .|........++|.|+.... .+|+-.      ..+.++||+||+||+|+     |.+|+++|+++||+|||||||+++.
T Consensus        26 ~~~s~~~~g~~tg~lv~~g~-~g~d~~------~~d~~GkIaLI~RG~c~~~~~~f~~Kv~~A~~aGA~avIIyNn~~~~   98 (139)
T cd04817          26 SYASMPVTGSATGSLYYCGT-SGGSYI------CGGMAGKICLIERGGNSKSVYPEIDKVKACQNAGAIAAIVYSNAALA   98 (139)
T ss_pred             cccccccCCcceEEEEEccC-CCcccc------CCCcCccEEEEECCCCCCCcccHHHHHHHHHHCCCeEEEEEeCCCCC
Confidence            34444444567899888774 347321      12457999999999999     9999999999999999999998432


Q ss_pred             -ceeeecCCCC-CceEEEEEEeccccchhhhhcCcc
Q 013394          114 -VLVAMAGNSA-GIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       114 -~~~~~~g~~~-~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                       .+..+.++.. .+.||+|+|++++|+.|+..+++.
T Consensus        99 g~~~~~lg~~~~~~~IP~v~is~~dG~~L~~~l~~~  134 (139)
T cd04817          99 GLQNPFLVDTNNDTTIPSVSVDRADGQALLAALGQS  134 (139)
T ss_pred             CcccccccCCCCCceEeEEEeeHHHHHHHHHHhcCC
Confidence             2333445443 789999999999999999987653

This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from the psychotroph Shewanella strain Ac10 and the Apa1 protease from the psychrotroph Pseudoalteromonas Sp. As-11. VapT is a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease showing high activity over a broad pH range and temperature. SapSh has a high level of protease activity at low temperatures. Apa1 is also cold-adapted. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>KOG3920 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]

Probab=99.55  E-value=2.7e-15  Score=132.05  Aligned_cols=113  Identities=26%  Similarity=0.339  Sum_probs=87.6

Q ss_pred             eeeEeecccc-ccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEe
Q 013394           29 VTLSFDDIEA-NFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVY  107 (444)
Q Consensus        29 ~~~~f~~~~A-~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~  107 (444)
                      ..++|...+| .||...+..-..-.|+.++|..||+.+.+.    -...+.|+|++||+|+|..|.++++++||.|+||-
T Consensus        43 l~Yty~~~pAkdfG~~F~~r~e~~~lV~adPp~aC~elrN~----~f~~d~vaL~eRGeCSFl~Ktl~~e~aGa~aiiit  118 (193)
T KOG3920|consen   43 LAYTYQMKPAKDFGVHFPDRFENLELVLADPPHACEELRNE----IFAPDSVALMERGECSFLVKTLNGEKAGATAIIIT  118 (193)
T ss_pred             EEEEEEecchhhhccccchhhcCcceeecCChhHHHHHhhc----ccCCCcEEEEecCCceeeehhhhhhhcCceEEEEe
Confidence            4567777777 788877654334468999999999998653    23458899999999999999999999999999998


Q ss_pred             ccCCCc----ceeeecCCC--CCceEEEEEEeccccchhhhhcC
Q 013394          108 DNEDDG----VLVAMAGNS--AGIKIHAVFVSKASGEKLKQYAG  145 (444)
Q Consensus       108 n~~~~~----~~~~~~g~~--~~i~Ip~v~Is~~~G~~L~~~l~  145 (444)
                      |+..+.    ..+.|..+.  +..+||++|+-+.+|-.++.-++
T Consensus       119 d~~~~~~sf~~YveMI~D~sq~~AniPa~fllg~~Gy~ir~sL~  162 (193)
T KOG3920|consen  119 DSQNYEYSFHQYVEMIPDESQDRANIPAVFLLGVTGYYIRVSLK  162 (193)
T ss_pred             cCCCCchhHHHHHHhcCcccccccCCceEEEeccceEEEehhHH
Confidence            865432    144555443  46789999999999988766544

>PF02225 PA: PA domain; InterPro: IPR003137 The PA (Protease associated) domain is found as an insert domain in diverse proteases, which include the MEROPS peptidase families A22B, M28, and S8A []

Probab=99.52  E-value=5e-15  Score=123.58  Aligned_cols=96  Identities=33%  Similarity=0.414  Sum_probs=67.2

Q ss_pred             CceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceE
Q 013394           48 GDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKI  127 (444)
Q Consensus        48 ~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~I  127 (444)
                      ...|.|+.+.+...+........+..+.+++||||+||+|+|.+|+++||++||+|+||+|..+...............|
T Consensus         5 ~~~~~lV~~~~~~~~~~~~~~~~~~~~~~gkIvlv~rg~~~~~~k~~~a~~~GA~gvIi~~~~~~~~~~~~~~~~~~~~i   84 (101)
T PF02225_consen    5 TVTGPLVPAGNGIDEGDCCPSDYNGSDVKGKIVLVERGSCSFDDKVRNAQKAGAKGVIIYNPPPNNGSMIDSEDPDPIDI   84 (101)
T ss_dssp             EEEEEEEEETTEEECCHHHHHHTSTSTCTTSEEEEESTSSCHHHHHHHHHHTTESEEEEE-TSCSCTTTTCEBTTTSTBS
T ss_pred             CEEEEEEEecCCCCcccccccccCCccccceEEEEecCCCCHHHHHHHHHHcCCEEEEEEeCCccccCcccccCCCCcEE
Confidence            45778885544433332222223344678999999999999999999999999999999993222222222334456799


Q ss_pred             EEEEEeccccchhhhh
Q 013394          128 HAVFVSKASGEKLKQY  143 (444)
Q Consensus       128 p~v~Is~~~G~~L~~~  143 (444)
                      |+++|++++|+.|+++
T Consensus        85 P~v~I~~~~g~~L~~~  100 (101)
T PF02225_consen   85 PVVFISYEDGEALLAY  100 (101)
T ss_dssp             EEEEE-HHHHHHHHHH
T ss_pred             EEEEeCHHHHhhhhcc
Confidence            9999999999999876

The PA domain is also found in a plant vacuolar sorting receptor O22925 from SWISSPROT and members of the RZF family, e.g. O43567 from SWISSPROT.; PDB: 3EIF_A 1XF1_B 3BXM_A 2C6P_A 1Z8L_C 3SJF_A 3BHX_A 2C6G_A 3D7F_A 2XEG_A ....

>cd02124 PA_PoS1_like PA_PoS1_like: Protease-associated (PA) domain PoS1-like

Probab=99.50  E-value=5.9e-14  Score=123.35  Aligned_cols=89  Identities=27%  Similarity=0.393  Sum_probs=67.7

Q ss_pred             EEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceEEEEE
Q 013394           52 VLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVF  131 (444)
Q Consensus        52 ~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~v~  131 (444)
                      .+..+++.+||+++..   +..+++++||||+||+|+|.+|+++|+++||++|||||+.++..  .+.+... ..+++++
T Consensus        34 ~~~~~~~~~gC~~~~~---~~~~~~g~IaLv~rg~c~f~~K~~nA~~aGA~aviiyn~~~~~~--~~~~~~~-~~~~~~~  107 (129)
T cd02124          34 SLDTSVADDACQPLPD---DTPDLSGYIVLVRRGTCTFATKAANAAAKGAKYVLIYNNGSGPT--DQVGSDA-DSIIAAV  107 (129)
T ss_pred             ecccCCCcccCcCCCc---ccccccCeEEEEECCCCCHHHHHHHHHHcCCcEEEEEECCCCcc--cccCCCC-cceeeEE
Confidence            3445578899998743   22356899999999999999999999999999999999876532  2223333 3455666


Q ss_pred             EeccccchhhhhcCcc
Q 013394          132 VSKASGEKLKQYAGST  147 (444)
Q Consensus       132 Is~~~G~~L~~~l~~~  147 (444)
                      + +++|+.|++.+..+
T Consensus       108 ~-~~~G~~l~~~l~~G  122 (129)
T cd02124         108 T-PEDGEAWIDALAAG  122 (129)
T ss_pred             e-HHHHHHHHHHHhcC
Confidence            6 99999999887654

This group includes various PA domain-containing proteins similar to Pleurotus ostreatus (Po)S1. PoSl, the main extracellular protease in P. ostreatus is a subtilisin-like serine protease belonging to the peptidase S8 family. Ca2+ and Mn2+ both stimulate the protease activity of (Po)S1. Ca2+ protects PoS1 from autolysis. PoS1 is a monomeric glycoprotein, which may play a role in the regulation of laccases in lignin formation. (Po)S1 participates in the degradation of POXA1b, and in the activation of POXA3, (POXA1b and POXA3 are laccase isoenzymes), but its effect may be indirect. The significance of the PA domain to PoS1 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>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=99.48  E-value=1.6e-14  Score=103.16  Aligned_cols=44  Identities=48%  Similarity=1.140  Sum_probs=39.6

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccc
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK  274 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR  274 (444)
                      ++|+||+++|..++.+..++|+|+||.+||.+|+++++ +||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~-~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNN-SCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSS-B-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCC-cCCccC
Confidence            47999999999999999999999999999999999965 599997

...

>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]

Probab=99.42  E-value=4.6e-13  Score=136.58  Aligned_cols=117  Identities=29%  Similarity=0.495  Sum_probs=86.6

Q ss_pred             eccccccCCCCCCCCceEEE---EecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccC
Q 013394           34 DDIEANFAPAIRGSGDCGVL---YVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNE  110 (444)
Q Consensus        34 ~~~~A~Fg~~~~~~~~~G~L---~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~  110 (444)
                      ....|.||...+...-...+   ..++|+|.|.+...+-      .+++++|.||+|+|.+|+++||++||.|++|.|+.
T Consensus        56 a~~~~~~~~t~~~~~~~a~~~~~a~~~pld~cs~~~~kl------~~~~~~v~RGnC~Ft~Ka~~Aq~aGAsaLliin~~  129 (541)
T KOG2442|consen   56 AGMLARFGITLPSKCKAADIPHLAQVDPLDSCSTLQSKL------SGKVALVFRGNCSFTEKAKLAQAAGASALLIINNK  129 (541)
T ss_pred             hhhhhhcCCcCCCCccccccchhhhcCCccccCCCCccc------cceeEEEecccceeehhhhhhhhcCceEEEEEcCc
Confidence            44568888776654322222   3458999999886543      68999999999999999999999999999999986


Q ss_pred             CCcceeeecCC---CCCceEEEEEEeccccchhhhh-cCcccceeeeeccc
Q 013394          111 DDGVLVAMAGN---SAGIKIHAVFVSKASGEKLKQY-AGSTDMEIWIIPSF  157 (444)
Q Consensus       111 ~~~~~~~~~g~---~~~i~Ip~v~Is~~~G~~L~~~-l~~~~v~v~I~P~~  157 (444)
                      ++ .+.+..++   ..++.||++||++++|+.+.+. ..+..+++.++.+.
T Consensus       130 ~d-~~~~~~~~~~~~~dv~IPv~mi~~~~~~~l~~~~~~~~~V~~~lYaPk  179 (541)
T KOG2442|consen  130 KD-LLFMPCGNKETSLDVTIPVAMISYSDGRDLNKSTRSNDNVELALYAPK  179 (541)
T ss_pred             hh-hccCCCCCCCccccccceEEEEEhhhHHHHHhhhccCCeEEEEEECCC
Confidence            64 22222222   2478999999999999998863 34456777766443

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

Probab=99.39  E-value=3.4e-13  Score=133.16  Aligned_cols=76  Identities=26%  Similarity=0.646  Sum_probs=57.0

Q ss_pred             CCcHHHHhhcccceeeccccccCCCcccccccccccc-C---------ceeEEeccCCeecHhHHHHHHhcCCCCCCccc
Q 013394          205 GMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSV-G---------EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK  274 (444)
Q Consensus       205 ~~~~~~~~~lp~~~~~~~~~~~~~~~~C~ICle~~~~-~---------~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR  274 (444)
                      +..+++.+.+|+.+..+.   ..++..|.||+|++-. +         .+.+.|||||+||..|++.|++++++ ||+||
T Consensus       266 r~~kdl~~~~~t~t~eql---~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQT-CPICr  341 (491)
T COG5243         266 RATKDLNAMYPTATEEQL---TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQT-CPICR  341 (491)
T ss_pred             HHhhHHHhhcchhhhhhh---cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccC-CCccc
Confidence            345677777776554433   2346899999999533 3         24589999999999999999999887 99999


Q ss_pred             cC-CcCCCCCC
Q 013394          275 RD-ARTSTGEP  284 (444)
Q Consensus       275 ~~-i~~~~~~~  284 (444)
                      .+ +.++.+..
T Consensus       342 ~p~ifd~~~~~  352 (491)
T COG5243         342 RPVIFDQSSPT  352 (491)
T ss_pred             CccccccCCCC
Confidence            99 55655543

>cd00538 PA PA: Protease-associated (PA) domain

Probab=99.31  E-value=3.9e-12  Score=110.07  Aligned_cols=92  Identities=40%  Similarity=0.547  Sum_probs=70.8

Q ss_pred             EecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcc-eeeecCC-CCCceEEEEE
Q 013394           54 YVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGV-LVAMAGN-SAGIKIHAVF  131 (444)
Q Consensus        54 ~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~-~~~~~g~-~~~i~Ip~v~  131 (444)
                      ....+.++|++... .....++++||||++||+|+|.+|+++|+++||+|+||+|+.+... ...+.++ .....||+++
T Consensus        25 ~~~~~~~~C~~~~~-~~~~~~~~GkIvl~~~g~~~~~~k~~~a~~~GA~gvii~~~~~~~~~~~~~~~~~~~~~~iP~~~  103 (126)
T cd00538          25 VVAGPLVGCGYGTT-DDSGADVKGKIVLVRRGGCSFSEKVKNAQKAGAKAVIIYNNGDDPGPQMGSVGLESTDPSIPTVG  103 (126)
T ss_pred             ccccceEEEecCcc-cccCCCccceEEEEECCCcCHHHHHHHHHHCCCEEEEEEECCCCcccccccccCCCCCCcEeEEE
Confidence            45567889988752 1223456899999999999999999999999999999999876421 1112221 2456799999


Q ss_pred             EeccccchhhhhcCc
Q 013394          132 VSKASGEKLKQYAGS  146 (444)
Q Consensus       132 Is~~~G~~L~~~l~~  146 (444)
                      |+.++|+.|++++..
T Consensus       104 is~~~g~~l~~~~~~  118 (126)
T cd00538         104 ISYADGEALLSLLEA  118 (126)
T ss_pred             eCHHHHHHHHHHHhc
Confidence            999999999998764

The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) g

>cd02133 PA_C5a_like PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase

Probab=99.26  E-value=3.5e-11  Score=107.56  Aligned_cols=100  Identities=27%  Similarity=0.262  Sum_probs=72.9

Q ss_pred             cccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceee
Q 013394           38 ANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVA  117 (444)
Q Consensus        38 A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~  117 (444)
                      ..|+...+..+..+.|+...   .|.+.+..   ..+++++|||++||+|+|.+|+++|+++||+|+||||+.++.  ..
T Consensus        15 ~~~~~~~~~~~~~~~lv~~g---~g~~~d~~---~~dv~GkIvL~~rg~c~~~~K~~~a~~aGA~gvIi~n~~~~~--~~   86 (143)
T cd02133          15 AFSGNPTDLLGKTYELVDAG---LGTPEDFE---GKDVKGKIALIQRGEITFVEKIANAKAAGAVGVIIYNNVDGL--IP   86 (143)
T ss_pred             ccCCCcCCCCCcEEEEEEcc---CCchhccC---CCCccceEEEEECCCCCHHHHHHHHHHCCCeEEEEeecCCCc--cc
Confidence            34555455556788887753   22322221   235689999999999999999999999999999999987653  22


Q ss_pred             ecCCCCCceEEEEEEeccccchhhhhcCc
Q 013394          118 MAGNSAGIKIHAVFVSKASGEKLKQYAGS  146 (444)
Q Consensus       118 ~~g~~~~i~Ip~v~Is~~~G~~L~~~l~~  146 (444)
                      +... ....||+++|++++|+.|++++..
T Consensus        87 ~~~~-~~~~iP~v~Is~~dG~~L~~~l~~  114 (143)
T cd02133          87 GTLG-EAVFIPVVFISKEDGEALKAALES  114 (143)
T ss_pred             ccCC-CCCeEeEEEecHHHHHHHHHHHhC
Confidence            2111 135799999999999999998865

This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from Bacillus subtilis, ii) a large molecular mass collagenolytic protease from Geobacillus collagenovorans MO-1, and iii) PrtS, a cell envelope protease from Streptococcus thermophilus CNRZ 385. Proteins in this group belong to the peptidase S8 family. C5a peptidase is a cell surface serine protease which specifically inactivates C5a [a chemotactic peptide, which attracts polymorphonuclear leukocytes (PMNs)], by cleaving it to release a 7-residue carboxy-terminal fragment which contains the PMN binding site. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promotin

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.19  E-value=1.4e-11  Score=118.35  Aligned_cols=74  Identities=26%  Similarity=0.543  Sum_probs=54.2

Q ss_pred             cCCcHHHHhhcccceeecccc-ccCCCccccccccccccCc----ee-EEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          204 HGMSRRLVKAMPSLIFTAVVE-DNCTSRTCAICLEDYSVGE----KL-RILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       204 ~~~~~~~~~~lp~~~~~~~~~-~~~~~~~C~ICle~~~~~~----~~-~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      ++..+.+++.+|.+...-... +...+.+|+||+|.+..++    .+ ..++|+|.||..||.+|+..+. +||+||.++
T Consensus       148 ~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~-tCPlCR~~~  226 (238)
T PHA02929        148 GKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKN-TCPVCRTPF  226 (238)
T ss_pred             cchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCC-CCCCCCCEe
Confidence            445778888899875432221 2234689999999987653    12 3446999999999999999855 599999977


Q ss_pred             c
Q 013394          278 R  278 (444)
Q Consensus       278 ~  278 (444)
                      .
T Consensus       227 ~  227 (238)
T PHA02929        227 I  227 (238)
T ss_pred             e
Confidence            5

>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=99.18  E-value=1.9e-11  Score=96.87  Aligned_cols=45  Identities=36%  Similarity=0.840  Sum_probs=35.4

Q ss_pred             CccccccccccccC----------ceeEEeccCCeecHhHHHHHHhcCCCCCCccc
Q 013394          229 SRTCAICLEDYSVG----------EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK  274 (444)
Q Consensus       229 ~~~C~ICle~~~~~----------~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR  274 (444)
                      ++.|+||++.|...          -.+...+|+|.||..||.+||+.++ +||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN-TCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS-B-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC-cCCCCC
Confidence            45699999999332          2455667999999999999999866 599997

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 ....

>cd04819 PA_2 PA_2: Protease-associated (PA) domain subgroup 2

Probab=99.09  E-value=5.4e-10  Score=97.97  Aligned_cols=96  Identities=19%  Similarity=0.098  Sum_probs=70.3

Q ss_pred             CCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCC--CHHHHHHHHHHcCCeEEEEeccCCCccee-eecCC--
Q 013394           47 SGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC--SFEDKVRNAQKAGFEAAIVYDNEDDGVLV-AMAGN--  121 (444)
Q Consensus        47 ~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~C--sF~~Kv~~Aq~aGA~avII~n~~~~~~~~-~~~g~--  121 (444)
                      .+++|.|+.+..  + .+.+..   ..++++|||||+||.|  +|.+|+++|+++||+|+||+|+.++.... ...+.  
T Consensus        21 ~~~~~~lV~~g~--G-~~~d~~---~~~v~GkIvlv~~g~~~~~~~~k~~~A~~~GA~avi~~~~~~g~~~~~~~~~~~~   94 (127)
T cd04819          21 GEAKGEPVDAGY--G-LPKDFD---GLDLEGKIAVVKRDDPDVDRKEKYAKAVAAGAAAFVVVNTVPGVLPATGDEGTED   94 (127)
T ss_pred             CCeeEEEEEeCC--C-CHHHcC---CCCCCCeEEEEEcCCCchhHHHHHHHHHHCCCEEEEEEeCCCCcCcccccccccC
Confidence            346888887652  2 111111   2356899999999999  99999999999999999999876653221 11122  


Q ss_pred             CCCceEEEEEEeccccchhhhhcCccc
Q 013394          122 SAGIKIHAVFVSKASGEKLKQYAGSTD  148 (444)
Q Consensus       122 ~~~i~Ip~v~Is~~~G~~L~~~l~~~~  148 (444)
                      .....||++.|+.+||+.|+++++.+.
T Consensus        95 ~~~~~IP~v~Is~edg~~L~~~l~~g~  121 (127)
T cd04819          95 GPPSPIPAASVSGEDGLRLARVAERND  121 (127)
T ss_pred             CCCCCCCEEEEeHHHHHHHHHHHhcCC
Confidence            234679999999999999999887643

A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuola

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.97  E-value=5.6e-10  Score=103.25  Aligned_cols=55  Identities=31%  Similarity=0.591  Sum_probs=44.3

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc---------------CCCCCCccccCCcCCCCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---------------WRTFCPVCKRDARTSTGEPP  285 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---------------~~~~CP~CR~~i~~~~~~~~  285 (444)
                      ++.+|+||++.++++   .+++|+|.||..||.+|+..               .+..||+||.++......+.
T Consensus        17 ~~~~CpICld~~~dP---VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPi   86 (193)
T PLN03208         17 GDFDCNICLDQVRDP---VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPI   86 (193)
T ss_pred             CccCCccCCCcCCCc---EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEe
Confidence            468999999998665   67889999999999999853               13469999999987655544

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

Probab=98.97  E-value=5.1e-10  Score=108.25  Aligned_cols=50  Identities=32%  Similarity=0.759  Sum_probs=43.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      ...|.+|||....+   -.+||||+||+.||..|...+.. ||+||.+..+++.
T Consensus       239 ~~kC~LCLe~~~~p---SaTpCGHiFCWsCI~~w~~ek~e-CPlCR~~~~pskv  288 (293)
T KOG0317|consen  239 TRKCSLCLENRSNP---SATPCGHIFCWSCILEWCSEKAE-CPLCREKFQPSKV  288 (293)
T ss_pred             CCceEEEecCCCCC---CcCcCcchHHHHHHHHHHccccC-CCcccccCCCcce
Confidence            58999999997766   78999999999999999998555 9999999887653

>cd04815 PA_M28_2 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2

Probab=98.94  E-value=1.3e-09  Score=96.40  Aligned_cols=104  Identities=17%  Similarity=0.150  Sum_probs=75.5

Q ss_pred             ccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCC------CHHHH-------HHHHHHcCCeEEE
Q 013394           39 NFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGC------SFEDK-------VRNAQKAGFEAAI  105 (444)
Q Consensus        39 ~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~C------sF~~K-------v~~Aq~aGA~avI  105 (444)
                      .|.+..++.+++|.++.....+   .++..  ...++++|||||.||.|      +|.+|       .++|+++||.|+|
T Consensus         7 ~~s~~t~~~gvta~vv~v~~~~---~~~~~--~~~~v~GKIvlv~~~~~~~~~~~~~~~k~~~r~~~~~~A~~~GA~avI   81 (134)
T cd04815           7 GGSVATPPEGITAEVVVVKSFD---ELKAA--PAGAVKGKIVFFNQPMVRTQTGSGYGPTVAYRRRGAVEAAKKGAVAVL   81 (134)
T ss_pred             CCCCCCCCCCcEEEEEEECCHH---HHHhc--chhhcCCeEEEecCCccccCchhhcCchhhhhhHHHHHHHhCCCEEEE
Confidence            3556666677999998776322   11111  12356899999999999      99999       7999999999999


Q ss_pred             EeccCCCc---ceeeecCC-CCCceEEEEEEeccccchhhhhcCcc
Q 013394          106 VYDNEDDG---VLVAMAGN-SAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       106 I~n~~~~~---~~~~~~g~-~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      |+|+.+..   ....+.+. .....||++.|+.++|+.|.+.++.+
T Consensus        82 v~s~~~~~~~~~~~G~~~~~~~~~~IP~v~is~ed~~~L~r~l~~g  127 (134)
T cd04815          82 IRSIGTDSHRSPHTGMMSYDDGVPKIPAAAISVEDADMLERLAARG  127 (134)
T ss_pred             EEecCcccCCCCcCCccccCCCCCCCCEEEechhcHHHHHHHHhCC
Confidence            99865331   11222333 33467999999999999999888765

A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies; relatively little is known a

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

Probab=98.93  E-value=4.8e-10  Score=105.54  Aligned_cols=59  Identities=29%  Similarity=0.514  Sum_probs=46.8

Q ss_pred             cCCCccccccccccccCceeEEeccCCeecHhHHHHHHhcC--CCCCCccccCCcCCCCCCCCC
Q 013394          226 NCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW--RTFCPVCKRDARTSTGEPPAS  287 (444)
Q Consensus       226 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~--~~~CP~CR~~i~~~~~~~~~~  287 (444)
                      +....+|.||||.-+++   +++.|||.||+.||.+||+.+  +..|||||..|...+-.|.-.
T Consensus        44 ~~~~FdCNICLd~akdP---VvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG  104 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP---VVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG  104 (230)
T ss_pred             CCCceeeeeeccccCCC---EEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence            34568999999985544   777799999999999999873  345999999998776665433

>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=98.92  E-value=8.7e-10  Score=77.44  Aligned_cols=45  Identities=42%  Similarity=1.082  Sum_probs=37.1

Q ss_pred             cccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      +|+||++.+  .+.+...+|+|.||..|++.|++..+..||+||.++
T Consensus         1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998  334566669999999999999998555699998764

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

Probab=98.87  E-value=5.4e-09  Score=112.76  Aligned_cols=54  Identities=35%  Similarity=0.811  Sum_probs=46.3

Q ss_pred             CCccccccccccccCce--eEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          228 TSRTCAICLEDYSVGEK--LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~--~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      .+..|.||+|++..++.  .++|||+|+||..|+..|+++.++ ||+||..+.....
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qt-CP~CR~~~~~~~~  345 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQT-CPTCRTVLYDYVL  345 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCc-CCcchhhhhcccc
Confidence            46899999999988765  789999999999999999999665 9999996655443

>cd02120 PA_subtilisin_like PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases

Probab=98.85  E-value=5.7e-09  Score=90.73  Aligned_cols=83  Identities=25%  Similarity=0.295  Sum_probs=65.9

Q ss_pred             CcCCCCCCCCCCcccCCCcceEEEEecCCC-CHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceEEEEEEeccc
Q 013394           58 PLDACSNLTSKVEKVSNMSSAFVLTIRGGC-SFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKAS  136 (444)
Q Consensus        58 p~~aC~~l~~~~~~~~~~~~~ivLV~RG~C-sF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~v~Is~~~  136 (444)
                      ....|++.....   .+.++||||++||.| +|.+|+++|+++||.|+|++++.++..  .+..  ....||+++|.+++
T Consensus        36 ~~~~C~~~~~~~---~~v~GkIVlc~~~~~~~~~~k~~~~~~~GA~gvI~~~~~~~~~--~~~~--~~~~iP~v~I~~~~  108 (126)
T cd02120          36 DASLCLPGSLDP---SKVKGKIVLCDRGGNTSRVAKGDAVKAAGGAGMILANDPTDGL--DVVA--DAHVLPAVHVDYED  108 (126)
T ss_pred             ccccCCCCCCCh---hhccccEEEEeCCCCccHHHHHHHHHHcCCcEEEEEecCCCCc--eecc--cccccceEEECHHH
Confidence            346898765433   345799999999999 999999999999999999998776532  1111  13579999999999


Q ss_pred             cchhhhhcCcc
Q 013394          137 GEKLKQYAGST  147 (444)
Q Consensus       137 G~~L~~~l~~~  147 (444)
                      |+.|++++...
T Consensus       109 g~~l~~y~~~~  119 (126)
T cd02120         109 GTAILSYINST  119 (126)
T ss_pred             HHHHHHHHHcC
Confidence            99999988654

This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from Alnus glutinosa ag12, members of the tomato P69 family, and tomato LeSBT2. These proteins belong to the peptidase S8 family. Cucumisin from the juice of melon fruits is a thermostable serine peptidase, with a broad substrate specificity for oligopeptides and proteins. A. thaliana Ara12 is a thermostable, extracellular serine protease, found chiefly in silique tissue and stem tissue. Ara12 is stimulated by Ca2+ ions. A. glutinosa ag12 is expressed at high levels in the nodules, and at low levels in the shoot tips; it is implicated in both symbiotic and non-symbiotic processes in plant development. The tomato P69 protease family is comprised of various protein isoforms of approximately 69KDa. These isoforms accu

>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=98.82  E-value=2e-09  Score=78.80  Aligned_cols=46  Identities=30%  Similarity=0.798  Sum_probs=37.9

Q ss_pred             CccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      +..|.||++.+..   +..+||+|. |+..|++.|+.... .||+||++|.
T Consensus         2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~-~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKK-KCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTS-BBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCC-CCCcCChhhc
Confidence            4789999998544   688999999 99999999999644 5999999875

...

>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=98.82  E-value=3e-09  Score=73.83  Aligned_cols=39  Identities=36%  Similarity=0.997  Sum_probs=32.9

Q ss_pred             ccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCcc
Q 013394          232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVC  273 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~C  273 (444)
                      |+||++.+.+  .+..++|||.|+..||.+|++. +..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEK-NPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence            8999999776  4678999999999999999999 5569998

>cd02128 PA_TfR PA_TfR: Protease-associated domain containing proteins like transferrin receptor (TfR)

Probab=98.80  E-value=8.6e-09  Score=95.41  Aligned_cols=108  Identities=22%  Similarity=0.230  Sum_probs=71.5

Q ss_pred             ccccCCCCCCCCceEEEEecCCcCCCCCCCCC--CcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcc
Q 013394           37 EANFAPAIRGSGDCGVLYVAEPLDACSNLTSK--VEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGV  114 (444)
Q Consensus        37 ~A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~--~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~  114 (444)
                      +..|.+..+...++|.|+.+.  .| ...+..  ....-+++++||||+||+|+|.+|+++|+++||+|||||++..+..
T Consensus        17 ~~~f~~~s~~G~v~g~lVyvn--~G-~~~Df~~L~~~gv~v~GkIvLvr~G~~~~~~Kv~~A~~~GA~gvIiy~Dp~d~~   93 (183)
T cd02128          17 PGGYVAYSAAGTVTGKLVYAN--YG-RKKDFEDLQSVGVSVNGSVVLVRAGKISFAEKVANAEKLGAVGVLIYPDPADFP   93 (183)
T ss_pred             cccccCCCCCCceEEEEEEcC--CC-CHHHHHHHHhcCCCCCCeEEEEECCCCCHHHHHHHHHHCCCEEEEEecCHHHcC
Confidence            345665555566899998873  22 222111  1112356899999999999999999999999999999998742210


Q ss_pred             e-------e----eecCC-----------------C--CCceEEEEEEeccccchhhhhcCcc
Q 013394          115 L-------V----AMAGN-----------------S--AGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       115 ~-------~----~~~g~-----------------~--~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      .       .    ...|+                 .  .--.||+.-|+..+++.|++.++..
T Consensus        94 ~~~~~~~~~g~~~~~~GDplTPG~ps~~~~~~~~~~~~~lP~IPs~PIS~~da~~lL~~l~G~  156 (183)
T cd02128          94 IDPSETALFGHVHLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPAQTISAAAAAKLLSKMGGP  156 (183)
T ss_pred             cccCcceeecceeccCCCcCCCCCccccccccCcccccCCCCCCEeccCHHHHHHHHHHcCCC
Confidence            0       0    00110                 0  1235899999999998888876543

This group contains various PA domain-containing proteins similar to human TfR1 and TfR2. TfR1 and TfR2 are type II membrane proteins, belonging to the peptidase M28 family. TfR1 is homodimeric, widely expressed, and a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and this complex is internalized. In addition to its role in iron uptake, TfR1 may participate in cell growth and proliferation. TfR2 also binds Tf but with a significantly lower affinity than does TfR1. TfR2 is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis. HFE and TfR2 interact in cells. By one model for serum iron sensing, at low or basal iron concentrations, HFE and TFR1 form a complex at the plasma membra

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

Probab=98.75  E-value=4.8e-09  Score=84.52  Aligned_cols=50  Identities=30%  Similarity=0.822  Sum_probs=38.4

Q ss_pred             Ccccccccccccc--------Cce--eEEeccCCeecHhHHHHHHhcC--CCCCCccccCCc
Q 013394          229 SRTCAICLEDYSV--------GEK--LRILPCRHKFHAFCVDSWLTSW--RTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~--------~~~--~~~lpC~H~FH~~Ci~~Wl~~~--~~~CP~CR~~i~  278 (444)
                      ++.|.||+..|..        +|.  +..-.|+|.||..||.+||.++  +..||+||++..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            5789999998873        332  2333499999999999999863  456999998754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.70  E-value=1e-08  Score=73.09  Aligned_cols=44  Identities=32%  Similarity=0.815  Sum_probs=38.0

Q ss_pred             cccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCcccc
Q 013394          231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR  275 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~  275 (444)
                      .|.||++.|...+..++++|+|+|+..|++.+. .....||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence            499999999666788999999999999999998 33456999985

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

Probab=98.68  E-value=9.8e-09  Score=92.91  Aligned_cols=51  Identities=25%  Similarity=0.597  Sum_probs=41.7

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ....|+|||+.+++... .-..|||+||..||+.-+...+. ||+||+.|...
T Consensus       130 ~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~-CP~C~kkIt~k  180 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNK-CPTCRKKITHK  180 (187)
T ss_pred             cccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCC-CCCcccccchh
Confidence            35899999999877522 23679999999999999998776 99999887643

>PHA02926 zinc finger-like protein; Provisional

Probab=98.66  E-value=1.2e-08  Score=95.60  Aligned_cols=52  Identities=29%  Similarity=0.758  Sum_probs=39.1

Q ss_pred             CCccccccccccccC-----ceeEEe-ccCCeecHhHHHHHHhcCC-----CCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVG-----EKLRIL-PCRHKFHAFCVDSWLTSWR-----TFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~-----~~~~~l-pC~H~FH~~Ci~~Wl~~~~-----~~CP~CR~~i~~  279 (444)
                      .+.+|.||+|..-.+     ....+| +|+|.||..||+.|...++     ..||+||..+..
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            458999999986432     233455 4999999999999998632     349999987653

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

Probab=98.66  E-value=1.6e-08  Score=71.49  Aligned_cols=39  Identities=33%  Similarity=0.784  Sum_probs=31.0

Q ss_pred             ccccccccccCceeEEeccCCeecHhHHHHHHhcCCC---CCCcc
Q 013394          232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRT---FCPVC  273 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~---~CP~C  273 (444)
                      |+||++.|+++   ..|+|||.|+..||..|.+..+.   .||.|
T Consensus         1 CpiC~~~~~~P---v~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999887   78999999999999999987533   49987

>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=98.65  E-value=1.4e-08  Score=70.95  Aligned_cols=40  Identities=43%  Similarity=1.035  Sum_probs=34.4

Q ss_pred             ccccccccccCceeEEeccCCeecHhHHHHHHh-cCCCCCCcc
Q 013394          232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLT-SWRTFCPVC  273 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~~~CP~C  273 (444)
                      |+||++.+...  .+.++|+|.||..||++|++ .....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998776  36899999999999999999 445569998

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 ....

>smart00184 RING Ring finger

Probab=98.61  E-value=2.7e-08  Score=67.33  Aligned_cols=39  Identities=44%  Similarity=1.088  Sum_probs=33.1

Q ss_pred             ccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCcc
Q 013394          232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVC  273 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~C  273 (444)
                      |+||++.   .+....++|+|.||..|++.|++..+..||+|
T Consensus         1 C~iC~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEE---LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccC---CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            8899988   34568899999999999999998545569987

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)

>smart00504 Ubox Modified RING finger domain

Probab=98.55  E-value=7.5e-08  Score=73.47  Aligned_cols=46  Identities=26%  Similarity=0.392  Sum_probs=40.0

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ..|+||++.|+++   .+++|||+|+..||.+|++.+ ..||+|+.++..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~-~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSH-GTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHC-CCCCCCcCCCCh
Confidence            5799999999886   678999999999999999984 459999988754

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

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

Probab=98.39  E-value=1.9e-07  Score=73.45  Aligned_cols=50  Identities=26%  Similarity=0.670  Sum_probs=36.6

Q ss_pred             ccccccccccccCceeEEe--ccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          230 RTCAICLEDYSVGEKLRIL--PCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~l--pC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +.|+-|...+..+++..+.  -|+|.||..||.+||.++. .||+||++..-+
T Consensus        32 ~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~-~CPld~q~w~~~   83 (88)
T COG5194          32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKG-VCPLDRQTWVLA   83 (88)
T ss_pred             CcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCC-CCCCCCceeEEe
Confidence            4555555555566655443  2999999999999999944 599999976443

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

Probab=98.37  E-value=2.7e-07  Score=65.46  Aligned_cols=39  Identities=38%  Similarity=0.780  Sum_probs=23.2

Q ss_pred             ccccccccccCc-eeEEeccCCeecHhHHHHHHhcC---CCCCC
Q 013394          232 CAICLEDYSVGE-KLRILPCRHKFHAFCVDSWLTSW---RTFCP  271 (444)
Q Consensus       232 C~ICle~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~---~~~CP  271 (444)
                      |+||+| |...+ ...+|+|||+|+.+||++|+...   ...||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 86644 55889999999999999999864   33476

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.35  E-value=2.4e-07  Score=95.31  Aligned_cols=49  Identities=31%  Similarity=0.756  Sum_probs=41.8

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ....|.||++.|...   .+++|+|.||..||..|+.... .||+||..+...
T Consensus        25 ~~l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~~~-~CP~Cr~~~~~~   73 (397)
T TIGR00599        25 TSLRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSNQP-KCPLCRAEDQES   73 (397)
T ss_pred             cccCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhCCC-CCCCCCCccccc
Confidence            358999999999776   5789999999999999998854 599999987654

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

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

Probab=98.34  E-value=1.4e-07  Score=90.40  Aligned_cols=55  Identities=29%  Similarity=0.725  Sum_probs=43.7

Q ss_pred             CCCccccccccccccCc-------eeEEeccCCeecHhHHHHHHhc-CCCCCCccccCCcCCC
Q 013394          227 CTSRTCAICLEDYSVGE-------KLRILPCRHKFHAFCVDSWLTS-WRTFCPVCKRDARTST  281 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~-------~~~~lpC~H~FH~~Ci~~Wl~~-~~~~CP~CR~~i~~~~  281 (444)
                      .++..|+||-..+....       +.-+|.|+|+||+.||+.|-.. ++.+||.||+.+.-+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            35689999998886544       6678999999999999999654 3445999998876543

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

Probab=98.30  E-value=6.7e-07  Score=91.94  Aligned_cols=52  Identities=27%  Similarity=0.844  Sum_probs=40.6

Q ss_pred             CCccccccccccccC---c-----------eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVG---E-----------KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~---~-----------~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...+|+||+.....-   .           .-..+||.|+||..|+.+|+...+-.||+||.++++
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            347899999876431   1           123569999999999999999766569999998864

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

Probab=98.29  E-value=2.9e-07  Score=88.34  Aligned_cols=51  Identities=29%  Similarity=0.687  Sum_probs=43.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHH-HHhcCCCCCCccccCCcCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDS-WLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~-Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      +..|+||+|.....   ..++|||+||..||-. |-.++-..||+||+.+.+.+.
T Consensus       215 d~kC~lC~e~~~~p---s~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         215 DYKCFLCLEEPEVP---SCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccceeeeecccCCc---ccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            68999999986665   7889999999999999 877755569999998876543

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

Probab=98.23  E-value=8.5e-07  Score=64.75  Aligned_cols=43  Identities=28%  Similarity=0.762  Sum_probs=33.7

Q ss_pred             cccccccccccCceeEEeccC-----CeecHhHHHHHHhcC-CCCCCccc
Q 013394          231 TCAICLEDYSVGEKLRILPCR-----HKFHAFCVDSWLTSW-RTFCPVCK  274 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~~-~~~CP~CR  274 (444)
                      .|.||++ +..++...++||.     |.+|..|+++|+... +..||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 4444555689985     889999999999764 44699995

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

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

Probab=98.20  E-value=3.8e-07  Score=71.22  Aligned_cols=50  Identities=32%  Similarity=0.831  Sum_probs=36.9

Q ss_pred             Ccccccccccccc--------CceeE-Eec-cCCeecHhHHHHHHhcC--CCCCCccccCCc
Q 013394          229 SRTCAICLEDYSV--------GEKLR-ILP-CRHKFHAFCVDSWLTSW--RTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~--------~~~~~-~lp-C~H~FH~~Ci~~Wl~~~--~~~CP~CR~~i~  278 (444)
                      +++|-||+-.|..        +|..- ++- |.|.||..||.+|+...  +..||+||++..
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            4689999888864        33322 222 99999999999999753  455999998753

>cd02121 PA_GCPII_like PA_GCPII_like: Protease-associated domain containing protein, glutamate carboxypeptidase II (GCPII)-like

Probab=98.13  E-value=4.4e-06  Score=79.87  Aligned_cols=61  Identities=25%  Similarity=0.192  Sum_probs=46.4

Q ss_pred             CCceEEEEecCCcCCCCCCCCC--CcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccC
Q 013394           47 SGDCGVLYVAEPLDACSNLTSK--VEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNE  110 (444)
Q Consensus        47 ~~~~G~L~~~~p~~aC~~l~~~--~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~  110 (444)
                      ..++|.|+.+.   .|...+..  ....-+++++|||+++|.|.+.+|+++|+++||+|||||++.
T Consensus        43 g~v~g~lVyvn---yG~~~D~~~L~~~gvdv~GKIvLvr~G~~~~~~Kv~~A~~~GA~gVIiy~Dp  105 (220)
T cd02121          43 GNVTAELVYAN---YGSPEDFEYLEDLGIDVKGKIVIARYGGIFRGLKVKNAQLAGAVGVIIYSDP  105 (220)
T ss_pred             CCceEEEEEcC---CCcHHHHHHHhhcCCCCCCeEEEEECCCccHHHHHHHHHHcCCEEEEEEeCc
Confidence            44788888764   34332221  112346789999999999999999999999999999999864

This group contains various PA domain-containing proteins similar to GCPII including, GCPIII (NAALADase2) and NAALADase L. These proteins belong to the peptidase M28 family. GCPII is also known N-acetylated-alpha-linked acidic dipeptidase (NAALDase1), folate hydrolase or prostate-specific membrane antigen (PSMA). GCPII is found in various human tissues including prostate, small intestine, and the central nervous system. In the brain, GCPII is known as NAALDase1, it functions as a NAALDase hydrolyzing the neuropeptide N-acetyl-L-aspartyl-L-glutamate (alpha-NAAG), to release free glutamate. In the small intestine, GCPII releases the terminal glutamate from poly-gamma-glutamated folates. GCPII (PSMA) is a useful cancer marker; its expression is markedly increased in prostate cancer and in tumor-associated neovasculature. GCPIII hydrolyzes alpha-NAAG with a lower

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

Probab=98.12  E-value=1.2e-06  Score=69.33  Aligned_cols=49  Identities=22%  Similarity=0.320  Sum_probs=38.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ...|+||.+-|.++   .++||||.|...||+.||.++...||+|++++...
T Consensus         4 ~f~CpIt~~lM~dP---Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    4 EFLCPITGELMRDP---VILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGB-TTTSSB-SSE---EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             ccCCcCcCcHhhCc---eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            47899999999887   78999999999999999999666699999887654

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 ....

>cd04822 PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3

Probab=98.12  E-value=9.7e-06  Score=73.12  Aligned_cols=63  Identities=17%  Similarity=0.168  Sum_probs=49.3

Q ss_pred             CCceEEEEecC---CcCCCCCCCCCCcccCCCcceEEEEecCC------------------CCHHHHHHHHHHcCCeEEE
Q 013394           47 SGDCGVLYVAE---PLDACSNLTSKVEKVSNMSSAFVLTIRGG------------------CSFEDKVRNAQKAGFEAAI  105 (444)
Q Consensus        47 ~~~~G~L~~~~---p~~aC~~l~~~~~~~~~~~~~ivLV~RG~------------------CsF~~Kv~~Aq~aGA~avI  105 (444)
                      ..++|.||.+.   ...+|...++..   -++++|||||.||+                  |+|..|+++|+++||+|||
T Consensus        18 g~vtg~lVfvGyGi~~~~~~~~Dy~g---iDVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~aVI   94 (151)
T cd04822          18 GAVTAPVVFAGYGITAPELGYDDYAG---LDVKGKIVLVLRHEPQEDDANSRFNGPGLTRHAGLRYKATNARRHGAAAVI   94 (151)
T ss_pred             CCceEeEEEecCCcCccccchhhccC---CCCCCeEEEEEcCCcccccccccccccccccccCHHHHHHHHHHCCCeEEE
Confidence            34788887764   345776554432   35679999999884                  9999999999999999999


Q ss_pred             EeccCCC
Q 013394          106 VYDNEDD  112 (444)
Q Consensus       106 I~n~~~~  112 (444)
                      ||++...
T Consensus        95 v~~d~~~  101 (151)
T cd04822          95 VVNGPNS  101 (151)
T ss_pred             EEeCCcc
Confidence            9997654

A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt

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

Probab=98.10  E-value=8.3e-07  Score=96.93  Aligned_cols=50  Identities=36%  Similarity=0.909  Sum_probs=39.2

Q ss_pred             CCCccccccccccccCceeEEec------cCCeecHhHHHHHHhc-CCCCCCccccCCc
Q 013394          227 CTSRTCAICLEDYSVGEKLRILP------CRHKFHAFCVDSWLTS-WRTFCPVCKRDAR  278 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lp------C~H~FH~~Ci~~Wl~~-~~~~CP~CR~~i~  278 (444)
                      .+..+|+||......-|  |.||      |+|.||..|+.+|+.. .+.+||+||.+++
T Consensus      1467 sG~eECaICYsvL~~vd--r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHh--ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            34689999998876332  3343      8999999999999987 4567999998775

>cd04820 PA_M28_1_1 PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1

Probab=98.10  E-value=1.1e-05  Score=71.48  Aligned_cols=63  Identities=17%  Similarity=0.140  Sum_probs=48.9

Q ss_pred             CCceEEEEecC---CcCCCCCCCCCCcccCCCcceEEEEecCCCC------------HHHHHHHHHHcCCeEEEEeccCC
Q 013394           47 SGDCGVLYVAE---PLDACSNLTSKVEKVSNMSSAFVLTIRGGCS------------FEDKVRNAQKAGFEAAIVYDNED  111 (444)
Q Consensus        47 ~~~~G~L~~~~---p~~aC~~l~~~~~~~~~~~~~ivLV~RG~Cs------------F~~Kv~~Aq~aGA~avII~n~~~  111 (444)
                      ..++|.|+.+.   ..++|.-.+..   .-+++||||||++|.|.            +.+|+++|+++||+|||||++..
T Consensus        20 g~v~gelVfvGyG~~~~~~~~~Dy~---~iDVkGKIVlv~~g~p~~~~~~~~~~~~~~~~K~~~A~~~GA~aVIi~~d~~   96 (137)
T cd04820          20 ASVEAPLVFVGYGLVAPELGHDDYA---GLDVKGKIVVVLSGGPAGIPSEEGAHAHSSNEKARYAAKAGAIGMITLTTPR   96 (137)
T ss_pred             CCceEeEEEecCCcCccCcCHhhcc---CCCCCCeEEEEEcCCCCccccccccccccHHHHHHHHHHCCCeEEEEEeCCc
Confidence            45788887763   34567654432   23668999999999995            88999999999999999999755


Q ss_pred             C
Q 013394          112 D  112 (444)
Q Consensus       112 ~  112 (444)
                      .
T Consensus        97 ~   97 (137)
T cd04820          97 S   97 (137)
T ss_pred             c
Confidence            4

A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt

>cd04814 PA_M28_1 PA_M28_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1

Probab=98.08  E-value=1.1e-05  Score=72.00  Aligned_cols=62  Identities=11%  Similarity=0.035  Sum_probs=47.9

Q ss_pred             CceEEEEecC---CcCCCCCCCCCCcccCCCcceEEEEecCCC------------------CHHHHHHHHHHcCCeEEEE
Q 013394           48 GDCGVLYVAE---PLDACSNLTSKVEKVSNMSSAFVLTIRGGC------------------SFEDKVRNAQKAGFEAAIV  106 (444)
Q Consensus        48 ~~~G~L~~~~---p~~aC~~l~~~~~~~~~~~~~ivLV~RG~C------------------sF~~Kv~~Aq~aGA~avII  106 (444)
                      .+.|.||.+.   ...+|.-.++..   -+++||||||.||+|                  +|..|+++|+++||+||||
T Consensus        19 ~~~aelVfvGyGi~a~~~~~dDYag---~DVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~gvIi   95 (142)
T cd04814          19 IKDAPLVFVGYGIKAPELSWDDYAG---LDVKGKVVVVLRNDPQGEPGAGDFGGKAMTYYGRWTYKYEEAARHGAAGVLI   95 (142)
T ss_pred             ccceeeEEecCCcCCCCCChhhcCC---CCCCCcEEEEEcCCCCcccccccccccccccccCHHHHHHHHHHCCCcEEEE
Confidence            3577776653   234666544432   356799999999999                  7999999999999999999


Q ss_pred             eccCCC
Q 013394          107 YDNEDD  112 (444)
Q Consensus       107 ~n~~~~  112 (444)
                      +++.+.
T Consensus        96 i~~~~~  101 (142)
T cd04814          96 VHELAP  101 (142)
T ss_pred             EeCCCc
Confidence            998654

A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies, relatively little is known a

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

Probab=98.04  E-value=2.2e-06  Score=89.11  Aligned_cols=54  Identities=28%  Similarity=0.507  Sum_probs=41.1

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcC----CCCCCccccCCcCCCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW----RTFCPVCKRDARTSTGEPP  285 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~~~CP~CR~~i~~~~~~~~  285 (444)
                      +..|+|||+....+   ..+.|||+||..||-+.+...    -..||+||..|....-.+.
T Consensus       186 ~~~CPICL~~~~~p---~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv  243 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPV  243 (513)
T ss_pred             CCcCCcccCCCCcc---cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeee
Confidence            68999999987766   344499999999998876542    2249999999887544443

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

Probab=98.01  E-value=2.4e-06  Score=87.33  Aligned_cols=48  Identities=31%  Similarity=0.794  Sum_probs=38.9

Q ss_pred             CCccccccccccccCc-eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGE-KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      +-.+|+||||.|.... .++...|.|.||..|+.+|-   ..+||+||.-..
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---DSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccccchHHHhhcc---cCcChhhhhhcC
Confidence            3579999999997753 45666799999999999994   446999998554

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.98  E-value=5.4e-06  Score=82.31  Aligned_cols=53  Identities=25%  Similarity=0.478  Sum_probs=40.1

Q ss_pred             Ccccccccccc-ccCc-eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          229 SRTCAICLEDY-SVGE-KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       229 ~~~C~ICle~~-~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      +..|+||..+- -.++ ++.+-+|||.||..||+..+......||.|+..+....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            47899999963 3332 33334799999999999977665667999998887665

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

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

Probab=97.93  E-value=5.1e-06  Score=83.16  Aligned_cols=52  Identities=27%  Similarity=0.651  Sum_probs=41.5

Q ss_pred             CCCccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      .+..+|.||+.+-+   ...+|||.|. .|..|-+.---+++. ||+||++|.....
T Consensus       288 ~~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~-CPICRqpi~~ll~  340 (349)
T KOG4265|consen  288 ESGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNN-CPICRQPIEELLE  340 (349)
T ss_pred             cCCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcC-CCccccchHhhhe
Confidence            34689999998744   4689999999 999999887666554 9999999876443

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

Probab=97.85  E-value=3.5e-06  Score=66.22  Aligned_cols=50  Identities=28%  Similarity=0.685  Sum_probs=23.6

Q ss_pred             CccccccccccccCceeEEe-----ccCCeecHhHHHHHHhcC---C-------CCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRIL-----PCRHKFHAFCVDSWLTSW---R-------TFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~l-----pC~H~FH~~Ci~~Wl~~~---~-------~~CP~CR~~i~  278 (444)
                      +.+|.||.+.+..++++-.+     .|++.||..|+.+||...   +       ..||.|+.+|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            36899999987633322111     389999999999999741   1       13999998875

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

Probab=97.78  E-value=8.6e-06  Score=79.18  Aligned_cols=43  Identities=37%  Similarity=0.799  Sum_probs=38.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK  274 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR  274 (444)
                      +...|+||++.|...   +++||+|.||..||..|+. ....||.||
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr   54 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCR   54 (386)
T ss_pred             ccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-CCcCCcccC
Confidence            357999999999998   8999999999999999988 455699999

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

Probab=97.73  E-value=1.1e-05  Score=79.69  Aligned_cols=48  Identities=31%  Similarity=0.832  Sum_probs=42.3

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ..|-||.|-|..+   .++||+|.||.-||+..|.. ++.||.|+.++.+..
T Consensus        24 LRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~   71 (442)
T KOG0287|consen   24 LRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESD   71 (442)
T ss_pred             HHHhHHHHHhcCc---eeccccchHHHHHHHHHhcc-CCCCCceecccchhh
Confidence            6899999999987   78899999999999999998 455999999876654

>cd02131 PA_hNAALADL2_like PA_hNAALADL2_like: Protease-associated domain containing proteins like human N-acetylated alpha-linked acidic dipeptidase-like 2 protein (hNAALADL2)

Probab=97.72  E-value=4.2e-05  Score=68.50  Aligned_cols=39  Identities=23%  Similarity=0.360  Sum_probs=35.8

Q ss_pred             CCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCC
Q 013394           74 NMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD  112 (444)
Q Consensus        74 ~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~  112 (444)
                      ++++||||++-|...+..|+++||++||.|||||.|..+
T Consensus        38 ~v~GkIvi~RyG~~~RG~Kv~~A~~~GA~GviIYsDP~d   76 (153)
T cd02131          38 NVTNQIALLKLGQAPLLYKLSLLEEAGFGGVLLYVDPCD   76 (153)
T ss_pred             CccceEEEEeccCcchHHHHHHHHHCCCeEEEEecChhh
Confidence            568999999999999999999999999999999987544

This group contains various PA domain-containing proteins similar to hNAALADL2. The function of hNAALADL2 is unknown. This gene has been mapped to a chromosomal region associated with Cornelia de Lange syndrome. The significance of the PA domain to hNAALADL2 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

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

Probab=97.71  E-value=1.6e-05  Score=77.06  Aligned_cols=47  Identities=32%  Similarity=0.706  Sum_probs=40.3

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|-||-+-|..+   .+++|||.||.-||...|..+ ..||+||.+..+
T Consensus        25 ~lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~q-p~CP~Cr~~~~e   71 (391)
T COG5432          25 MLRCRICDCRISIP---CETTCGHTFCSLCIRRHLGTQ-PFCPVCREDPCE   71 (391)
T ss_pred             HHHhhhhhheeecc---eecccccchhHHHHHHHhcCC-CCCccccccHHh
Confidence            36899999998887   788899999999999999984 559999986543

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]

Probab=97.69  E-value=2e-05  Score=65.29  Aligned_cols=28  Identities=32%  Similarity=0.948  Sum_probs=24.7

Q ss_pred             cCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          250 CRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       250 C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      |.|.||..||.+||++++. ||+|.++-.
T Consensus        81 CNHaFH~hCisrWlktr~v-CPLdn~eW~  108 (114)
T KOG2930|consen   81 CNHAFHFHCISRWLKTRNV-CPLDNKEWV  108 (114)
T ss_pred             cchHHHHHHHHHHHhhcCc-CCCcCccee
Confidence            9999999999999999665 999987643

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.69  E-value=1.6e-05  Score=77.81  Aligned_cols=53  Identities=23%  Similarity=0.466  Sum_probs=43.8

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEP  284 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~~  284 (444)
                      ..+|+||+....-+   ..|+|+|.||.-||+.-....+.+|++||.+|...-...
T Consensus         7 ~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~~~   59 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTIDFE   59 (324)
T ss_pred             CCcceeeeccCCcC---ccccccchhhhhhhcchhhcCCCCCceecCCCCcchhcc
Confidence            47899999987665   778999999999999877776667999999997765443

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

Probab=97.60  E-value=2.4e-05  Score=76.30  Aligned_cols=55  Identities=25%  Similarity=0.700  Sum_probs=44.7

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHh------------------c----CCCCCCccccCCcCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLT------------------S----WRTFCPVCKRDARTSTG  282 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~------------------~----~~~~CP~CR~~i~~~~~  282 (444)
                      ...+|+|||..|..++.+.+++|-|.||..|+-..|.                  .    .+..||+||..|.....
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~  190 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN  190 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc
Confidence            3579999999999999999999999999999876543                  1    12359999998865543

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.60  E-value=2.4e-05  Score=78.76  Aligned_cols=47  Identities=28%  Similarity=0.769  Sum_probs=35.5

Q ss_pred             ccccccccccccCceeEEec-cCCeecHhHHHHHHhcCC--CCCCccccC
Q 013394          230 RTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWR--TFCPVCKRD  276 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~--~~CP~CR~~  276 (444)
                      -.|.||.+-+-..+++.-.. |||+||..|+.+|++.-.  ..||.||-.
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik   54 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIK   54 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeec
Confidence            57999955554555666565 999999999999998632  259999833

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

Probab=97.37  E-value=7.2e-05  Score=75.83  Aligned_cols=51  Identities=29%  Similarity=0.839  Sum_probs=38.8

Q ss_pred             CCccccccccccccCc----eeEEec-cCCeecHhHHHHHHhcCC------CCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGE----KLRILP-CRHKFHAFCVDSWLTSWR------TFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~----~~~~lp-C~H~FH~~Ci~~Wl~~~~------~~CP~CR~~i~  278 (444)
                      .+.+|.||+|...+.-    ...+|| |.|.||..||+.|-...+      ..||.||....
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            3589999999865542    235566 999999999999984433      45999998654

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

Probab=97.30  E-value=4.1e-05  Score=56.20  Aligned_cols=48  Identities=23%  Similarity=0.528  Sum_probs=34.3

Q ss_pred             CccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +++|.||+|.-.+.   ....|||. .|.+|-.+-++..+..||+||++|.+
T Consensus         7 ~dECTICye~pvds---VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDS---VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchH---HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            48999999874442   34459999 78888655444345569999998754

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

Probab=97.27  E-value=5.7e-05  Score=75.40  Aligned_cols=51  Identities=25%  Similarity=0.512  Sum_probs=41.3

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      +..|.|||+-++..  +....|.|.||.+||..-+......||.||+.+....
T Consensus        43 ~v~c~icl~llk~t--mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr   93 (381)
T KOG0311|consen   43 QVICPICLSLLKKT--MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR   93 (381)
T ss_pred             hhccHHHHHHHHhh--cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence            57999999987664  2333499999999999999987777999999775444

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

Probab=97.25  E-value=6.3e-05  Score=81.34  Aligned_cols=48  Identities=27%  Similarity=0.475  Sum_probs=41.7

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      ...|++|+..+.++...-.-+|+|.||..||+.|-..-++ ||+||..+
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqT-CPiDR~EF  170 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQT-CPVDRGEF  170 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhccc-Cchhhhhh
Confidence            4689999999988876667779999999999999988776 99999854

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

Probab=97.25  E-value=7.1e-05  Score=57.14  Aligned_cols=47  Identities=28%  Similarity=0.619  Sum_probs=24.7

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ..|.+|.+-++++  +..-.|.|+|+..||..-+..   .||+|+.+...++
T Consensus         8 LrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~~---~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIGS---ECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--SS---B---SSS--B-TTTGGGGTTT---B-SSS--B-S-SS
T ss_pred             cCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcCC---CCCCcCChHHHHH
Confidence            6799999998776  455569999999999886654   3999998876554

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.21  E-value=0.00021  Score=72.51  Aligned_cols=48  Identities=33%  Similarity=0.930  Sum_probs=37.8

Q ss_pred             CccccccccccccC--ceeEEeccCCeecHhHHHHHHhcC-CCCCCccccC
Q 013394          229 SRTCAICLEDYSVG--EKLRILPCRHKFHAFCVDSWLTSW-RTFCPVCKRD  276 (444)
Q Consensus       229 ~~~C~ICle~~~~~--~~~~~lpC~H~FH~~Ci~~Wl~~~-~~~CP~CR~~  276 (444)
                      ..+|+|||+.+...  ..+..+.|+|.|-..||++||.+. ...||.|..+
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            47899999999764  355666699999999999999632 2359999653

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

Probab=96.90  E-value=0.0003  Score=71.11  Aligned_cols=50  Identities=28%  Similarity=0.747  Sum_probs=39.7

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcC-CCCCCccccCCcCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-RTFCPVCKRDARTST  281 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~~~CP~CR~~i~~~~  281 (444)
                      -..|-||-|.   ++.+++=||||..|..|+..|-... ...||.||.+|..-.
T Consensus       369 FeLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  369 FELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            3679999886   4557888999999999999998552 334999999875443

>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]

Probab=96.90  E-value=0.00055  Score=78.03  Aligned_cols=69  Identities=23%  Similarity=0.475  Sum_probs=49.0

Q ss_pred             HhhcccceeeccccccCCCccccccccccccCceeEEeccCCeecHhHHHHHHhcC-C--------CCCCccccCCcC
Q 013394          211 VKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-R--------TFCPVCKRDART  279 (444)
Q Consensus       211 ~~~lp~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~--------~~CP~CR~~i~~  279 (444)
                      .+.||-+.-.+.......++.|.||..+--.....+.|.|+|+||..|.+.-|++. .        ..||+|+.+|..
T Consensus      3468 E~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3468 EHCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             hhcccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            34566554333332333478999999876666678899999999999999877752 1        149999998754

>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.90  E-value=0.00034  Score=62.71  Aligned_cols=28  Identities=39%  Similarity=0.905  Sum_probs=26.7

Q ss_pred             CccccccccccccCceeEEeccCCeecH
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHA  256 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~  256 (444)
                      ..+|.||||+++.+|++..|||-++||+
T Consensus       177 kGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  177 KGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             CCcEEEEhhhccCCCceeccceEEEeec
Confidence            5799999999999999999999999996

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

Probab=96.89  E-value=0.00025  Score=77.37  Aligned_cols=48  Identities=23%  Similarity=0.549  Sum_probs=39.1

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ..|++|-..+++   +.+..|+|+||..||..-+...+..||.|-..+...
T Consensus       644 LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  644 LKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             eeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            689999977655   355669999999999999988777799998766543

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

Probab=96.87  E-value=0.00053  Score=51.67  Aligned_cols=42  Identities=24%  Similarity=0.498  Sum_probs=29.3

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhc-CCCCCCc
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS-WRTFCPV  272 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~~~CP~  272 (444)
                      ...|+|.+..|+++  ++-..|+|+|-++.|.+||.+ ....||+
T Consensus        11 ~~~CPiT~~~~~~P--V~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFEDP--VKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SSE--EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhCC--cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            57899999998765  677789999999999999943 3445998

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.85  E-value=0.00051  Score=69.42  Aligned_cols=47  Identities=34%  Similarity=0.798  Sum_probs=39.4

Q ss_pred             CccccccccccccC-ceeEEeccCCeecHhHHHHHHhcCC-CCCCcccc
Q 013394          229 SRTCAICLEDYSVG-EKLRILPCRHKFHAFCVDSWLTSWR-TFCPVCKR  275 (444)
Q Consensus       229 ~~~C~ICle~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~-~~CP~CR~  275 (444)
                      +.-|-.|-|.+... +.+..|||.|+||..|+...|+++- .+||.||+
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            46899999998665 5788999999999999999998742 34999984

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

Probab=96.67  E-value=0.0012  Score=68.44  Aligned_cols=49  Identities=27%  Similarity=0.626  Sum_probs=41.5

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ..+.+|.||..-+...   ..+||||.||..||++-+.+ .+.||.||.++..
T Consensus        82 ~sef~c~vc~~~l~~p---v~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCC---ccccccccccHHHHHHHhcc-CCCCccccccccc
Confidence            4578999998887776   67799999999999997775 5569999998875

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.49  E-value=0.0023  Score=60.42  Aligned_cols=54  Identities=24%  Similarity=0.577  Sum_probs=43.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCC-------CCCCccccCCcCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWR-------TFCPVCKRDARTSTGE  283 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-------~~CP~CR~~i~~~~~~  283 (444)
                      ...|..|--.+..+|.+| |-|-|+||.+|++.|-..-.       -.||.|-.+|++....
T Consensus        50 ~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~Nl  110 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINL  110 (299)
T ss_pred             CCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccc
Confidence            467999998888888766 55999999999999976521       1399999999876543

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=96.43  E-value=0.0012  Score=58.01  Aligned_cols=35  Identities=20%  Similarity=0.484  Sum_probs=30.8

Q ss_pred             CccccccccccccCceeEEeccC------CeecHhHHHHHH
Q 013394          229 SRTCAICLEDYSVGEKLRILPCR------HKFHAFCVDSWL  263 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~------H~FH~~Ci~~Wl  263 (444)
                      ..+|+||++.....+.+..++|+      |+||..|+++|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence            37899999999886678888885      899999999994

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

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

Probab=96.20  E-value=0.0024  Score=66.43  Aligned_cols=54  Identities=26%  Similarity=0.604  Sum_probs=43.3

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEP  284 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~~  284 (444)
                      .+..|++|...+.++-  ....|+|.||..|+..|+..++. ||.|+..+......+
T Consensus        20 ~~l~C~~C~~vl~~p~--~~~~cgh~fC~~C~~~~~~~~~~-cp~~~~~~~~~~~~~   73 (391)
T KOG0297|consen   20 ENLLCPICMSVLRDPV--QTTTCGHRFCAGCLLESLSNHQK-CPVCRQELTQAEELP   73 (391)
T ss_pred             ccccCccccccccCCC--CCCCCCCcccccccchhhccCcC-CcccccccchhhccC
Confidence            4589999999987762  22579999999999999999554 999998876655444

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

Probab=95.97  E-value=0.0063  Score=62.24  Aligned_cols=48  Identities=29%  Similarity=0.579  Sum_probs=39.3

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcC-------CCCCCcccc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-------RTFCPVCKR  275 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-------~~~CP~CR~  275 (444)
                      .-..|.||.++..-.+.+..|||+|+||+.|+...+..+       .-.||-|+-
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            458999999998877899999999999999999998642       234876654

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A

Probab=95.83  E-value=0.006  Score=44.08  Aligned_cols=41  Identities=37%  Similarity=0.853  Sum_probs=27.6

Q ss_pred             ccccccccccCceeEEeccC--C---eecHhHHHHHHhc-CCCCCCcc
Q 013394          232 CAICLEDYSVGEKLRILPCR--H---KFHAFCVDSWLTS-WRTFCPVC  273 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lpC~--H---~FH~~Ci~~Wl~~-~~~~CP~C  273 (444)
                      |-||+++-...+ ..+.||+  -   ..|..|+++|+.. .+..|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999876655 4567864  2   6899999999985 34459887

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

Probab=95.78  E-value=0.0042  Score=44.95  Aligned_cols=45  Identities=24%  Similarity=0.630  Sum_probs=22.6

Q ss_pred             ccccccccccCceeEEec--cCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          232 CAICLEDYSVGEKLRILP--CRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lp--C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      |++|.+++...+ ...+|  |++..+..|...-++.....||-||++.
T Consensus         1 cp~C~e~~d~~d-~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETD-KDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCC-TT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCC-CccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999984433 34455  7899999998888875566799999863

>PHA02862 5L protein; Provisional

Probab=95.77  E-value=0.0057  Score=54.11  Aligned_cols=47  Identities=26%  Similarity=0.536  Sum_probs=34.9

Q ss_pred             CccccccccccccCceeEEeccCC-----eecHhHHHHHHhc-CCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRH-----KFHAFCVDSWLTS-WRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H-----~FH~~Ci~~Wl~~-~~~~CP~CR~~i~~  279 (444)
                      ++.|-||+++-.  ++  .-||++     .-|.+|+.+|+.. ++..|++||.+..-
T Consensus         2 ~diCWIC~~~~~--e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          2 SDICWICNDVCD--ER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CCEEEEecCcCC--CC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            368999999842  22  467754     5899999999975 34569999987643

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

Probab=95.69  E-value=0.0062  Score=61.46  Aligned_cols=45  Identities=27%  Similarity=0.635  Sum_probs=33.0

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      ...+.|.||+++...   ...+||||+-|  |..--.  |...||+||+.|.
T Consensus       303 ~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIR  347 (355)
T ss_pred             CCCCceEEecCCccc---eeeecCCcEEE--chHHHh--hCCCCchhHHHHH
Confidence            346899999998665   58899999965  544332  2345999998764

>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=95.66  E-value=0.0052  Score=51.49  Aligned_cols=32  Identities=25%  Similarity=0.685  Sum_probs=27.7

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHH
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVD  260 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~  260 (444)
                      ++..|++|-..+.. ....+.||||+||..|++
T Consensus        77 ~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            35789999999877 578899999999999975

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 [].

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=95.54  E-value=0.0098  Score=53.60  Aligned_cols=49  Identities=20%  Similarity=0.602  Sum_probs=36.2

Q ss_pred             CCccccccccccccCceeEEeccCC-----eecHhHHHHHHhcC-CCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRH-----KFHAFCVDSWLTSW-RTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H-----~FH~~Ci~~Wl~~~-~~~CP~CR~~i~~~  280 (444)
                      .+..|-||.++-.  +  ..-||.+     ..|.+|++.|+... ...|+.|+.+....
T Consensus         7 ~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          7 MDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4589999998843  2  2357654     46999999999864 45699999876544

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

Probab=95.42  E-value=0.0058  Score=64.11  Aligned_cols=55  Identities=27%  Similarity=0.602  Sum_probs=41.2

Q ss_pred             cCCCccccccccccccCceeEEeccCCeecHhHHHHHHhc----CCCCCCccccCCcCCCCC
Q 013394          226 NCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS----WRTFCPVCKRDARTSTGE  283 (444)
Q Consensus       226 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~----~~~~CP~CR~~i~~~~~~  283 (444)
                      +.+..+|-+|-+.-   +...+..|.|.||.-||..+...    .+.+||+|...+.-+...
T Consensus       533 nk~~~~C~lc~d~a---ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse  591 (791)
T KOG1002|consen  533 NKGEVECGLCHDPA---EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSE  591 (791)
T ss_pred             ccCceeecccCChh---hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccc
Confidence            44567999999863   33477789999999999887653    456799998877655333

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

Probab=95.30  E-value=0.018  Score=56.17  Aligned_cols=50  Identities=20%  Similarity=0.484  Sum_probs=38.4

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcC-CCCCCccccCCc
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-RTFCPVCKRDAR  278 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~~~CP~CR~~i~  278 (444)
                      ..+.+|++|-+.-..+  ....+|+|+||..||..-+... ..+||.|-.++.
T Consensus       237 t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            3468999999986666  4566799999999999876642 245999976655

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.17  E-value=0.0015  Score=66.09  Aligned_cols=52  Identities=25%  Similarity=0.601  Sum_probs=44.8

Q ss_pred             CccccccccccccC-ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          229 SRTCAICLEDYSVG-EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       229 ~~~C~ICle~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ...|+||.+.++.. +++..+-|+|.+|..||.+||..... ||.||+++....
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~k-l~~~~rel~~~~  248 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRK-LPSCRRELPKNG  248 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHH-hHHHHhhhhhhh
Confidence            46899999999887 77888889999999999999998554 999999876543

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

Probab=95.07  E-value=0.016  Score=56.95  Aligned_cols=43  Identities=28%  Similarity=0.556  Sum_probs=35.5

Q ss_pred             ccccccccccccCceeEEec-cCCeecHhHHHHHHhcCCCCCCcccc
Q 013394          230 RTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKR  275 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~~~CP~CR~  275 (444)
                      ..|+.|..-....   ..+| |+|.||.+||..-|......||.|.+
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            7899998877666   3446 89999999999998877777999955

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.89  E-value=0.032  Score=53.52  Aligned_cols=55  Identities=13%  Similarity=0.218  Sum_probs=45.8

Q ss_pred             CCccccccccccccCceeEEec-cCCeecHhHHHHHHhcCCCCCCccccCCcCCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE  283 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~  283 (444)
                      ..+.|+||.+.+.+...+.+|. |||+|+.+|+++.+.. ...||+|-+++.+....
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRDII  275 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccceE
Confidence            3589999999999998888775 9999999999998876 44599998887665443

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

Probab=94.79  E-value=0.0098  Score=55.19  Aligned_cols=44  Identities=27%  Similarity=0.602  Sum_probs=37.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD  276 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~  276 (444)
                      ...|-||-++|+.+   .+..|||.||..|...-.+... .|-+|-+.
T Consensus       196 PF~C~iCKkdy~sp---vvt~CGH~FC~~Cai~~y~kg~-~C~~Cgk~  239 (259)
T COG5152         196 PFLCGICKKDYESP---VVTECGHSFCSLCAIRKYQKGD-ECGVCGKA  239 (259)
T ss_pred             ceeehhchhhccch---hhhhcchhHHHHHHHHHhccCC-cceecchh
Confidence            47899999999887   6778999999999888777644 49999664

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=94.77  E-value=0.017  Score=57.63  Aligned_cols=48  Identities=35%  Similarity=0.795  Sum_probs=41.7

Q ss_pred             ccccccccccccCc---eeEEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          230 RTCAICLEDYSVGE---KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       230 ~~C~ICle~~~~~~---~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      ..|-||-++|+..+   ..|+|.|||.|+..|+.+-+......||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            67999999998874   3478889999999999998888777799999875

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=94.70  E-value=0.011  Score=56.79  Aligned_cols=49  Identities=27%  Similarity=0.602  Sum_probs=37.3

Q ss_pred             cccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCC
Q 013394          231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE  283 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~  283 (444)
                      .|.-|..--. ++...++.|.|+||..|...-...   .||+||+.+......
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~~---~C~lCkk~ir~i~l~   53 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSPD---VCPLCKKSIRIIQLN   53 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhcccCCcc---ccccccceeeeeecc
Confidence            4777765444 888999999999999997764332   599999987655543

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

Probab=94.64  E-value=0.026  Score=56.55  Aligned_cols=62  Identities=23%  Similarity=0.512  Sum_probs=43.4

Q ss_pred             HhhcccceeeccccccCCCccccccccccccCceeEEeccCCeecHhHHHHH--HhcCCCCCCccccC
Q 013394          211 VKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW--LTSWRTFCPVCKRD  276 (444)
Q Consensus       211 ~~~lp~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~W--l~~~~~~CP~CR~~  276 (444)
                      +..-|.++....++.+.+...|.||-+...-   ..++||+|..|.-|--.-  |...+ .||+||.+
T Consensus        43 lsaEPnlttsSaddtDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K-~C~~CrTE  106 (493)
T COG5236          43 LSAEPNLTTSSADDTDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQK-GCPLCRTE  106 (493)
T ss_pred             cccCCccccccccccccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhcc-CCCccccc
Confidence            3445655555555555567899999887544   589999999999996442  44434 49999985

>cd04821 PA_M28_1_2 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2

Probab=94.31  E-value=0.12  Score=47.07  Aligned_cols=39  Identities=15%  Similarity=0.266  Sum_probs=31.3

Q ss_pred             CCCcceEEEEecCCCCH-------------------HHHHHHHHHcCCeEEEEeccCC
Q 013394           73 SNMSSAFVLTIRGGCSF-------------------EDKVRNAQKAGFEAAIVYDNED  111 (444)
Q Consensus        73 ~~~~~~ivLV~RG~CsF-------------------~~Kv~~Aq~aGA~avII~n~~~  111 (444)
                      -|++||||+|.+|+=.|                   ..|.+.|+++||+|||+.++..
T Consensus        46 ~DVkGKiVvvl~~~P~~~~~~~~~f~~~~~~~~~~~~~K~~~A~~~GA~gvi~v~~~~  103 (157)
T cd04821          46 LDVKGKTVVILVNDPGFATPDSGLFNGKAMTYYGRWTYKYEEAARQGAAGALIVHETE  103 (157)
T ss_pred             CCcCCcEEEEEcCCCCcccccccccCcccccccccHHHHHHHHHHCCCeEEEEEeCCC
Confidence            46789999998776533                   3599999999999999997643

A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt

>PHA03096 p28-like protein; Provisional

Probab=94.25  E-value=0.02  Score=56.95  Aligned_cols=46  Identities=33%  Similarity=0.732  Sum_probs=33.5

Q ss_pred             ccccccccccccC----ceeEEec-cCCeecHhHHHHHHhcCC--CCCCcccc
Q 013394          230 RTCAICLEDYSVG----EKLRILP-CRHKFHAFCVDSWLTSWR--TFCPVCKR  275 (444)
Q Consensus       230 ~~C~ICle~~~~~----~~~~~lp-C~H~FH~~Ci~~Wl~~~~--~~CP~CR~  275 (444)
                      ..|.||+|.....    .....|+ |.|.||..||..|-....  ..||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            6899999987653    2445777 999999999999986532  22555543

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

Probab=93.87  E-value=0.022  Score=56.06  Aligned_cols=46  Identities=22%  Similarity=0.461  Sum_probs=38.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      .+.|-||.+.|..+   ++..|+|.||..|-..-++.... |.+|-+++.
T Consensus       241 Pf~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~qk~~~-c~vC~~~t~  286 (313)
T KOG1813|consen  241 PFKCFICRKYFYRP---VVTKCGHYFCEVCALKPYQKGEK-CYVCSQQTH  286 (313)
T ss_pred             Cccccccccccccc---hhhcCCceeehhhhccccccCCc-ceecccccc
Confidence            47899999999887   77789999999999888877554 999977553

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

Probab=93.82  E-value=0.015  Score=57.99  Aligned_cols=49  Identities=24%  Similarity=0.557  Sum_probs=39.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ..+|.+|-.-|-+..  .+..|-|.||+.||.+.|+.. .+||+|...|...
T Consensus        15 ~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~~-~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   15 HITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEES-KYCPTCDIVIHKT   63 (331)
T ss_pred             ceehhhccceeecch--hHHHHHHHHHHHHHHHHHHHh-ccCCccceeccCc
Confidence            578999988877663  344699999999999999994 4599998766443

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=93.80  E-value=0.038  Score=41.06  Aligned_cols=46  Identities=26%  Similarity=0.494  Sum_probs=33.4

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ..|..|...   +.+-.++||+|+.+..|.+.|--  + -||.|-+++...+
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~rY--n-gCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGERY--N-GCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccChhhc--c-CCCCCCCcccCCC
Confidence            456666654   33448899999999999887633  2 4999988876544

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

Probab=93.53  E-value=0.066  Score=53.87  Aligned_cols=49  Identities=22%  Similarity=0.493  Sum_probs=39.6

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      .+++.|+||.-.--.   ....||+|.=|..||.+-|...+. |=.|+..+.+
T Consensus       420 sEd~lCpICyA~pi~---Avf~PC~H~SC~~CI~qHlmN~k~-CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAGPIN---AVFAPCSHRSCYGCITQHLMNCKR-CFFCKTTVID  468 (489)
T ss_pred             cccccCcceecccch---hhccCCCCchHHHHHHHHHhcCCe-eeEecceeee
Confidence            457899999865333   367799999999999999998555 9999987764

>PF04641 Rtf2: Rtf2 RING-finger

Probab=93.47  E-value=0.093  Score=51.63  Aligned_cols=55  Identities=18%  Similarity=0.314  Sum_probs=41.8

Q ss_pred             CCCccccccccccccCceeEEe-ccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCC
Q 013394          227 CTSRTCAICLEDYSVGEKLRIL-PCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE  283 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~  283 (444)
                      .....|+|+..+|........| ||||+|-..+|++--  ....||+|-.++...+..
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~~~DiI  166 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFTEEDII  166 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccccCCEE
Confidence            4468999999999666555544 799999999999973  233599998887755433

>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]

Probab=93.23  E-value=0.043  Score=60.79  Aligned_cols=49  Identities=29%  Similarity=0.632  Sum_probs=35.9

Q ss_pred             CCCccccccccccccCcee-EEeccCCeecHhHHHHHHhcC------CCCCCcccc
Q 013394          227 CTSRTCAICLEDYSVGEKL-RILPCRHKFHAFCVDSWLTSW------RTFCPVCKR  275 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~-~~lpC~H~FH~~Ci~~Wl~~~------~~~CP~CR~  275 (444)
                      ....+|.||+|.+...+.+ -.-.|-|+||..||..|-.+.      ...||-|+.
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            3468999999998766533 222378999999999997641      135999973

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans

Probab=93.19  E-value=0.071  Score=54.61  Aligned_cols=29  Identities=28%  Similarity=0.776  Sum_probs=23.1

Q ss_pred             cCCeecHhHHHHHHhcCC------------CCCCccccCCc
Q 013394          250 CRHKFHAFCVDSWLTSWR------------TFCPVCKRDAR  278 (444)
Q Consensus       250 C~H~FH~~Ci~~Wl~~~~------------~~CP~CR~~i~  278 (444)
                      |.-.+|.+|+-+|+..++            ..||+||+.+.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            677899999999997543            24999999754

They are purported to be transmembrane protein-precursors but their function is unknown.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.87  E-value=0.058  Score=53.98  Aligned_cols=52  Identities=23%  Similarity=0.632  Sum_probs=37.1

Q ss_pred             CccccccccccccCce-eEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEK-LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ++.|+.|+|++...|+ ..--|||...|.-|...--+.-+..||-||+...+.
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            3569999999988764 445568877777775554444456799999976544

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

Probab=92.77  E-value=0.03  Score=55.04  Aligned_cols=42  Identities=29%  Similarity=0.661  Sum_probs=31.9

Q ss_pred             CccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      ...|+||++.   +.....|+|||. =|.+|-...    + .||+||+.|.
T Consensus       300 ~~LC~ICmDa---P~DCvfLeCGHmVtCt~CGkrm----~-eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDA---PRDCVFLECGHMVTCTKCGKRM----N-ECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcC---CcceEEeecCcEEeehhhcccc----c-cCchHHHHHH
Confidence            5789999986   455789999998 577785432    2 4999998664

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

Probab=92.50  E-value=0.033  Score=61.67  Aligned_cols=42  Identities=21%  Similarity=0.657  Sum_probs=32.4

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      ..|..|--.+..+  ..-.-|+|.||..|++    .+...||-|+-+.
T Consensus       841 skCs~C~~~LdlP--~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLP--FVHFLCGHSYHQHCLE----DKEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccc--eeeeecccHHHHHhhc----cCcccCCccchhh
Confidence            6899998776665  4555699999999998    3345699998744

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)

Probab=92.45  E-value=0.066  Score=37.92  Aligned_cols=42  Identities=24%  Similarity=0.634  Sum_probs=24.1

Q ss_pred             ccccccccccCceeEEeccCCeecHhHHHHHHhcCCC-CCCcc
Q 013394          232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRT-FCPVC  273 (444)
Q Consensus       232 C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~-~CP~C  273 (444)
                      |.+|.+-...|.....-.|+=.+|..|++.++...+. .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            6788888777744333348889999999999987553 49987

; PDB: 3NW0_A 2CT0_A.

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=91.88  E-value=0.082  Score=48.42  Aligned_cols=49  Identities=27%  Similarity=0.716  Sum_probs=34.1

Q ss_pred             ccccccccccccC----ceeEEeccCCeecHhHHHHHHhc----CCC------CCCccccCCc
Q 013394          230 RTCAICLEDYSVG----EKLRILPCRHKFHAFCVDSWLTS----WRT------FCPVCKRDAR  278 (444)
Q Consensus       230 ~~C~ICle~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~----~~~------~CP~CR~~i~  278 (444)
                      ..|-||+.---.|    ..+.-..|+.-||.-|+..||..    .+.      .||.|-.+|.
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            6788987533222    23344569999999999999863    221      3999988764

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

Probab=91.45  E-value=0.31  Score=48.82  Aligned_cols=47  Identities=21%  Similarity=0.431  Sum_probs=35.1

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      +...|+||+..-.++.  ...--|-+||..||-..+.+++. ||+=-.++
T Consensus       299 ~~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~~~~~-CPVT~~p~  345 (357)
T KOG0826|consen  299 DREVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVVNYGH-CPVTGYPA  345 (357)
T ss_pred             ccccChhHHhccCCCc--eEEecceEEeHHHHHHHHHhcCC-CCccCCcc
Confidence            3579999998865552  22225999999999999998766 99865543

>KOG1940 consensus Zn-finger protein [General function prediction only]

Probab=90.93  E-value=0.098  Score=51.64  Aligned_cols=46  Identities=26%  Similarity=0.639  Sum_probs=38.8

Q ss_pred             CccccccccccccCc-eeEEeccCCeecHhHHHHHHhcCCCCCCcccc
Q 013394          229 SRTCAICLEDYSVGE-KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR  275 (444)
Q Consensus       229 ~~~C~ICle~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~  275 (444)
                      ...|+||.|.+.... .+..++|+|.-|..|.+.....+ -+||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence            345999999887764 56789999999999999988887 66999987

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

Probab=90.60  E-value=0.12  Score=49.30  Aligned_cols=40  Identities=38%  Similarity=0.953  Sum_probs=29.9

Q ss_pred             cccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCc
Q 013394          231 TCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      .|-.|.+.   +..+..+||.|. +|..|=+. +   + .||+|+....
T Consensus       160 ~Cr~C~~~---~~~VlllPCrHl~lC~~C~~~-~---~-~CPiC~~~~~  200 (207)
T KOG1100|consen  160 SCRKCGER---EATVLLLPCRHLCLCGICDES-L---R-ICPICRSPKT  200 (207)
T ss_pred             cceecCcC---CceEEeecccceEeccccccc-C---c-cCCCCcChhh
Confidence            38888775   556899999987 88899655 1   2 3999987654

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

Probab=90.45  E-value=0.11  Score=57.79  Aligned_cols=48  Identities=23%  Similarity=0.584  Sum_probs=38.6

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCC-CCCCccccCCcCCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWR-TFCPVCKRDARTST  281 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-~~CP~CR~~i~~~~  281 (444)
                      ..|.||++    .+...+.+|+|.||..|+.+-++... ..||+||..+....
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            79999999    56678888999999999998876532 24999998776544

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

Probab=90.00  E-value=0.11  Score=51.61  Aligned_cols=43  Identities=30%  Similarity=0.669  Sum_probs=27.3

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA  277 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i  277 (444)
                      ..|.-|-...  .-.-|.+||+|+||.+|-..  .. .+.||.|-..|
T Consensus        91 HfCd~Cd~PI--~IYGRmIPCkHvFCl~CAr~--~~-dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPI--AIYGRMIPCKHVFCLECARS--DS-DKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcc--eeeecccccchhhhhhhhhc--Cc-cccCcCcccHH
Confidence            3565564332  22237889999999999654  22 23499995543

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

Probab=88.95  E-value=0.26  Score=49.53  Aligned_cols=44  Identities=23%  Similarity=0.526  Sum_probs=34.6

Q ss_pred             CccccccccccccCceeEEecc--CCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPC--RHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC--~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      -.+|+||.+.+..+    ++.|  ||+-|..|-.+-    ...||.||.++...
T Consensus        48 lleCPvC~~~l~~P----i~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~   93 (299)
T KOG3002|consen   48 LLDCPVCFNPLSPP----IFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNI   93 (299)
T ss_pred             hccCchhhccCccc----ceecCCCcEehhhhhhhh----cccCCccccccccH
Confidence            47899999998886    5668  799999997542    34499999988743

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

Probab=87.70  E-value=0.25  Score=55.39  Aligned_cols=35  Identities=23%  Similarity=0.607  Sum_probs=28.1

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHH
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWL  263 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl  263 (444)
                      .++.|.+|...+-. +...+.||||.||.+||.+-.
T Consensus       816 p~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  816 PQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             CccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence            35899999877654 367889999999999998753

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=86.77  E-value=0.22  Score=57.81  Aligned_cols=49  Identities=29%  Similarity=0.552  Sum_probs=38.5

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ...|.||++.+....  .+.-|+|.+|..|+..|+..+. .||.|+....+.
T Consensus      1153 ~~~c~ic~dil~~~~--~I~~cgh~~c~~c~~~~l~~~s-~~~~~ksi~~df 1201 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQG--GIAGCGHEPCCRCDELWLYASS-RCPICKSIKGDF 1201 (1394)
T ss_pred             ccchHHHHHHHHhcC--CeeeechhHhhhHHHHHHHHhc-cCcchhhhhhhh
Confidence            468999999988431  4556999999999999999855 499998544433

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=84.97  E-value=0.29  Score=52.98  Aligned_cols=43  Identities=35%  Similarity=0.695  Sum_probs=31.2

Q ss_pred             ccccccccccccCc-eeEEeccCCeecHhHHHHHHhcCCCCCCccccC
Q 013394          230 RTCAICLEDYSVGE-KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD  276 (444)
Q Consensus       230 ~~C~ICle~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~  276 (444)
                      ..|.||+..|.... ..+-|-|||..|..|++.-..+   +|| |+++
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~---scp-~~~D   55 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA---SCP-TKRD   55 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc---cCC-CCcc
Confidence            57999988887764 3344559999999999876543   488 6553

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=84.43  E-value=0.73  Score=45.54  Aligned_cols=48  Identities=31%  Similarity=0.553  Sum_probs=35.6

Q ss_pred             ccccccccc-ccCc-eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          231 TCAICLEDY-SVGE-KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       231 ~C~ICle~~-~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      .|++|..+- ..++ .+.+=+|+|..|..|++.-+..+...||.|-..+.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR   51 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR   51 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence            588887543 3333 33333799999999999999998888999965443

>KOG0260 consensus RNA polymerase II, large subunit [Transcription]

Probab=84.21  E-value=25  Score=41.39  Aligned_cols=23  Identities=13%  Similarity=0.336  Sum_probs=12.5

Q ss_pred             CCHHHHHHHHHH-cCCeEEEEecc
Q 013394           87 CSFEDKVRNAQK-AGFEAAIVYDN  109 (444)
Q Consensus        87 CsF~~Kv~~Aq~-aGA~avII~n~  109 (444)
                      -+..+|++.-++ .|-....|+++
T Consensus      1194 ltm~~ia~~i~~~f~~d~~~i~~d 1217 (1605)
T KOG0260|consen 1194 LTMEQIAEKINRGFGSDLACIFSD 1217 (1605)
T ss_pred             ccHHHHHHHHHhhccCCCceeecc
Confidence            566666666553 34444445543

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.95  E-value=0.41  Score=46.41  Aligned_cols=52  Identities=23%  Similarity=0.597  Sum_probs=36.0

Q ss_pred             CCccccccccccccCcee-EEecc-----CCeecHhHHHHHHhcCC-------CCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKL-RILPC-----RHKFHAFCVDSWLTSWR-------TFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~-~~lpC-----~H~FH~~Ci~~Wl~~~~-------~~CP~CR~~i~~  279 (444)
                      .+..|=||++.=++...- =+-||     .|..|..|+..|+.+++       ..||-|+.+...
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii   83 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII   83 (293)
T ss_pred             cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence            357899999874443211 24566     37899999999997643       249999886543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=83.87  E-value=1.1  Score=33.28  Aligned_cols=33  Identities=21%  Similarity=0.716  Sum_probs=27.6

Q ss_pred             CccccccccccccCceeEEec-cCCeecHhHHHH
Q 013394          229 SRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDS  261 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~  261 (444)
                      ...|.+|-+.|+.++.+.+-| |+=.||..|-+.
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            468999999999777777777 999999999544

>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=82.51  E-value=1  Score=46.29  Aligned_cols=46  Identities=20%  Similarity=0.293  Sum_probs=38.9

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCC--CCCCccc
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWR--TFCPVCK  274 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~--~~CP~CR  274 (444)
                      -..|+|=.+.=.+......|.|||+..++-+.+-.+.+.  ..||.|=
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP  381 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCP  381 (394)
T ss_pred             eeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCC
Confidence            368999888777777789999999999999999888766  5699993

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

Probab=81.41  E-value=0.8  Score=50.75  Aligned_cols=50  Identities=20%  Similarity=0.243  Sum_probs=37.7

Q ss_pred             CCccccccccccccC-ceeEEec---cCCeecHhHHHHHHhc-----CCCCCCccccCC
Q 013394          228 TSRTCAICLEDYSVG-EKLRILP---CRHKFHAFCVDSWLTS-----WRTFCPVCKRDA  277 (444)
Q Consensus       228 ~~~~C~ICle~~~~~-~~~~~lp---C~H~FH~~Ci~~Wl~~-----~~~~CP~CR~~i  277 (444)
                      ....|.||.-++..+ |..-.+|   |.|-||..||..|+.+     ....|+.|..-|
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            457889998888873 2345556   9999999999999875     344589987644

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]

Probab=80.97  E-value=0.91  Score=50.12  Aligned_cols=25  Identities=28%  Similarity=0.662  Sum_probs=21.1

Q ss_pred             EeccCCeecHhHHHHHHhcCCCCCCc
Q 013394          247 ILPCRHKFHAFCVDSWLTSWRTFCPV  272 (444)
Q Consensus       247 ~lpC~H~FH~~Ci~~Wl~~~~~~CP~  272 (444)
                      ..-|+|+.|..|...|+..+.. ||.
T Consensus      1045 Cg~C~Hv~H~sc~~eWf~~gd~-Cps 1069 (1081)
T KOG0309|consen 1045 CGTCGHVGHTSCMMEWFRTGDV-CPS 1069 (1081)
T ss_pred             hccccccccHHHHHHHHhcCCc-CCC
Confidence            4559999999999999998664 884

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=80.89  E-value=0.83  Score=45.55  Aligned_cols=52  Identities=27%  Similarity=0.595  Sum_probs=37.9

Q ss_pred             CccccccccccccCce-eEEeccC-----CeecHhHHHHHHhcC-CCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEK-LRILPCR-----HKFHAFCVDSWLTSW-RTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~-~~~lpC~-----H~FH~~Ci~~Wl~~~-~~~CP~CR~~i~~~  280 (444)
                      +..|-||.++...... ..+.||.     +..|..|++.|+..+ +..|-+|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            4789999998655422 4677864     457999999999853 44599998766544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	444
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		1e-09
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		6e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		7e-07
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-06
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		6e-06
2ek8_A	421	Aminopeptidase From Aneurinibacillus Sp. Strain Am-		1e-05
3eif_A	936	1.9 Angstrom Crystal Structure Of The Active Form O		3e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		5e-05

>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein 38 Length = 75

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 36/51 (70%), Gaps = 1/51 (1%)
Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG 282
           C +C+ D+   + LR+LPC H+FHA CVD WL + RT CP+C+ D+  S+G
Sbjct: 26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRT-CPICRADSGPSSG 75

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 21/44 (47%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR 275
           C +C EDY++GE +R LPC H FH  C+  WL    + CPVC++
Sbjct: 18  CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRK 60

>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain Length = 69

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 22/45 (48%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
           C ICL     GE +R LPC H FH  CVD WL + +  CP+C+ D
Sbjct: 17  CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVD 60

>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5 Length = 55

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/44 (54%), Positives = 29/44 (65%), Gaps = 2/44 (4%)
Query: 232 CAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCK 274
           CA+CL +   GE+ R LP C H FHA CVD WL S  T CP+C+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCR 50

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 232 CAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVC 273
           CA+CLED+   ++L I PC+H FH  C+  WL   R  CP+C
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEV-RKVCPLC 58

>pdb|2EK8|A Chain A, Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 Length = 421

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 73  SNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFV 132
            +++    L  RG  SF DKVRNA K G +A I+Y+N  DG L    G S    + AV +
Sbjct: 111 KDLNGKIALIQRGNISFADKVRNAAKQGAKAVIIYNNT-DGKLNGTLGGSDASFVAAVGI 169
Query: 133 SKASGEKL 140
           +K  G+ L
Sbjct: 170 TKQEGDAL 177

>pdb|3EIF|A Chain A, 1.9 Angstrom Crystal Structure Of The Active Form Of The C5a Peptidase From Streptococcus Pyogenes (Scpa) Length = 936

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 3/87 (3%)
Query: 61  ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAG 120
           A +N   K +   ++     L  RG   F+DK+ NA+KAG    ++YDN+D G  + +  
Sbjct: 274 AYANRGMKEDDFKDVKGKIALIERGDIDFKDKIANAKKAGAVGVLIYDNQDKGFPIELPN 333
Query: 121 NSAGIKIHAVFVSKASGEKLKQYAGST 147
                ++ A F+S+  G  LK  +  T
Sbjct: 334 VD---QMPAAFISRKDGLLLKDNSKKT 357

>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3 Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4710b Length = 91

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 207 SRRLVKAMPSLIFT----AVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW 262
           S+  + A+P ++ T    AV ++ C    C IC  +Y  G+    LPC H FH  CV  W
Sbjct: 18  SKESIDALPEILVTEDHGAVGQEMC----CPICCSEYVKGDVATELPCHHYFHKPCVSIW 73
Query: 263 LTSWRTFCPVCK 274
           L    T CPVC+
Sbjct: 74  LQKSGT-CPVCR 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	444
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	3e-27
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	5e-25
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-22
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	7e-21
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	7e-21
2ect_A	78	Ring finger protein 126; metal binding protein, st	8e-19
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	5e-17
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-14
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	4e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-12
1xf1_A	926	C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {St	6e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	1e-08
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	8e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-07
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	3e-07
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-06
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	3e-05
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	4e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-05
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	4e-05
2ek8_A	421	Aminopeptidase; metalloproteinase, hydrolase; 1.80	4e-05
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	7e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	9e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	9e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	9e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	1e-04
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-04
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-04
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	3e-04
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	3e-04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	3e-04
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-04
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	9e-04

>3icu_A E3 ubiquitin-protein ligase RNF128; E3 ligase, energy, PA domain, transmembrane,protein turnover conjugation pathway; HET: NAG; 2.10A {Homo sapiens} Length = 194

 Score =  106 bits (266), Expect = 3e-27
 Identities = 34/153 (22%), Positives = 55/153 (35%), Gaps = 9/153 (5%)

Query: 19  SANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYV---AEPLDACSNLT----SKVEK 71
           S  V   G N T+     E  +          GVL        L+AC+  T      V  
Sbjct: 40  SWRVPHTGVNRTVWELSEEGVYGQDSPLEPVAGVLVPPDGPGALNACNPHTNFTVPTVWG 99

Query: 72  VSNMSSAFVLTIRGG-CSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAV 130
            +   S   L  RGG C+F DK+  A + G   A++++       V    +   + I A+
Sbjct: 100 STVQVSWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAVDIVAI 159

Query: 131 FVSKASGEKLKQY-AGSTDMEIWIIPSFENSAW 162
            +    G K+ Q       + + I    ++  W
Sbjct: 160 MIGNLKGTKILQSIQRGIQVTMVIEVGKKHGPW 192

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75

 Score = 96.6 bits (241), Expect = 5e-25
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 207 SRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW 266
           S      +PS  F            C +C+ D+   + LR+LPC H+FHA CVD WL + 
Sbjct: 2   SSGSSGQLPSYRFNPN-NHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 267 RTFCPVCKRDARTSTG 282
           RT CP+C+ D+  S+G
Sbjct: 61  RT-CPICRADSGPSSG 75

>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} Length = 69

 Score = 90.1 bits (224), Expect = 1e-22
 Identities = 26/66 (39%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 224 EDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE 283
            +  T   C ICL     GE +R LPC H FH  CVD WL + +  CP+C+ D       
Sbjct: 9   TEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDIEA---- 63

Query: 284 PPASES 289
              SES
Sbjct: 64  QLPSES 69

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74

 Score = 85.2 bits (211), Expect = 7e-21
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 223 VEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG 282
           V++      CA+CLED+   ++L I PC+H FH  C+  WL   +  CP+C         
Sbjct: 9   VKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKV-CPLCNMPVLQLAQ 67

Query: 283 EPPASE 288
               S 
Sbjct: 68  LSGPSS 73

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91

 Score = 85.9 bits (213), Expect = 7e-21
 Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 205 GMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLT 264
             S+  + A+P ++ T           C IC  +Y  G+    LPC H FH  CV  WL 
Sbjct: 16  PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQ 75

Query: 265 SWRTFCPVCKRD 276
              T CPVC+  
Sbjct: 76  KSGT-CPVCRCM 86

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78

 Score = 79.4 bits (196), Expect = 8e-19
 Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART--STGEPPASE 288
            C +C EDY++GE +R LPC H FH  C+  WL    + CPVC++      +   PP   
Sbjct: 17  ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRKSLTGQNTATNPPGLT 75

Query: 289 ST 290
             
Sbjct: 76  GV 77

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55

 Score = 73.8 bits (182), Expect = 5e-17
 Identities = 24/46 (52%), Positives = 29/46 (63%), Gaps = 2/46 (4%)

Query: 232 CAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRD 276
           CA+CL +   GE+ R LP C H FHA CVD WL S  T CP+C+  
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLT 52

>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 Length = 55

 Score = 66.1 bits (162), Expect = 2e-14
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 226 NCTSRTCAICLEDYSVGEKL-RILPCRHKFHAFCVDSWLTSWRTFCPVCKRDA 277
           +  S  C ICLED      +  +LPC H  H  C +  L      CP+C   +
Sbjct: 2   SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYR-CPLCSGPS 53

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 63.2 bits (154), Expect = 4e-13
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 6/58 (10%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD-ARTSTGEPPAS 287
            C IC++  +      ILPC H F   C+D W    R  CP+C+      +    P+S
Sbjct: 17  ECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRN-CPICRLQMTGANESSGPSS 69

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 60.9 bits (148), Expect = 2e-12
 Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            +  C ICLED S       LPC H F   C+  W+    T CP+CK  
Sbjct: 4   VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPT-CPLCKVP 49

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 61.1 bits (148), Expect = 3e-12
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)

Query: 222 VVEDNCT------SRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCK 274
           V  D C          C  C  +    + + +   C H FH  C+  W+      CP+C+
Sbjct: 13  VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQ-NNRCPLCQ 71

Query: 275 RD 276
           +D
Sbjct: 72  QD 73

>1xf1_A C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {Streptococcus pyogenes} PDB: 3eif_A* Length = 926

 Score = 67.0 bits (163), Expect = 6e-12
 Identities = 26/130 (20%), Positives = 46/130 (35%), Gaps = 6/130 (4%)

Query: 18  ASANVVLIGNNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSS 77
           + +    +   V +   D +    P +  +                      + V     
Sbjct: 225 SYSPDKQLTETVRVKTADQQDKEMPVLSTNRFEPNKAYDYAYANRGTKEDDFKDVKG--- 281

Query: 78  AFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASG 137
              L  RG   F+DK+  A+KAG    ++YDN+D G  + +       ++ A F+S+  G
Sbjct: 282 KIALIERGDIDFKDKIAKAKKAGAVGVLIYDNQDKGFPIELPNVD---QMPAAFISRKDG 338

Query: 138 EKLKQYAGST 147
             LK     T
Sbjct: 339 LLLKDNPQKT 348

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 5/51 (9%)

Query: 229 SRTCAICLEDYS----VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR 275
           + +C IC++ YS     G  +    C H F + C+   L +  T CP C++
Sbjct: 15  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRK 64

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 5/54 (9%)

Query: 231 TCAICLEDYS----VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS 280
           +C IC++ YS     G  +    C H F + C+   L +  T CP C++     
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHK 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 = 50.2 bits (120), Expect = 2e-08
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 229 SRTCAICLEDYS----VGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS 280
           + +C IC++ YS     G  +    C H F + C+   L +  T CP C++     
Sbjct: 10  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHK 64

>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 = 53.2 bits (127), Expect = 8e-08
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 3/53 (5%)

Query: 224 EDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
           E   T + C IC E+      ++I PC H     C+ SW  S    CP C+ +
Sbjct: 327 EMGSTFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 376

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWL-TSWRTFCPVCKRD 276
           + C IC      G+      C  + H  CV  +  ++    CP C   
Sbjct: 16  KICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 53.2 bits (127), Expect = 1e-07
 Identities = 48/165 (29%), Positives = 64/165 (38%), Gaps = 9/165 (5%)

Query: 277  ARTSTGEPPASESTPLLSSSPASSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVAS 336
              TS      S    L S S + SS   S   +   SS  + P S S+SP+ S  +S  S
Sbjct: 1538 GYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPT-SPSYSPTS 1596

Query: 337  TPYIPQSLRSYCQSPPIS-----VSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNS 391
              Y P S      SP  S      S +S      S   S  S   S  S  Y   SP  S
Sbjct: 1597 PSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1656

Query: 392  RYMSPYLPSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQS 436
                 Y P+  + SP+   S S+      YS ++ S+SP + + S
Sbjct: 1657 PTSPSYSPTSPSYSPT---SPSYSPTSPSYSPTSPSYSPTSPSYS 1698

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 52.4 bits (125), Expect = 3e-07
 Identities = 41/158 (25%), Positives = 59/158 (37%), Gaps = 5/158 (3%)

Query: 279  TSTGEPPASESTPLLSSSPASSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVASTP 338
             + GE P S    + S   + +S   S  S   S ++    P+       S  +S  S  
Sbjct: 1524 GAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1583

Query: 339  YIPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYL 398
            Y P S      SP  S +  S      S   S  S   S  S  Y   SP  S     Y 
Sbjct: 1584 YSPTSPSYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1641

Query: 399  PSPSNASPSLVGSSSHQQHPLHYSESATSFSPFASAQS 436
            P+  + SP+   S S+      YS ++ S+SP + + S
Sbjct: 1642 PTSPSYSPT---SPSYSPTSPAYSPTSPSYSPTSPSYS 1676

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 50.5 bits (120), Expect = 1e-06
 Identities = 43/164 (26%), Positives = 58/164 (35%), Gaps = 12/164 (7%)

Query: 277  ARTSTGEPPASESTPLLSSSPASSSILSSIRSSLASSSALHIPPSMSHSPSVSHIHSVAS 336
               S      +        +    +         A +S      S   SP+ S  +S  S
Sbjct: 1495 LVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPT-SPTYSPTS 1553

Query: 337  TPYIPQSLRSYCQSP---PISVSRSSLDLRHASSQRSHG--SYIMSSHSIGY----PSIS 387
              Y P S      SP   P S S S     ++ +  S+   S   S  S  Y    PS S
Sbjct: 1554 PAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1613

Query: 388  PLNSRYMSPYLPSPSNASPSL-VGSSSHQQHPLHYSESATSFSP 430
            P +  Y SP  PS S  SPS    S S+      YS ++ S+SP
Sbjct: 1614 PTSPSY-SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1656

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 45.5 bits (107), Expect = 3e-05
 Identities = 48/158 (30%), Positives = 66/158 (41%), Gaps = 19/158 (12%)

Query: 284  PPASESTPLLSSSPASSSILSSIRSSLAS----SSALHIPPSMSHSPSVSHIHSVASTPY 339
            P  S ++P  S +  S S  S   S  +     +S  + P S S+SP+ S  +S  S  Y
Sbjct: 1554 PAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSY 1612

Query: 340  IPQSLRSYCQSPPISVSRSSLDLRHASSQRSHGSYIMSSHSIGYPSISPLNSRYMSPYLP 399
             P S      SP  S S +S      S   S  S          PS SP +  Y SP  P
Sbjct: 1613 SPTSPSYSPTSP--SYSPTSPSYSPTSPSYSPTS----------PSYSPTSPSY-SPTSP 1659

Query: 400  SPSNASPSLVGSS-SHQQHPLHYSESATSFSPFASAQS 436
            + S  SPS   +S S+      YS ++ S+SP +   S
Sbjct: 1660 AYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS 1697

>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 = 46.0 bits (109), Expect = 1e-06
 Identities = 15/59 (25%), Positives = 20/59 (33%), Gaps = 2/59 (3%)

Query: 222 VVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS 280
            VE       C IC+E     +      C       C+  WLT  R  CP C+   +  
Sbjct: 15  SVESIAEVFRCFICMEKLR--DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR 71

>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 Length = 114

 Score = 45.2 bits (106), Expect = 3e-06
 Identities = 18/74 (24%), Positives = 23/74 (31%), Gaps = 19/74 (25%)

Query: 231 TCAICLEDYSVGEK---------------LRILPCRHKFHAFCVDSWL----TSWRTFCP 271
            C IC+E  +V                   R+  C H FH  C+ +            CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 272 VCKRDARTSTGEPP 285
            CK      TG  P
Sbjct: 87  SCKTIYGEKTGTQP 100

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 43.5 bits (102), Expect = 4e-06
 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 1/47 (2%)

Query: 231 TCAICLEDYSVGEK-LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            C +C+E   + +       C ++   FC     T     CP C++ 
Sbjct: 13  ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 59

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381

 Score = 46.4 bits (109), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 15/67 (22%)

Query: 232 CAICLEDYSVGEKLRI-----LPCRHKFHAFCVDSWLTSWRTF----------CPVCKRD 276
           C IC      G ++ +       C  K HA C++ W  +              CP CK  
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 277 ARTSTGE 283
             TS   
Sbjct: 371 LSTSFAA 377

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

 Score = 46.4 bits (109), Expect = 2e-05
 Identities = 59/414 (14%), Positives = 117/414 (28%), Gaps = 120/414 (28%)

Query: 27  NNVTLSFDDIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSK-VEKVSNMSSAFVLTIRG 85
                 + DI + F  A   + DC    V +   +   L+ + ++ +     A   T+R 
Sbjct: 12  GEHQYQYKDILSVFEDAFVDNFDCK--DVQDMPKSI--LSKEEIDHIIMSKDAVSGTLR- 66

Query: 86  GCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQ-YA 144
                  + + Q+   +                            FV     E L+  Y 
Sbjct: 67  ---LFWTLLSKQEEMVQK---------------------------FV----EEVLRINYK 92

Query: 145 GSTDMEIWIIPSF--ENSAWSIMAISFISL---LAMSAVLATCFFVRR----HRIRREAP 195
                  +++     E    S+M   +I     L     +   + V R     ++R+   
Sbjct: 93  -------FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145

Query: 196 RASRGRE--FHGM--------------SRRLVKAMPSLIF-------------------- 219
                +     G+              S ++   M   IF                    
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205

Query: 220 TAVVEDNCTSR---TCAICLEDYSVGEKLRILPCRHKF-HAFCV--DSW-LTSWRTFCPV 272
              ++ N TSR   +  I L  +S+  +LR L     + +   V  +     +W  F   
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265

Query: 273 CK-----RDAR-------TSTGEPPASESTPLLSSSPASSSILSSIRSSLASSSALHIPP 320
           CK     R  +        +T        +  L +     S+L              +P 
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTL-TPDEVKSLLLKY----LDCRPQDLPR 320

Query: 321 SM-SHSP-SVSHI-HSVASTPYIPQSLRSYCQSPPISVSRSSLDLRHASSQRSH 371
            + + +P  +S I  S+        + +        ++  SSL++   +  R  
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM 374

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 4/53 (7%)

Query: 224 EDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
           E+      C IC + +       +  CRH F   C      +    C +C + 
Sbjct: 10  EEEEIPFRCFICRQAFQNP---VVTKCRHYFCESCALEHFRA-TPRCYICDQP 58

>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 Length = 94

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 10/40 (25%), Positives = 18/40 (45%)

Query: 226 NCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS 265
           +  S  C +CL +Y V +   I  C+  F   C+  ++  
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVEL 41

>2ek8_A Aminopeptidase; metalloproteinase, hydrolase; 1.80A {Aneurinibacillus SP} PDB: 2ek9_A* Length = 421

 Score = 44.7 bits (105), Expect = 4e-05
 Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 73  SNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFV 132
            +++    L  RG  SF DKVRNA K G +A I+Y N  DG L    G S    + AV +
Sbjct: 111 KDLNGKIALIQRGNISFADKVRNAAKQGAKAVIIY-NNTDGKLNGTLGGSDASFVAAVGI 169

Query: 133 SKASGEKLKQYAG 145
           +K  G+ L     
Sbjct: 170 TKQEGDALAANLR 182

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 40.2 bits (94), Expect = 6e-05
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEPPASE 288
            CAICL+          LPC+H F   CV       +  C +C+++      +   S 
Sbjct: 17  ECAICLQTC---VHPVSLPCKHVFCYLCVKGASWLGKR-CALCRQEIPEDFLDSGPSS 70

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens} Length = 238

 Score = 43.2 bits (101), Expect = 7e-05
 Identities = 23/161 (14%), Positives = 43/161 (26%), Gaps = 25/161 (15%)

Query: 130 VFVSKASGEKLKQYAGSTDMEI--------WIIPSFENSAWSIMAISFISL-----LAMS 176
             V+ A+    K      + E+         II S    A S   ++ +       +   
Sbjct: 77  ALVNLATTSISKMATDFAENELDLFRKALELIIDSETGFASSTNILNLVDQLKGKKMRKK 136

Query: 177 AVLATCFFVRRHRIRREAPRASRGREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICL 236
                     +++   E            +  R +  M   I     +       C IC 
Sbjct: 137 EAEQVLQKFVQNKWLIEKEG------EFTLHGRAILEMEQYIRETYPDAVKI---CNICH 187

Query: 237 EDYSVGEKLRILPCRHKFHAFCVDSWL-TSWRTFCPVCKRD 276
               + +      C  + H  CV  +  ++    CP C   
Sbjct: 188 S--LLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 39.3 bits (92), Expect = 9e-05
 Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 7/48 (14%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR 278
            C  C  +    +  ++LPC H   + C    L +    CP+C+    
Sbjct: 8   RCQQCQAEA---KCPKLLPCLHTLCSGC----LEASGMQCPICQAPWP 48

>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 = 40.6 bits (95), Expect = 9e-05
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            C +C   +   +   I+ C H F   C+  +L +   +CP+C   
Sbjct: 17  MCVLCGGYFI--DATTIIECLHSFCKTCIVRYLET-SKYCPICDVQ 59

>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 = 41.1 bits (96), Expect = 9e-05
 Identities = 19/92 (20%), Positives = 29/92 (31%), Gaps = 10/92 (10%)

Query: 204 HGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWL 263
             +  R     P  +F + VE+      C  C E      +     C+H     C+D   
Sbjct: 30  ASLKDRPASGSPFQLFLSKVEETFQ---CICCQELV---FRPITTVCQHNVCKDCLDRSF 83

Query: 264 TSWRTFCPVCKRDARTSTGEPPASESTPLLSS 295
            +    CP C    R   G   A +    L +
Sbjct: 84  RAQVFSCPAC----RYDLGRSYAMQVNQPLQT 111

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 231 TCAICLEDYSVGEKL-RILPCRHKFHAFCVDSWLT-SWRTF-CPVCKR 275
            C IC+E ++  +   ++L C H     C++  L  S     CP C +
Sbjct: 17  ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSK 64

>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 = 39.9 bits (93), Expect = 2e-04
 Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR 278
            C+ C       E + +  C H F + CV        T CPVC   A 
Sbjct: 24  RCSRCTNILR--EPVCLGGCEHIFCSNCVSDC---IGTGCPVCYTPAW 66

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 11/44 (25%), Positives = 14/44 (31%), Gaps = 3/44 (6%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCK 274
            C+IC       +   I  C H F   C+          CP C 
Sbjct: 17  LCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNR-CPKCN 57

>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 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 39.0 bits (90), Expect = 3e-04
 Identities = 16/66 (24%), Positives = 22/66 (33%), Gaps = 16/66 (24%)

Query: 226 NCTSRTCAICL---------------EDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFC 270
           +     CAIC                   S    +    C H FH  C+  WL + R  C
Sbjct: 34  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVC 92

Query: 271 PVCKRD 276
           P+  R+
Sbjct: 93  PLDNRE 98

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 39.4 bits (91), Expect = 3e-04
 Identities = 15/66 (22%), Positives = 21/66 (31%), Gaps = 16/66 (24%)

Query: 226 NCTSRTCAICLEDYSV---------------GEKLRILPCRHKFHAFCVDSWLTSWRTFC 270
           +     CAIC                        +    C H FH  C+  WL + R  C
Sbjct: 45  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVC 103

Query: 271 PVCKRD 276
           P+  R+
Sbjct: 104 PLDNRE 109

>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 = 38.0 bits (88), Expect = 3e-04
 Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 2/51 (3%)

Query: 230 RTCAICLEDYSVGEKLRIL--PCRHKFHAFCVDSWLTSWRTFCPVCKRDAR 278
           + C  C         L+++   C H     CVD         CP C    R
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR 54

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 7/52 (13%)

Query: 229 SRTCAICLEDYSVGEKLRILPCR-----HKFHAFCVDSWL-TSWRTFCPVCK 274
              C IC  +      L I PC      H  H  C+  W+ +S    C +CK
Sbjct: 15  QDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCK 65

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 40.0 bits (93), Expect = 4e-04
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST 281
            C IC E +        L C H F ++C++ W+      CP+C++D ++ T
Sbjct: 66  QCIICSEYFIEA---VTLNCAHSFCSYCINEWMKRKIE-CPICRKDIKSKT 112

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 39.4 bits (91), Expect = 4e-04
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)

Query: 231 TCAICLEDYSVGEKLR----ILPCRHKFHAFCVDSWLTSWRTFCPVCKR 275
           +C IC++ YS   +         C H F + C+   L +  T CP C++
Sbjct: 9   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRK 56

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66

 Score = 36.7 bits (85), Expect = 9e-04
 Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 3/46 (6%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            C  C     V    +   C H+F   C+ + L+S    C  C+  
Sbjct: 17  KCEKCHL---VLCSPKQTECGHRFCESCMAALLSSSSPKCTACQES 59

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	444
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	99.85
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.66
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.59
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.5
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.5
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.47
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.45
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.38
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.38
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.37
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.37
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.31
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.31
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.29
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.28
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.26
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.25
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.23
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.23
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.21
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.18
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.17
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.16
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.16
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.15
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.14
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.12
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.11
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.08
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.07
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.07
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.05
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.03
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.03
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.01
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.01
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.96
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.95
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.95
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.93
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.93
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.9
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.89
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.89
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.88
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.87
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.83
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.82
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.8
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.79
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.76
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.75
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.73
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.72
2ek8_A	421	Aminopeptidase; metalloproteinase, hydrolase; 1.80	98.68
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.66
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.64
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.61
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.58
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.56
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.55
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.54
3iib_A	444	Peptidase M28; YP_926796.1, structural genomics, J	98.52
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.49
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.46
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.45
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.4
3fed_A	707	Glutamate carboxypeptidase III; metallopeptidase,	98.37
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.27
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.26
3kas_A	640	Transferrin receptor protein 1; transferrin recept	98.25
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.16
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.11
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.06
1y9z_A	441	Alkaline serine protease; subtilisin-like alpha/be	97.67
3nw0_A	238	Non-structural maintenance of chromosomes element	97.66
3i6s_A	649	Subtilisin-like protease; PA-domain, FN3-domain, h	97.64
1xf1_A	926	C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {St	97.58
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.7
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	93.03
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	90.14
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	89.93
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	87.12
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	86.72
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	85.7
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	85.47
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	85.2
1we9_A	64	PHD finger family protein; structural genomics, PH	84.22
2yt5_A	66	Metal-response element-binding transcription facto	82.54
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	82.45
3vta_A	621	Cucumisin; subtilisin-like fold, serine protease,	82.33
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	81.6
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	81.48
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	81.46
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	81.32

>3icu_A E3 ubiquitin-protein ligase RNF128; E3 ligase, energy, PA domain, transmembrane,protein turnover conjugation pathway; HET: NAG; 2.10A {Homo sapiens}

Probab=99.85  E-value=5.7e-21  Score=176.85  Aligned_cols=134  Identities=22%  Similarity=0.322  Sum_probs=105.2

Q ss_pred             ceeeEeeccccccCCCCCCCCceEEEEecC---CcCCCCCCCCCCcccC----CCcceEEEEecCC-CCHHHHHHHHHHc
Q 013394           28 NVTLSFDDIEANFAPAIRGSGDCGVLYVAE---PLDACSNLTSKVEKVS----NMSSAFVLTIRGG-CSFEDKVRNAQKA   99 (444)
Q Consensus        28 ~~~~~f~~~~A~Fg~~~~~~~~~G~L~~~~---p~~aC~~l~~~~~~~~----~~~~~ivLV~RG~-CsF~~Kv~~Aq~a   99 (444)
                      |.++.+.+.+|.||...+..++.|.|+.+.   +.+||++.++......    ..+++||||+||+ |+|.+|+++||++
T Consensus        49 n~t~~~~~e~a~FG~~~p~~~v~G~lv~~~~~~~~~GC~~~~~~~~~~~~~~~~~~gkIaLV~RG~~CsF~~Kv~nAq~a  128 (194)
T 3icu_A           49 NRTVWELSEEGVYGQDSPLEPVAGVLVPPDGPGALNACNPHTNFTVPTVWGSTVQVSWLALIQRGGGCTFADKIHLAYER  128 (194)
T ss_dssp             TCEEEEEEEEEEECTTSCCSCEEEEEECBSSTTCTTCCSTTCCBCCCBCTTSSCBCCEEEEEESCTTCCHHHHHHHHHHT
T ss_pred             cceeeecccccccCCCCCCCCcEEEEEecCCCCCcCCCCCCccccCCcccccccCCCeEEEEECCCCcCHHHHHHHHHHC
Confidence            677788999999999999999999998874   7899999876432211    2368999999999 9999999999999


Q ss_pred             CCeEEEEeccC-CCcceeeecCCCCCceEEEEEEeccccchhhhhcCcc-cceeeeeccccccch
Q 013394          100 GFEAAIVYDNE-DDGVLVAMAGNSAGIKIHAVFVSKASGEKLKQYAGST-DMEIWIIPSFENSAW  162 (444)
Q Consensus       100 GA~avII~n~~-~~~~~~~~~g~~~~i~Ip~v~Is~~~G~~L~~~l~~~-~v~v~I~P~~~~s~~  162 (444)
                      ||+||||||++ ++.....|.... ...||++||++.+|+.|++.++++ .+.+.+........|
T Consensus       129 GA~avIIyNn~~~g~~~~~m~~~~-~~~IPsv~Is~~~G~~L~~~L~~G~~Vtvti~vg~~h~pw  192 (194)
T 3icu_A          129 GASGAVIFNFPGTRNEVIPMSHPG-AVDIVAIMIGNLKGTKILQSIQRGIQVTMVIEVGKKHGPW  192 (194)
T ss_dssp             TCSEEEEECCTTCTTCCCCCCCTT-CCSSEEEEECHHHHHHHHHHHHTTCCEEEEEEEEEEECCC
T ss_pred             CCcEEEEEeCCCCCCceeeecCCC-CCceeEEEECHHHHHHHHHHHHCCCeEEEEEECCCccCCC
Confidence            99999999985 333445555433 457999999999999999988765 455555544443334

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=99.66  E-value=8.8e-17  Score=131.48  Aligned_cols=79  Identities=29%  Similarity=0.555  Sum_probs=68.4

Q ss_pred             cccccCCcHHHHhhcccceeeccccccCCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          200 GREFHGMSRRLVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       200 ~r~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      .....+++++.++.||.+.+.........+..|+||+++|..++.++.|||+|.||..||++|+..+. .||+||+++..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~-~CP~Cr~~~~~   89 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSG-TCPVCRCMFPP   89 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTC-BCTTTCCBSSC
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCC-cCcCcCccCCC
Confidence            34457789999999999888776655556789999999999999999999999999999999999855 59999998864

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.8e-16  Score=122.19  Aligned_cols=70  Identities=37%  Similarity=0.854  Sum_probs=57.2

Q ss_pred             HHhhcccceeeccccccCCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          210 LVKAMPSLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       210 ~~~~lp~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      .++.+|...+.... ...++.+|+||+++|..++.++.+||+|.||..||++|++.+. .||+||+++.+..
T Consensus         5 ~i~~lp~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~-~CP~Cr~~~~~~~   74 (75)
T 1x4j_A            5 SSGQLPSYRFNPNN-HQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR-TCPICRADSGPSS   74 (75)
T ss_dssp             CCSSCCCEEBCSSS-CSSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCS-SCTTTCCCCCCCC
T ss_pred             hHhhCCcEEecCcc-ccCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCC-cCcCcCCcCCCCC
Confidence            34577877776433 2234689999999999999999999999999999999999865 5999999887643

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=2.1e-14  Score=112.24  Aligned_cols=54  Identities=35%  Similarity=0.869  Sum_probs=47.8

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      .+.+|+||++.|..++.+++|+|+|.||..||++|++.+. .||+||+++.....
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRK-VCPLCNMPVLQLAQ   67 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCS-BCTTTCCBCSSCCS
T ss_pred             CCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCC-cCCCcCcccccccc
Confidence            4589999999999999999999999999999999999865 59999999876433

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.50  E-value=2.2e-14  Score=113.33  Aligned_cols=57  Identities=37%  Similarity=0.915  Sum_probs=49.6

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCCC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEP  284 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~~  284 (444)
                      ..+.+|+||++.|..++.++.++|+|.||..||.+|++.+. .||+||+++......+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHD-SCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTC-SCTTTCCCCCCSCSCC
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCC-cCcCcCCccCCcccCC
Confidence            34689999999999999999999999999999999998754 5999999988765443

>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=99.47  E-value=4.4e-14  Score=108.93  Aligned_cols=54  Identities=43%  Similarity=0.960  Sum_probs=47.7

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ..+..|+||++.|..++.++.++|+|.||..||.+|+..+.. ||+||.++....
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~~   65 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDIEAQL   65 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSB-CTTTCSBSCSCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCC-CcCcCccccCcC
Confidence            346789999999998888999999999999999999998654 999999987644

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=99.45  E-value=3.3e-14  Score=104.58  Aligned_cols=49  Identities=47%  Similarity=1.023  Sum_probs=44.4

Q ss_pred             CccccccccccccCceeEEec-cCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      +.+|+||+++|..++.++.++ |+|.||..||++|++.+. .||+||+++.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~-~CP~Cr~~~~   54 (55)
T 1iym_A            5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV   54 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCC-SCSSSCCCSC
T ss_pred             CCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCC-cCcCCCCEeE
Confidence            578999999999999999998 999999999999999854 5999998874

>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=99.38  E-value=5.2e-13  Score=113.03  Aligned_cols=59  Identities=31%  Similarity=0.620  Sum_probs=46.5

Q ss_pred             CccccccccccccCc---------------eeEEeccCCeecHhHHHHHHhc----CCCCCCccccCCcCCCCCCCCC
Q 013394          229 SRTCAICLEDYSVGE---------------KLRILPCRHKFHAFCVDSWLTS----WRTFCPVCKRDARTSTGEPPAS  287 (444)
Q Consensus       229 ~~~C~ICle~~~~~~---------------~~~~lpC~H~FH~~Ci~~Wl~~----~~~~CP~CR~~i~~~~~~~~~~  287 (444)
                      +.+|+||++.|..++               .++.++|+|+||..||+.|+..    .+..||+||..+....+..+..
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~g  102 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWG  102 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCCC
Confidence            468999999997653               4558899999999999999952    2446999999988766655443

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=1.6e-13  Score=109.66  Aligned_cols=51  Identities=29%  Similarity=0.719  Sum_probs=40.2

Q ss_pred             Cccccccccccc-----------cCceeEEec-cCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYS-----------VGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~-----------~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +++|+||+++|.           .++.++.++ |+|.||..||++||++++ +||+||+++...
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~~~   77 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNN-RCPLCQQDWVVQ   77 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCC-BCTTTCCBCCEE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCC-CCCCcCCCcchh
Confidence            456777777774           445567776 999999999999999865 599999987643

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=3.7e-13  Score=107.46  Aligned_cols=60  Identities=27%  Similarity=0.551  Sum_probs=48.3

Q ss_pred             ccCCCccccccccccccCceeEEeccC-----CeecHhHHHHHHhcCC-CCCCccccCCcCCCCCCC
Q 013394          225 DNCTSRTCAICLEDYSVGEKLRILPCR-----HKFHAFCVDSWLTSWR-TFCPVCKRDARTSTGEPP  285 (444)
Q Consensus       225 ~~~~~~~C~ICle~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~~~-~~CP~CR~~i~~~~~~~~  285 (444)
                      ...++..|.||+++|..++.+ ++||+     |.||..||++||..++ .+||+||.++.......+
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~~P   76 (80)
T 2d8s_A           11 TPSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLSG   76 (80)
T ss_dssp             CCTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCSCC
T ss_pred             CCCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcccCC
Confidence            334468999999999887776 69996     9999999999998753 469999999876554443

>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=99.37  E-value=4.3e-13  Score=98.47  Aligned_cols=50  Identities=34%  Similarity=0.721  Sum_probs=43.0

Q ss_pred             CCccccccccccccC-ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVG-EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      ++.+|+||++.|..+ +.++.++|+|.||..||++|+... ..||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG-YRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT-CCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC-CcCCCCCCcCC
Confidence            357899999999664 467889999999999999999986 45999998874

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.31  E-value=8.6e-13  Score=101.92  Aligned_cols=53  Identities=25%  Similarity=0.605  Sum_probs=45.0

Q ss_pred             CCccccccccccccC----ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          228 TSRTCAICLEDYSVG----EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       228 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ++.+|+||++.|...    +.+..++|+|.||..||++|+..+. .||+||.++....
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHKR   65 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCS-BCTTTCCBCCCCS
T ss_pred             CCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCC-CCCCCCCccChhh
Confidence            358899999999763    5668899999999999999999865 5999999887543

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=1.3e-12  Score=100.14  Aligned_cols=51  Identities=25%  Similarity=0.630  Sum_probs=43.3

Q ss_pred             CCccccccccccccC----ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVG----EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +...|+||++.|...    +.+..++|+|.||..||++|+..+. .||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCS-SCTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCC-CCCCCCCccCc
Confidence            458999999999764    4558899999999999999999854 59999998753

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.29  E-value=1.4e-12  Score=98.45  Aligned_cols=51  Identities=25%  Similarity=0.619  Sum_probs=43.7

Q ss_pred             CccccccccccccC----ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVG----EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +.+|+||++.|..+    +.+..++|+|.||..||++|++.+. .||+||+++...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   57 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   57 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCS-BCTTTCCBCTTT
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCC-CCCCCCccCCcc
Confidence            57899999999764    4568899999999999999999854 599999988754

>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=99.28  E-value=1.9e-12  Score=108.73  Aligned_cols=50  Identities=28%  Similarity=0.627  Sum_probs=42.1

Q ss_pred             CCccccccccccccC---------------ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVG---------------EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~---------------~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      +++.|+||++.|...               ..++.++|+|.||..||++||..+. +||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ-VCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCS-BCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCC-cCcCCCCcce
Confidence            468899999999854               1367889999999999999999854 5999999854

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=2.1e-12  Score=99.74  Aligned_cols=50  Identities=32%  Similarity=0.857  Sum_probs=42.7

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      +...|+||++.+..    ..++|+|.||..||.+|+..+. .||+||+++.....
T Consensus        14 ~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHR-NCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCS-SCHHHHHCTTCCCC
T ss_pred             CCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcC-cCCCcCCcccCCCc
Confidence            45899999999876    7899999999999999999744 59999999876543

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=7.2e-12  Score=97.41  Aligned_cols=54  Identities=20%  Similarity=0.351  Sum_probs=43.5

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEP  284 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~~  284 (444)
                      +...|+||++.|.+.  +..++|+|.||..||+.|+..+. .||+||+++.......
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~~~~~   67 (72)
T 2djb_A           14 PYILCSICKGYLIDA--TTITECLHTFCKSCIVRHFYYSN-RCPKCNIVVHQTQPLS   67 (72)
T ss_dssp             GGGSCTTTSSCCSSC--EECSSSCCEECHHHHHHHHHHCS-SCTTTCCCCCSSCSCC
T ss_pred             CCCCCCCCChHHHCc--CEECCCCCHHHHHHHHHHHHcCC-cCCCcCcccCcccccc
Confidence            357999999998774  33349999999999999998844 5999999987655443

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=1.9e-12  Score=100.48  Aligned_cols=49  Identities=31%  Similarity=0.633  Sum_probs=42.0

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ++.+|+||++.|...   ..++|+|.||..||+.|+..+. .||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~---~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~   62 (71)
T 2d8t_A           14 TVPECAICLQTCVHP---VSLPCKHVFCYLCVKGASWLGK-RCALCRQEIPED   62 (71)
T ss_dssp             SCCBCSSSSSBCSSE---EEETTTEEEEHHHHHHCTTCSS-BCSSSCCBCCHH
T ss_pred             CCCCCccCCcccCCC---EEccCCCHHHHHHHHHHHHCCC-cCcCcCchhCHh
Confidence            458899999998664   7789999999999999999854 599999988654

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=99.23  E-value=7.1e-12  Score=96.02  Aligned_cols=48  Identities=38%  Similarity=0.825  Sum_probs=41.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +..|+||++.+..+  ...++|+|.||..||.+|+..+. .||+||.++..
T Consensus         5 ~~~C~IC~~~~~~~--~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   52 (68)
T 1chc_A            5 AERCPICLEDPSNY--SMALPCLHAFCYVCITRWIRQNP-TCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCSC--EEETTTTEEESTTHHHHHHHHSC-STTTTCCCCCC
T ss_pred             CCCCeeCCccccCC--cEecCCCCeeHHHHHHHHHhCcC-cCcCCChhhHh
Confidence            57899999998653  57899999999999999999865 59999998864

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.21  E-value=1.1e-11  Score=99.60  Aligned_cols=53  Identities=26%  Similarity=0.655  Sum_probs=45.2

Q ss_pred             CCccccccccccccCce-eEEeccCCeecHhHHHHHHhcC--CCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEK-LRILPCRHKFHAFCVDSWLTSW--RTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~~--~~~CP~CR~~i~~~  280 (444)
                      +..+|+||++.|...+. .+.++|+|.||..||..|+..+  ...||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             CCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            45889999999988664 7889999999999999999975  35699999987654

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.18  E-value=1e-11  Score=94.81  Aligned_cols=50  Identities=20%  Similarity=0.454  Sum_probs=42.0

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.+..+   ..++|||.||..||.+|+...+..||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           14 DKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCEECTTTCCEESSC---CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             cCCCCCCCChHhcCe---eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            357899999999876   34799999999999999965555699999988654

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.7e-11  Score=95.18  Aligned_cols=50  Identities=26%  Similarity=0.545  Sum_probs=41.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc--CCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS--WRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|...   ..++|+|.||..||..|++.  .+..||+||+++...
T Consensus        19 ~~~~C~IC~~~~~~~---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           19 EEVICPICLDILQKP---VTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCBCTTTCSBCSSE---EECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             cCCEeccCCcccCCe---EEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            458999999998754   66799999999999999973  344699999988654

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.16  E-value=3.1e-11  Score=94.38  Aligned_cols=49  Identities=20%  Similarity=0.573  Sum_probs=41.2

Q ss_pred             CCccccccccccccCceeEEec-cCCeecHhHHHHHHhcCC-CCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWR-TFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~-~~CP~CR~~i~~  279 (444)
                      +...|+||++.|..+   ..++ |+|.||..||+.|+.... ..||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           14 DELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             GGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            357999999999876   6699 999999999999998742 469999997543

>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=99.16  E-value=3.7e-12  Score=108.75  Aligned_cols=51  Identities=29%  Similarity=0.643  Sum_probs=1.0

Q ss_pred             CCccccccccccccC-------------c--eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVG-------------E--KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~-------------~--~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      .++.|+||+++|...             +  .+..++|+|.||..||++||..+. +||+||+++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~-~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ-VCPLDNREWEF  112 (117)
T ss_dssp             CC-----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCC-cCCCCCCeeee
Confidence            458999999999752             2  233458999999999999999855 59999998643

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.15  E-value=2.2e-11  Score=96.75  Aligned_cols=47  Identities=21%  Similarity=0.499  Sum_probs=40.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      ....|+||++.|...   .+++|+|.||..||..|+.... .||+||.++.
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~   60 (81)
T 2csy_A           14 IPFRCFICRQAFQNP---VVTKCRHYFCESCALEHFRATP-RCYICDQPTG   60 (81)
T ss_dssp             CCSBCSSSCSBCCSE---EECTTSCEEEHHHHHHHHHHCS-BCSSSCCBCC
T ss_pred             CCCCCcCCCchhcCe---eEccCCCHhHHHHHHHHHHCCC-cCCCcCcccc
Confidence            457899999998664   5789999999999999998744 5999999885

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.14  E-value=2.7e-11  Score=92.15  Aligned_cols=53  Identities=26%  Similarity=0.503  Sum_probs=43.6

Q ss_pred             Ccccccccc-ccccCce-eEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          229 SRTCAICLE-DYSVGEK-LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       229 ~~~C~ICle-~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      +..|+||++ .|..+.. ...++|||.||..||++|+.+.+..||+||+++....
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCcccccc
Confidence            578999999 7777653 3567999999999999998876667999999887543

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.12  E-value=4.4e-11  Score=94.15  Aligned_cols=50  Identities=18%  Similarity=0.337  Sum_probs=42.7

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|.++   ..++|||.||..||..|+...+..||+||+++...
T Consensus         7 ~~~~C~IC~~~~~~P---v~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            7 EYFRCPISLELMKDP---VIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSSE---EEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCCCccccccCC---EEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            458999999999765   66899999999999999987555699999988643

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.11  E-value=5.1e-11  Score=93.40  Aligned_cols=53  Identities=23%  Similarity=0.466  Sum_probs=43.2

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcC-CCCCCccccCCcCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-RTFCPVCKRDARTSTGE  283 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~~~CP~CR~~i~~~~~~  283 (444)
                      ..+|+||++.+..+++.  ..|+|.||..||++||+++ +.+||+||+++..+.++
T Consensus        15 i~~C~IC~~~i~~g~~C--~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~~   68 (74)
T 2ct0_A           15 VKICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK   68 (74)
T ss_dssp             SCBCSSSCCBCSSSEEC--SSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCCC
T ss_pred             CCcCcchhhHcccCCcc--CCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCCC
Confidence            47899999999877544  3899999999999999875 25699999987755444

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=9.7e-11  Score=88.39  Aligned_cols=43  Identities=26%  Similarity=0.561  Sum_probs=36.8

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc--CCCCCCcc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS--WRTFCPVC  273 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~~~CP~C  273 (444)
                      ++..|+||++.|.+.   ..++|+|.||..||++|++.  .+..||+|
T Consensus        19 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQKP---VTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSSC---EECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCCe---EEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            458999999999875   66799999999999999985  34469998

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.07  E-value=4.6e-11  Score=104.73  Aligned_cols=47  Identities=30%  Similarity=0.890  Sum_probs=40.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +..|+||++.|..+   ..+||||.||..||..|+..+. .||+||.++..
T Consensus        53 ~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLNCAHSFCSYCINEWMKRKI-ECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEETTSCEEEHHHHHHHTTTCS-BCTTTCCBCCC
T ss_pred             cCCCcccCcccCCc---eECCCCCCccHHHHHHHHHcCC-cCCCCCCcCCC
Confidence            36899999998764   7789999999999999999855 49999998753

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.07  E-value=1.1e-10  Score=92.76  Aligned_cols=50  Identities=30%  Similarity=0.521  Sum_probs=42.4

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcC-----CCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-----RTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-----~~~CP~CR~~i~~~  280 (444)
                      ++..|+||++.|..+   ..++|+|.||..||..|+...     ...||+||.++...
T Consensus        18 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           18 EEVTCPICLELLKEP---VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTTSCTTTCSCCSSC---EECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             cCCCCcCCChhhCcc---eeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            458999999998776   578999999999999999873     45699999988653

>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=99.07  E-value=5e-11  Score=98.78  Aligned_cols=49  Identities=27%  Similarity=0.560  Sum_probs=41.4

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|+||++.|..+  +..++|||.||..||..|+...+..||+||.++..
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           22 VFRCFICMEKLRDA--RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HTBCTTTCSBCSSE--EECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCccCCccccCc--cccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            47899999999754  33389999999999999999865569999998854

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.05  E-value=7.9e-11  Score=101.36  Aligned_cols=53  Identities=25%  Similarity=0.605  Sum_probs=45.0

Q ss_pred             CCccccccccccccC----ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          228 TSRTCAICLEDYSVG----EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       228 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      +..+|+||++.|..+    +.++.++|||.||..||++|++.++ .||+||+.+....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCS-BCTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCC-CCCCCCCcCcccc
Confidence            357899999999764    5668899999999999999999865 4999999886543

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=1.3e-10  Score=92.23  Aligned_cols=50  Identities=30%  Similarity=0.585  Sum_probs=41.9

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc-----CCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS-----WRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-----~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|...   ..++|+|.||..||..|+..     ....||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           18 EEVTCPICLELLTQP---LSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCTTTCSCCSSC---BCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             CCCCCCCCCcccCCc---eeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            358999999999775   55799999999999999987     244599999988753

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.03  E-value=3.8e-11  Score=94.54  Aligned_cols=49  Identities=29%  Similarity=0.511  Sum_probs=41.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcC------CCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW------RTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~------~~~CP~CR~~i~~  279 (444)
                      +...|+||++.|...   ..++|||.||..||..|+...      ...||+||.++..
T Consensus        11 ~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           11 EEVTCPICLELLTEP---LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCEETTTTEECSSC---CCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cCCCCcCCCcccCCe---eECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            458899999999775   458999999999999999863      4569999998865

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=1.1e-10  Score=86.33  Aligned_cols=43  Identities=33%  Similarity=0.842  Sum_probs=36.3

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc--CCCCCCcc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS--WRTFCPVC  273 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~~~CP~C  273 (444)
                      +...|+||++.|..+   ..++|+|.||..||++|+..  .+..||+|
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKEP---VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSSC---CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCcc---EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            457999999999876   55899999999999999754  45569998

>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=99.01  E-value=2e-10  Score=98.62  Aligned_cols=48  Identities=23%  Similarity=0.411  Sum_probs=41.8

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|+||++.|..+   ..++|||.||..||..|+..+...||+||.++..
T Consensus        52 ~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFRP---ITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSSE---EECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcCc---EEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            47899999999865   6789999999999999998656569999998865

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.01  E-value=2.4e-10  Score=92.77  Aligned_cols=48  Identities=21%  Similarity=0.575  Sum_probs=41.0

Q ss_pred             CCccccccccccccCceeEEec-cCCeecHhHHHHHHhcCC-CCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWR-TFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~-~~CP~CR~~i~  278 (444)
                      ++..|+||++.|..+   ..++ |||.||..||..|+.... ..||+||.++.
T Consensus        12 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           12 DELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             TTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             cCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            468999999999876   6889 999999999999997643 46999999863

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=98.96  E-value=2.9e-10  Score=93.74  Aligned_cols=47  Identities=26%  Similarity=0.753  Sum_probs=40.0

Q ss_pred             CccccccccccccCceeEEe-ccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRIL-PCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|+||++.|..+   ..+ +|||.||..||..|+..+. .||+||..+..
T Consensus        22 ~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKT-QCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHTTCC-BCTTTCCBCCG
T ss_pred             CCCcccCChhhCCc---CEECCCCCHhhHHHHHHHHHCCC-CCCCCCCcCCh
Confidence            47899999998764   455 8999999999999999754 59999998765

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.95  E-value=3.4e-10  Score=97.36  Aligned_cols=52  Identities=25%  Similarity=0.618  Sum_probs=43.9

Q ss_pred             CCccccccccccccC----ceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVG----EKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|...    +....++|+|.||..||++|++.++ +||+||.++...
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~  126 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK  126 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCS-BCTTTCCBCCGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCC-CCCCCCCcCChh
Confidence            357899999999763    4457889999999999999999865 499999988654

>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=98.95  E-value=3.5e-10  Score=94.74  Aligned_cols=49  Identities=22%  Similarity=0.663  Sum_probs=40.8

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +..|+||++.|..+  +..++|||.||..||..|+... ..||+||..+...
T Consensus        15 ~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~~-~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFIDA--TTIIECLHSFCKTCIVRYLETS-KYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCSSE--EEETTTCCEEEHHHHHHHHTSC-SBCTTTCCBSCSS
T ss_pred             cCCCccCChHHhCc--CEeCCCCChhhHHHHHHHHHhC-CcCcCCCcccccc
Confidence            47899999998764  3334999999999999999985 4599999988653

>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=98.93  E-value=5.4e-10  Score=99.48  Aligned_cols=49  Identities=22%  Similarity=0.399  Sum_probs=42.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ...|+||++.|..+   ..++|+|.||..||..|+......||+||.++...
T Consensus        78 ~~~C~IC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQP---VTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSE---EECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCC---EEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            47899999998765   56899999999999999997665699999998764

>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=98.93  E-value=4.3e-10  Score=101.32  Aligned_cols=49  Identities=29%  Similarity=0.600  Sum_probs=41.2

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|+||++.|...  +..++|||.||..||+.|+...+..||+||.++..
T Consensus        54 ~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           54 ELMCPICLDMLKNT--MTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHBCTTTSSBCSSE--EEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCcccChHhhCc--CEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            46899999998764  44459999999999999999755669999998854

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=98.90  E-value=1.1e-09  Score=86.66  Aligned_cols=54  Identities=20%  Similarity=0.613  Sum_probs=42.4

Q ss_pred             CCccccccccccccCceeEEec--cCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILP--CRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lp--C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      ++.+|+||+|.+...+. +.+|  |||.||..|+..|+......||+||+++.....
T Consensus        10 ~~~~CpICle~~~~~d~-~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A           10 DPVECPLCMEPLEIDDI-NFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCBCTTTCCBCCTTTT-TCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             cCCcCCccCccCccccc-cccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            45799999999865432 3444  999999999999986655679999998876443

>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=98.89  E-value=2.9e-10  Score=96.29  Aligned_cols=48  Identities=29%  Similarity=0.648  Sum_probs=41.7

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +..|+||++.|...   ..++|||.||..||..|+...+..||+||..+..
T Consensus        15 ~~~C~iC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           15 ECQCGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHBCTTTCSBCSSC---EECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCccCCcccCce---eEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            47899999999865   6789999999999999998756679999998863

>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=98.89  E-value=7e-10  Score=93.09  Aligned_cols=49  Identities=33%  Similarity=0.648  Sum_probs=41.1

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCC--CCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWR--TFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~--~~CP~CR~~i~~~  280 (444)
                      ...|+||++.|..+   ..++|||.||..||..|+....  ..||+||.++...
T Consensus        21 ~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcCe---EECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            36899999999765   4579999999999999998643  3599999988754

>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=98.88  E-value=6.6e-10  Score=94.67  Aligned_cols=49  Identities=24%  Similarity=0.455  Sum_probs=42.2

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ...|+||++.|..+   ..++|||.||..||.+|+......||+||.++...
T Consensus        18 ~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           18 KYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             GGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCcCChhhcCe---EECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            47999999998765   66899999999999999998664699999988653

>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=98.87  E-value=9.8e-10  Score=93.13  Aligned_cols=50  Identities=24%  Similarity=0.553  Sum_probs=42.2

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST  281 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~  281 (444)
                      ...|+||++.|..+   ..++|||.||..||..|+......||+||.++....
T Consensus        23 ~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           23 SISCQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcHhcCc---EEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            47899999998764   558999999999999999985556999999887543

>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=98.83  E-value=1e-09  Score=96.69  Aligned_cols=49  Identities=22%  Similarity=0.489  Sum_probs=42.2

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +...|+||++.|..+   ..++|||.||..||.+|+......||+||.++..
T Consensus        30 ~~~~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           30 AKYLCSACRNVLRRP---FQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCcCCCCCChhhcCc---EECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            358999999999876   5689999999999999998766569999998743

>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=98.82  E-value=1.9e-09  Score=81.96  Aligned_cols=46  Identities=24%  Similarity=0.469  Sum_probs=38.1

Q ss_pred             CccccccccccccCceeEEe--ccCCe-ecHhHHHHHHhcCCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRIL--PCRHK-FHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~l--pC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      +.+|.||++.+.+.   ..+  ||||. |+..|++.|.+.+. .||+||+++.
T Consensus         8 ~~~C~IC~~~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~-~CPiCR~~i~   56 (64)
T 2vje_A            8 IEPCVICQGRPKNG---CIVHGKTGHLMACFTCAKKLKKRNK-PCPVCRQPIQ   56 (64)
T ss_dssp             GSCCTTTSSSCSCE---EEEETTEEEEEECHHHHHHHHHTTC-CCTTTCCCCC
T ss_pred             cCCCCcCCCCCCCE---EEECCCCCChhhHHHHHHHHHHcCC-cCCCcCcchh
Confidence            47899999986543   445  99999 89999999998755 4999999885

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.80  E-value=9.6e-10  Score=81.28  Aligned_cols=46  Identities=22%  Similarity=0.582  Sum_probs=38.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|...   +.|+|+|.||..||..|    ...||+||+++...
T Consensus         5 ~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~----~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            5 QFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS----GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCC
T ss_pred             cCCCceEeCCccCCe---EEcCCCCcccHHHHccC----CCCCCcCCcEeecC
Confidence            457899999999876   67899999999999885    34599999988653

>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=98.79  E-value=2.2e-09  Score=108.81  Aligned_cols=49  Identities=31%  Similarity=0.712  Sum_probs=41.7

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ..+|+||++.+..   ...+||||.||..||..|+......||+||.++...
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            4799999999855   478999999999999999995455699999988754

>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=98.76  E-value=3.6e-09  Score=80.18  Aligned_cols=47  Identities=21%  Similarity=0.524  Sum_probs=38.2

Q ss_pred             CccccccccccccCceeEEe--ccCCe-ecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRIL--PCRHK-FHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~l--pC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +..|.||++.+.+.   ..+  ||||. |+..|+..|.+.. ..||+||+++..
T Consensus         7 ~~~C~IC~~~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~-~~CPiCR~~i~~   56 (63)
T 2vje_B            7 LKPCSLCEKRPRDG---NIIHGRTGHLVTCFHCARRLKKAG-ASCPICKKEIQL   56 (63)
T ss_dssp             GSBCTTTSSSBSCE---EEEETTEEEEEECHHHHHHHHHTT-CBCTTTCCBCCE
T ss_pred             CCCCcccCCcCCCe---EEEecCCCCHhHHHHHHHHHHHhC-CcCCCcCchhhc
Confidence            57899999986543   445  99999 9999999999875 459999998853

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=98.75  E-value=4.5e-09  Score=84.47  Aligned_cols=48  Identities=8%  Similarity=-0.101  Sum_probs=42.0

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +...|+||++.|+++   .+++|||.|+..||..|+..+ .+||+||.++..
T Consensus        13 ~~~~CpI~~~~m~dP---V~~~cGhtf~r~~I~~~l~~~-~~cP~~~~~l~~   60 (85)
T 2kr4_A           13 DEFRDPLMDTLMTDP---VRLPSGTVMDRSIILRHLLNS-PTDPFNRQMLTE   60 (85)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHC-SBCTTTCCBCCG
T ss_pred             hheECcccCchhcCC---eECCCCCEECHHHHHHHHhcC-CCCCCCcCCCCh
Confidence            358999999999886   788999999999999999975 459999988754

>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=98.73  E-value=4.4e-09  Score=87.23  Aligned_cols=48  Identities=8%  Similarity=-0.083  Sum_probs=42.1

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +...|+||++.|.++   .+++|||.|+..||..|+..+ .+||+||.++..
T Consensus        28 ~~~~CpI~~~~m~dP---V~~~cGhtf~r~~I~~~l~~~-~~cP~~~~~l~~   75 (100)
T 2kre_A           28 DEFRDPLMDTLMTDP---VRLPSGTIMDRSIILRHLLNS-PTDPFNRQTLTE   75 (100)
T ss_dssp             TTTBCTTTCSBCSSE---EEETTTEEEEHHHHHHHTTSC-SBCSSSCCBCCT
T ss_pred             HhhCCcCccCcccCC---eECCCCCEEchHHHHHHHHcC-CCCCCCCCCCCh
Confidence            358999999999887   788999999999999999964 559999998764

>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=98.72  E-value=5.2e-09  Score=86.47  Aligned_cols=49  Identities=12%  Similarity=-0.033  Sum_probs=42.5

Q ss_pred             CCccccccccccccCceeEEeccC-CeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCR-HKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~-H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|+++   .+++|| |.|+..||.+|+..+ .+||+||.++...
T Consensus        21 ~~~~CpI~~~~m~dP---V~~~cG~htf~r~cI~~~l~~~-~~cP~~~~~l~~~   70 (98)
T 1wgm_A           21 DEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSD-QTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTS-CBCTTTCSBCCTT
T ss_pred             HhcCCcCccccccCC---eECCCCCeEECHHHHHHHHHhC-CCCCCCCCCCChh
Confidence            358999999999887   778999 999999999999974 4599999988653

>2ek8_A Aminopeptidase; metalloproteinase, hydrolase; 1.80A {Aneurinibacillus SP} PDB: 2ek9_A*

Probab=98.68  E-value=5.2e-08  Score=100.39  Aligned_cols=91  Identities=31%  Similarity=0.384  Sum_probs=67.4

Q ss_pred             CCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCce
Q 013394           47 SGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIK  126 (444)
Q Consensus        47 ~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~  126 (444)
                      .+++|.|+...-- ..+++  .   ..++++|||||+||+|.|.+|+++|+++||+|||||++.+.. .....+......
T Consensus        91 g~v~a~lv~~~~G-~~~D~--~---~~dv~GkIvlv~~g~~~~~~k~~~A~~~GA~gvIi~~~~~~~-~~g~~~~~~~~~  163 (421)
T 2ek8_A           91 SDVTAELVYVGLG-TTADV--A---GKDLNGKIALIQRGNISFADKVRNAAKQGAKAVIIYNNTDGK-LNGTLGGSDASF  163 (421)
T ss_dssp             EEEEEEEEECTTC-CTTTT--T---TSCCTTSEEEEECCSSCHHHHHHHHHHTTCSEEEEECSSSSC-CCCBCSSCCTTC
T ss_pred             CCcceEEEECCCC-Chhhc--C---CCCcCceEEEEeCCCCCHHHHHHHHHHCCCeEEEEEeCCCcc-cccccCCCCCCC
Confidence            4678888765321 11221  1   225689999999999999999999999999999999987542 222233334568


Q ss_pred             EEEEEEeccccchhhhhc
Q 013394          127 IHAVFVSKASGEKLKQYA  144 (444)
Q Consensus       127 Ip~v~Is~~~G~~L~~~l  144 (444)
                      ||++.|+.++++.|++.+
T Consensus       164 IP~~~Is~~~a~~L~~~l  181 (421)
T 2ek8_A          164 VAAVGITKQEGDALAANL  181 (421)
T ss_dssp             CEEEEECHHHHHHHHHHH
T ss_pred             ccEEEeCHHHHHHHHHHh
Confidence            999999999999988776

>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=98.66  E-value=8.4e-09  Score=99.59  Aligned_cols=49  Identities=16%  Similarity=0.135  Sum_probs=42.9

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ....|+||++.|.++   .++||||.||..||..|+..+..+||+||.++..
T Consensus       207 ~~~~c~i~~~~~~dP---v~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSSE---EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcCC---eECCCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            468999999999886   7899999999999999998755559999998854

>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=98.64  E-value=5.7e-09  Score=88.69  Aligned_cols=45  Identities=31%  Similarity=0.543  Sum_probs=38.8

Q ss_pred             CccccccccccccCceeEEe-ccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRIL-PCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|+||++.|..+   ..+ +|||.||..||..|+.   ..||+||..+..
T Consensus        22 ~~~C~IC~~~~~~p---v~~~~CgH~fC~~Ci~~~~~---~~CP~Cr~~~~~   67 (117)
T 1jm7_B           22 LLRCSRCTNILREP---VCLGGCEHIFCSNCVSDCIG---TGCPVCYTPAWI   67 (117)
T ss_dssp             TTSCSSSCSCCSSC---BCCCSSSCCBCTTTGGGGTT---TBCSSSCCBCSC
T ss_pred             CCCCCCCChHhhCc---cEeCCCCCHHHHHHHHHHhc---CCCcCCCCcCcc
Confidence            47899999999776   566 8999999999999998   359999998743

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.61  E-value=9.7e-09  Score=80.23  Aligned_cols=43  Identities=23%  Similarity=0.641  Sum_probs=36.6

Q ss_pred             CccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +..|.||++.+.+   ...+||||. ||..|+..|     ..||+||.++..
T Consensus        24 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~-----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV-----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC-----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC-----ccCCCcCcCccC
Confidence            4789999998765   477899999 999999999     349999998754

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.58  E-value=2.5e-08  Score=74.90  Aligned_cols=48  Identities=29%  Similarity=0.654  Sum_probs=37.5

Q ss_pred             CCccccccccccccCceeEEeccC--C---eecHhHHHHHHhc-CCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCR--H---KFHAFCVDSWLTS-WRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~--H---~FH~~Ci~~Wl~~-~~~~CP~CR~~i~  278 (444)
                      +...|.||+++.  ++++ ++||.  |   .||..|+++|+.. ++.+||+||.++.
T Consensus         5 ~~~~CrIC~~~~--~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEEC--SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCC--CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            457899999983  3344 68965  4   8999999999975 3566999998764

>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=98.56  E-value=2.5e-08  Score=90.02  Aligned_cols=50  Identities=24%  Similarity=0.456  Sum_probs=42.5

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|+||++.|..+   ..++|||.||..||.+|+......||+||.++...
T Consensus        17 ~~~~C~IC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcCc---EECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            358999999998775   56899999999999999987554699999988653

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=98.55  E-value=8.2e-09  Score=102.16  Aligned_cols=53  Identities=28%  Similarity=0.619  Sum_probs=40.7

Q ss_pred             CCCccccccccccccCcee----E-EeccCCeecHhHHHHHHhcCC----------CCCCccccCCcC
Q 013394          227 CTSRTCAICLEDYSVGEKL----R-ILPCRHKFHAFCVDSWLTSWR----------TFCPVCKRDART  279 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~----~-~lpC~H~FH~~Ci~~Wl~~~~----------~~CP~CR~~i~~  279 (444)
                      ....+|+||++.+..+.++    . -..|+|.||..||.+||.+..          ..||.||++|..
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            3467999999999873322    2 246999999999999998631          249999998764

>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=98.54  E-value=4.2e-08  Score=80.19  Aligned_cols=46  Identities=22%  Similarity=0.495  Sum_probs=38.7

Q ss_pred             CCccccccccccccCceeEEec-cCCeecHhHHHHHHhcC-----CCCCCc--cccC
Q 013394          228 TSRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSW-----RTFCPV--CKRD  276 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~-----~~~CP~--CR~~  276 (444)
                      ....|+||++.|.++   .+++ |||.|+..||..|+..+     ..+||+  |+..
T Consensus         6 ~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            6 SGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             cEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            357899999999876   6776 99999999999999864     246999  9865

>3iib_A Peptidase M28; YP_926796.1, structural genomics, J center for structural genomics, JCSG, protein structure INI PSI-2; HET: PGE; 1.70A {Shewanella amazonensis SB2B}

Probab=98.52  E-value=1.5e-07  Score=97.71  Aligned_cols=105  Identities=11%  Similarity=0.041  Sum_probs=74.8

Q ss_pred             cccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCC---------HHHHH----HHHHHcCCeEE
Q 013394           38 ANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCS---------FEDKV----RNAQKAGFEAA  104 (444)
Q Consensus        38 A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~Cs---------F~~Kv----~~Aq~aGA~av  104 (444)
                      ..+++..+..+++|.|+.....+.|....     ..+++||||||.||.|.         |..|.    .+|+++||+|+
T Consensus        95 l~~s~~tp~~~vta~lV~v~~~~~~~~~~-----~~dvkGKIVlv~~~~~~~~~~~~y~~~~~kr~~~a~~A~~aGA~av  169 (444)
T 3iib_A           95 LGGSIATPAQGLSATIVRFDTLQDLQNAE-----AGSLNDKIAFIDAKTERHRDGKGYGQTASGRSRGAVAAAEKGAVGI  169 (444)
T ss_dssp             CBTCCCCCTTCEEEEEEEESSHHHHHTSC-----TTTTTTCEEEECCCCCCCTTCHHHHHHHHHHHHHHHHHHHTTCSEE
T ss_pred             ccCCCCCCCCCeEEEEEecCCHHHHhhcc-----ccccCccEEEEeCCCCCCcccccccchhhhhhhHHHHHHHCCCeEE
Confidence            34566566678999998887666665431     23567999999999995         77774    57999999999


Q ss_pred             EEeccCCCcc---eeeecC-CCCCceEEEEEEeccccchhhhhcCcc
Q 013394          105 IVYDNEDDGV---LVAMAG-NSAGIKIHAVFVSKASGEKLKQYAGST  147 (444)
Q Consensus       105 II~n~~~~~~---~~~~~g-~~~~i~Ip~v~Is~~~G~~L~~~l~~~  147 (444)
                      ||+|+..+..   .....+ ......||++.|+.++|+.|++.+..+
T Consensus       170 Ii~~~~~~~~~~~~tg~~~~~~~~~~IP~~~Is~~da~~L~~~l~~g  216 (444)
T 3iib_A          170 IIRSIGTDHDRMAHTGMMRYEEGVTAIPAAAISNPDADLINAMLKRD  216 (444)
T ss_dssp             EEECSCSCCSSCCCCCBCCCCTTSCCCCEEEECHHHHHHHHHHHTTT
T ss_pred             EEEccCCcccccccCCccccCCCCCCCCeEEecHHHHHHHHHHHhCC
Confidence            9998754321   111112 223468999999999999998876543

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.49  E-value=4.4e-08  Score=89.43  Aligned_cols=49  Identities=16%  Similarity=0.125  Sum_probs=42.2

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ....|+||++.|.++   .++||||.|+..||..|+..+..+||+||.++..
T Consensus       105 ~~f~CPI~~elm~DP---V~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          105 DYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             GGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             HhhcccCccccCCCC---eECCCCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            458999999999876   7789999999999999998754469999988754

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.46  E-value=1e-07  Score=73.28  Aligned_cols=45  Identities=31%  Similarity=0.790  Sum_probs=36.7

Q ss_pred             CCccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +...|.||++.+..   +..+||+|. |+..|+..    .+ .||+||++|...
T Consensus        14 ~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~-~CP~CR~~i~~~   59 (68)
T 2ea5_A           14 NSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQ-QCPMCRQFVQES   59 (68)
T ss_dssp             CSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CS-SCTTTCCCCCCE
T ss_pred             CCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CC-CCCCCCcchhce
Confidence            45899999998654   588999999 99999984    23 499999988653

>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=98.45  E-value=7.3e-08  Score=78.56  Aligned_cols=48  Identities=27%  Similarity=0.736  Sum_probs=39.9

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcC-------CCCCCc--cccC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-------RTFCPV--CKRD  276 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-------~~~CP~--CR~~  276 (444)
                      ..+|.||++++..++.+...+|+|.||..|+..+++..       ...||.  ||..
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            57899999999877666666899999999999998741       235999  9987

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.40  E-value=6.8e-08  Score=75.48  Aligned_cols=43  Identities=23%  Similarity=0.585  Sum_probs=35.2

Q ss_pred             CccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +.+|.||++.+...   ..+||+|. ||..|+..+     ..||+||+++..
T Consensus        25 ~~~C~IC~~~~~~~---~~~pCgH~~~C~~C~~~~-----~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIAI---VFVPCGHLVTCKQCAEAV-----DKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCCB---CCSSSCCCCBCHHHHHHC-----SBCTTTCCBCCC
T ss_pred             CCCCCcCCCCCCCE---EEecCCCHHHHHHHhhCC-----CCCccCCceecC
Confidence            36899999987654   67899999 999999642     349999998865

>3fed_A Glutamate carboxypeptidase III; metallopeptidase, bimetallic active site, N-glycosylation, C cation, chloride anion, zinc IONS, dipept glycoprotein; HET: NAG BIX; 1.29A {Homo sapiens} PDB: 3fec_A* 3fee_A* 3ff3_A* 2c6c_A* 2c6g_A* 2c6p_A* 2cij_A* 2jbj_A* 2jbk_A* 3rbu_A* 3bi1_A* 2oot_A* 2pvv_A* 2pvw_A* 2xei_A* 2or4_A* 3bi0_A* 3bhx_A* 3d7d_A* 3d7f_A* ...

Probab=98.37  E-value=2.5e-07  Score=101.11  Aligned_cols=104  Identities=24%  Similarity=0.240  Sum_probs=69.8

Q ss_pred             cCCCCCCCCceEEEEecCCcCCCCCCCCCCc-c-cCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCC-----
Q 013394           40 FAPAIRGSGDCGVLYVAEPLDACSNLTSKVE-K-VSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDD-----  112 (444)
Q Consensus        40 Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~-~-~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~-----  112 (444)
                      |.+-.+..+++|.|+.+.  .||...-.... + ..++.|+||||+||+|+|.+|+++|+++||+|||||++..+     
T Consensus       118 f~ays~~G~v~g~lV~v~--~G~~~Df~~L~~~~~~~v~GkIvlv~~G~~~~~~Kv~~A~~~GA~gviiy~dp~d~~~~g  195 (707)
T 3fed_A          118 YNAFSAQGMPEGDLVYVN--YARTEDFFKLEREMGINCTGKIVIARYGKIFRGNKVKNAMLAGAIGIILYSDPADYFAPE  195 (707)
T ss_dssp             CCTTCCCBCCEECEEECT--TCCHHHHHHHHHTSCCCCTTCEEEEECCSSCHHHHHHHHHHTTCSEEEEECCHHHHCCTT
T ss_pred             ccccCCCCceEEEEEEec--CCchhhHHHHHhccCCCCCCeEEEEECCCCCHhHHHHHHHHCCCEEEEEEcCchhccccc
Confidence            433334456889998874  45532111000 1 33578999999999999999999999999999999986221     


Q ss_pred             -----------------cceeee--cCCC--------------------CCceEEEEEEeccccchhhhhcC
Q 013394          113 -----------------GVLVAM--AGNS--------------------AGIKIHAVFVSKASGEKLKQYAG  145 (444)
Q Consensus       113 -----------------~~~~~~--~g~~--------------------~~i~Ip~v~Is~~~G~~L~~~l~  145 (444)
                                       +.+..+  .|+.                    ....||++-|+..+|+.|++.++
T Consensus       196 ~~~yP~~~~~p~~~vqrGsv~~~~~~GDp~TPG~ps~~~~~r~~~~~~~~~p~IP~~pIS~~da~~Ll~~l~  267 (707)
T 3fed_A          196 VQPYPKGWNLPGTAAQRGNVLNLNGAGDPLTPGYPAKEYTFRLDVEEGVGIPRIPVHPIGYNDAEILLRYLG  267 (707)
T ss_dssp             CCBTTTSSBCCTTCCCCCCCCCCTTCCSTTCTTSCCCTTCCCCCGGGCTTCCSSCEEEECHHHHHHHHHTBC
T ss_pred             cccCCCCccCCCccccccceecccCCCCCCCCCCcccCCCcccChhhccCCCCCCeEecCHHHHHHHHHHhc
Confidence                             000000  1211                    12479999999999999987654

>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=98.27  E-value=1.7e-07  Score=74.14  Aligned_cols=44  Identities=25%  Similarity=0.629  Sum_probs=36.7

Q ss_pred             CccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      +..|.||++.+..   ...+||||. |+..|+..|    . .||+||.++...
T Consensus        18 ~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----Q-SCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----S-BCTTTCCBCCEE
T ss_pred             CCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----C-cCCCCCchhhCe
Confidence            3689999998655   578999999 999999987    2 499999988654

>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=98.26  E-value=3.3e-07  Score=68.91  Aligned_cols=50  Identities=12%  Similarity=0.091  Sum_probs=41.6

Q ss_pred             CccccccccccccCceeEEe-ccCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRIL-PCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      ...|+||++.|.++   .++ +|||+|...||++||..+.+ ||++++++.....
T Consensus         3 ~~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~-cP~t~~~L~~~~L   53 (61)
T 2bay_A            3 HMLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGN-DPITNEPLSIEEI   53 (61)
T ss_dssp             -CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSB-CTTTCCBCCGGGC
T ss_pred             eEEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCC-CcCCcCCCChhhc
Confidence            36899999999865   566 89999999999999998655 9999998865443

>3kas_A Transferrin receptor protein 1; transferrin receptor 1, arenavirus, cell MEMB disulfide bond, endocytosis, HOST-virus inter receptor, secreted, transmembrane; HET: NAG FUC BMA MAN; 2.40A {Homo sapiens} PDB: 1de4_C* 3s9l_A* 3s9m_A* 3s9n_A* 1cx8_A* 1suv_A 2nsu_A

Probab=98.25  E-value=8.5e-07  Score=95.91  Aligned_cols=95  Identities=20%  Similarity=0.194  Sum_probs=65.0

Q ss_pred             CCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCc-c------eee--
Q 013394           47 SGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDG-V------LVA--  117 (444)
Q Consensus        47 ~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~-~------~~~--  117 (444)
                      ..++|.||.+.  .||... ..... -+++||||||+||+|.|.+|+++|+++||+|||||++..+. .      ..+  
T Consensus       106 g~v~g~lV~vg--~G~~~D-~~~l~-vdv~GkIvlv~~g~~~~~~K~~~A~~~GA~gvii~~~~~~~~~~~~~~~~~G~~  181 (640)
T 3kas_A          106 ATVTGKLVHAN--FGTKKD-FEDLY-TPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHA  181 (640)
T ss_dssp             EEEEECEEECT--TCCHHH-HHTCS-SCCTTSEEEEESCSSCHHHHHHHHHTTTCSEEEEECCTTTCCCSCTTCCCCEEC
T ss_pred             CceEEEEEEec--CCChhh-HHHhh-cccCCcEEEEecCCCCHHHHHHHHHHCCCeEEEEEecccccccccccccccccc
Confidence            44778887763  444321 11000 25689999999999999999999999999999999975421 1      000  


Q ss_pred             --ecCC-------------------CCCceEEEEEEeccccchhhhhcC
Q 013394          118 --MAGN-------------------SAGIKIHAVFVSKASGEKLKQYAG  145 (444)
Q Consensus       118 --~~g~-------------------~~~i~Ip~v~Is~~~G~~L~~~l~  145 (444)
                        ..|+                   .....||++.|+.++++.|.+.++
T Consensus       182 ~~~~Gdp~tpg~ps~~~~~~~~~~~~~~p~IP~~~Is~~~a~~Ll~~l~  230 (640)
T 3kas_A          182 HLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNME  230 (640)
T ss_dssp             CSSSSCSCCCSSCC---CCCCCCSSCCCCSSCEEECCHHHHHHHHTTEE
T ss_pred             ccCCCCCCCCCcccccccccccccccCCCCCCEEecCHHHHHHHHHHcc
Confidence              0011                   012369999999999999877543

>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=98.16  E-value=6.5e-07  Score=85.89  Aligned_cols=49  Identities=24%  Similarity=0.507  Sum_probs=40.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcC-CCCCCc--cccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-RTFCPV--CKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~~~CP~--CR~~i~~  279 (444)
                      ...|+||++.|..+  |+.+.|||.|+..||..|+..+ ...||+  ||+.+..
T Consensus       181 el~CPIcl~~f~DP--Vts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          181 ELTCPITCKPYEAP--LISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             CSBCTTTSSBCSSE--EEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             eeECcCccCcccCC--eeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            57899999999766  5556899999999999999863 346999  9987654

>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=98.11  E-value=5.9e-07  Score=90.19  Aligned_cols=44  Identities=30%  Similarity=0.764  Sum_probs=37.3

Q ss_pred             CCccccccccccccCceeEEeccCCe-ecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHK-FHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ++..|+||++.+..   ...+||||. ||..|+..|    . .||+||.++..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~----~-~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL----R-KCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC----S-BCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC----C-cCCCCCCCccC
Confidence            35799999999865   477899999 999999988    3 49999998754

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.06  E-value=2.4e-06  Score=69.77  Aligned_cols=48  Identities=23%  Similarity=0.425  Sum_probs=39.1

Q ss_pred             cccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      .|.+|--.+  ....|.+||+|+||.+|+..|.++....||+|+.+|...
T Consensus         3 fC~~C~~Pi--~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPI--KVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBC--SEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCe--EEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            477786554  345799999999999999999987666799999988654

>1y9z_A Alkaline serine protease; subtilisin-like alpha/beta domain, insert beta barrel domain hydrolase; HET: PMS; 1.40A {Pseudoalteromonas SP} PDB: 1v6c_A* 1wvm_A*

Probab=97.67  E-value=5.5e-05  Score=78.16  Aligned_cols=86  Identities=24%  Similarity=0.302  Sum_probs=62.9

Q ss_pred             CCCCCCCCCCcccCCCcceEEEEecCCC-----CHHHHHHHHHHcCCeEEEEeccCCCccee--eecCCCCCceEEEEEE
Q 013394           60 DACSNLTSKVEKVSNMSSAFVLTIRGGC-----SFEDKVRNAQKAGFEAAIVYDNEDDGVLV--AMAGNSAGIKIHAVFV  132 (444)
Q Consensus        60 ~aC~~l~~~~~~~~~~~~~ivLV~RG~C-----sF~~Kv~~Aq~aGA~avII~n~~~~~~~~--~~~g~~~~i~Ip~v~I  132 (444)
                      ++|.+... ..+..++++||+|++||.|     .|.+|+.+|+++||+++||||+.+.....  ..........||+++|
T Consensus       258 ~~C~~~~~-~~~~~~~~gkivl~~rg~~~~~~~~~~~~~~~~~~aGa~gvii~~~~~~~g~~~~~~~~~~~~~~~p~~~v  336 (441)
T 1y9z_A          258 AECTVNGT-SFSCGNMANKICLVERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSV  336 (441)
T ss_dssp             EEEEEETT-EEECCCCTTEEEEEECCSCSSSSCTHHHHHHHHHHTTCSEEEEECCTTSCSCCCCEEECTTCCCCSCEEEE
T ss_pred             hccccccc-cccCCCccccEEEEeccccCcccccHHHHHHHHHhcCCeEEEEEeCCCccccccccccccccCccccEEEE
Confidence            45664421 1233467899999999987     89999999999999999999886532111  1111223457999999


Q ss_pred             eccccchhhhhcCc
Q 013394          133 SKASGEKLKQYAGS  146 (444)
Q Consensus       133 s~~~G~~L~~~l~~  146 (444)
                      +.++|+.|+++++.
T Consensus       337 ~~~~g~~l~~~~~~  350 (441)
T 1y9z_A          337 DRATGLALKAKLGQ  350 (441)
T ss_dssp             CHHHHHHHHTTTTS
T ss_pred             eHHHHHHHHHHhcC
Confidence            99999999988765

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=97.66  E-value=2.3e-05  Score=74.62  Aligned_cols=53  Identities=23%  Similarity=0.460  Sum_probs=42.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCC-CCCCccccCCcCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWR-TFCPVCKRDARTSTGE  283 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-~~CP~CR~~i~~~~~~  283 (444)
                      ...|.||.+-...+.++  -.|+|.||..|++.|+..+. ..||.|+.+.....+.
T Consensus       180 i~~C~iC~~iv~~g~~C--~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~~  233 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK  233 (238)
T ss_dssp             CCBCTTTCSBCSSCEEC--SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCCC
T ss_pred             CCcCcchhhHHhCCccc--CccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCC
Confidence            57899999998887433  33999999999999998743 4699999987665444

>3i6s_A Subtilisin-like protease; PA-domain, FN3-domain, hydrolase; HET: NAG FUC; 2.50A {Solanum lycopersicum} PDB: 3i74_A*

Probab=97.64  E-value=3.5e-05  Score=83.61  Aligned_cols=88  Identities=16%  Similarity=0.142  Sum_probs=66.5

Q ss_pred             EEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceEEEE
Q 013394           51 GVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAV  130 (444)
Q Consensus        51 G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~v  130 (444)
                      -.|+.+...+.|.+....+.. -+++++|||++||.|.|.+|..+++++||+++|++|+...  +.     .....+|++
T Consensus       259 ~plv~~~~~~~C~~~~l~~~~-vdl~GkIvlc~~g~~~~~~k~~~~~~~Ga~g~i~~n~~~~--~~-----~~~~~~P~~  330 (649)
T 3i6s_A          259 SPVIYNKTLSDCSSEELLSQV-ENPENTIVICDDNGDFSDQMRIITRARLKAAIFISEDPGV--FR-----SATFPNPGV  330 (649)
T ss_dssp             EEEECCTTTTTCCCHHHHTTS-SSGGGCEEEECCCSCHHHHHHHHHHHTCSEEEEECCCGGG--GG-----CCCCCSCEE
T ss_pred             eeeEecccccccccccccccc-cccCCcEEEEeCCCccHHHHHHHHHhcCceEEEEecCccc--cc-----cccCcCCEE
Confidence            345555567789875322211 1237999999999999999999999999999999998622  11     123478999


Q ss_pred             EEeccccchhhhhcCc
Q 013394          131 FVSKASGEKLKQYAGS  146 (444)
Q Consensus       131 ~Is~~~G~~L~~~l~~  146 (444)
                      +|+.++|+.|++++..
T Consensus       331 ~v~~~~g~~i~~yi~s  346 (649)
T 3i6s_A          331 VVNKKEGKQVINYVKN  346 (649)
T ss_dssp             EECHHHHHHHHHHHHT
T ss_pred             EEcHHHHHHHHHHHhc
Confidence            9999999999987653

>1xf1_A C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {Streptococcus pyogenes} PDB: 3eif_A*

Probab=97.58  E-value=8.5e-05  Score=83.73  Aligned_cols=75  Identities=28%  Similarity=0.468  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceEEEEEEeccccch
Q 013394           60 DACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEK  139 (444)
Q Consensus        60 ~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~v~Is~~~G~~  139 (444)
                      ++|.+...     .+++++|||++||.|+|.+|+.+|+++||.++|+||+..+.....+.   ....||+++|+.++|+.
T Consensus       269 ~g~~~~~~-----~~v~Gkivl~~rg~~~~~~k~~~~~~~Ga~gvi~~n~~~~~~~~~~~---~~~~iP~~~i~~~~g~~  340 (926)
T 1xf1_A          269 RGTKEDDF-----KDVKGKIALIERGDIDFKDKIAKAKKAGAVGVLIYDNQDKGFPIELP---NVDQMPAAFISRKDGLL  340 (926)
T ss_dssp             TSCSTTTT-----TTCTTSEEEEECCSSCHHHHHHHHHHTTCSEEEEECSSTTCCCEECC---CSTTCCEEEECHHHHHH
T ss_pred             CCCCccch-----hhcCCeEEEEECCCCCHHHHHHHHHhCCCcEEEEEecCCCCcccccC---ccccccEEEEeHHHHHH
Confidence            46764322     35689999999999999999999999999999999987654333221   23578999999999987


Q ss_pred             hhh
Q 013394          140 LKQ  142 (444)
Q Consensus       140 L~~  142 (444)
                      |+.
T Consensus       341 l~~  343 (926)
T 1xf1_A          341 LKD  343 (926)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            764

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=94.70  E-value=0.022  Score=43.09  Aligned_cols=47  Identities=28%  Similarity=0.470  Sum_probs=34.0

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhcC---CCCCCccccC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW---RTFCPVCKRD  276 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~~~CP~CR~~  276 (444)
                      ..+..|.||.+.   ++-+..=.|...||..|+++.|...   .-.||.|+..
T Consensus        10 ~~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           10 APGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             CTTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            345789999853   4444433489999999999988752   3469999754

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=93.03  E-value=0.045  Score=44.23  Aligned_cols=34  Identities=15%  Similarity=0.368  Sum_probs=27.1

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHH
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW  262 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~W  262 (444)
                      +..|.||++++...-....+.|+|.|+..|+..|
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            4689999987544444556899999999999984

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=89.93  E-value=0.16  Score=39.88  Aligned_cols=35  Identities=17%  Similarity=0.471  Sum_probs=24.6

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHH
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW  262 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~W  262 (444)
                      ..+..|.||- .|..++....=-|+-+||..|+++-
T Consensus        13 ~~D~~C~VC~-~~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceeccccccccccHhhcccc
Confidence            3578999994 5555533222227899999999996

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=87.12  E-value=0.15  Score=39.14  Aligned_cols=51  Identities=20%  Similarity=0.395  Sum_probs=33.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~~i~  278 (444)
                      +...|.||.........+..=-|.-.||..|+..-+..   ..-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            34679999876532222222238889999999865543   2446999987654

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=86.72  E-value=0.3  Score=36.04  Aligned_cols=46  Identities=24%  Similarity=0.671  Sum_probs=32.4

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccccC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKRD  276 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~~  276 (444)
                      .+..|.||.+.   ++.+..-.|...||..|+..-+..   ..-.||.|+..
T Consensus        10 ~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A           10 HQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            46789999873   443333348889999999986543   24469999763

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=85.70  E-value=0.15  Score=37.70  Aligned_cols=49  Identities=27%  Similarity=0.596  Sum_probs=32.9

Q ss_pred             cCCCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccccCC
Q 013394          226 NCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKRDA  277 (444)
Q Consensus       226 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~~i  277 (444)
                      +.++..|.||.+.   ++-+..-.|...||..|+.+-|..   ..-.||.|+...
T Consensus         6 d~~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            3456889999863   333333338889999999865543   234699997654

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=85.47  E-value=0.16  Score=46.80  Aligned_cols=48  Identities=27%  Similarity=0.493  Sum_probs=32.7

Q ss_pred             cCCCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccccC
Q 013394          226 NCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKRD  276 (444)
Q Consensus       226 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~~  276 (444)
                      +.+++.|.+|.+.   ++-+..=.|...||..|+.+.|..   ....||.|+..
T Consensus         4 d~~~~~C~~C~~~---g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~   54 (207)
T 3u5n_A            4 DPNEDWCAVCQNG---GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI   54 (207)
T ss_dssp             CSSCSSBTTTCCC---EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCCCCCCCCCCC---CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCc
Confidence            3456889999853   332222238899999999887654   23469999764

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=85.20  E-value=0.75  Score=39.93  Aligned_cols=48  Identities=21%  Similarity=0.479  Sum_probs=33.6

Q ss_pred             ccCCCccccccccccccCceeEEeccCCeecHhHHHHHHh----------cCCCCCCcccc
Q 013394          225 DNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLT----------SWRTFCPVCKR  275 (444)
Q Consensus       225 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~----------~~~~~CP~CR~  275 (444)
                      ++..++.|.||.+.   ++-+..=.|...||..||++=+.          .....||+|+.
T Consensus        59 ~Dg~~d~C~vC~~G---G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           59 SDGMDEQCRWCAEG---GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TTSCBCSCSSSCCC---SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCCeecccCCC---CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            34457899999874   44333334889999999997552          23456999964

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=84.22  E-value=0.35  Score=35.80  Aligned_cols=48  Identities=29%  Similarity=0.493  Sum_probs=32.9

Q ss_pred             CCccccccccccccCcee-EEeccCCeecHhHHHHHHh----cCCCCCCcccc
Q 013394          228 TSRTCAICLEDYSVGEKL-RILPCRHKFHAFCVDSWLT----SWRTFCPVCKR  275 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~-~~lpC~H~FH~~Ci~~Wl~----~~~~~CP~CR~  275 (444)
                      +...|+||...+..++.. ..-.|...||..|+..-..    ...-.||.|+.
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            357899999888654433 3334899999999865432    13456999975

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=82.54  E-value=0.26  Score=36.73  Aligned_cols=49  Identities=27%  Similarity=0.596  Sum_probs=33.0

Q ss_pred             CCcccccccccccc--CceeEEeccCCeecHhHHHHHHh------cCCCCCCccccC
Q 013394          228 TSRTCAICLEDYSV--GEKLRILPCRHKFHAFCVDSWLT------SWRTFCPVCKRD  276 (444)
Q Consensus       228 ~~~~C~ICle~~~~--~~~~~~lpC~H~FH~~Ci~~Wl~------~~~~~CP~CR~~  276 (444)
                      ++..|.||.+....  ++.+..-.|.-.||..|+.+-+.      ...-.|+.|+..
T Consensus         5 ~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~   61 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFA   61 (66)
T ss_dssp             CCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCc
Confidence            46889999987543  22222223889999999986442      234569999764

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=82.45  E-value=0.3  Score=44.02  Aligned_cols=46  Identities=30%  Similarity=0.545  Sum_probs=32.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccccC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKRD  276 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~~  276 (444)
                      +++.|.||.+.   ++-+..=.|.-.||..|+.+-|..   ..-.||.|+..
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~   51 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDL   51 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCc
Confidence            35789999854   543333348899999999887664   23469999764

>3vta_A Cucumisin; subtilisin-like fold, serine protease, hydrolase; HET: DFP NAG FUC BMA MAN; 2.75A {Cucumis melo}

Probab=82.33  E-value=0.96  Score=48.44  Aligned_cols=69  Identities=12%  Similarity=0.118  Sum_probs=50.0

Q ss_pred             CCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEeccCCCcceeeecCCCCCceEEEEEEeccccchh
Q 013394           61 ACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDNEDDGVLVAMAGNSAGIKIHAVFVSKASGEKL  140 (444)
Q Consensus        61 aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~~~~~~~~~~~g~~~~i~Ip~v~Is~~~G~~L  140 (444)
                      .|.+....+   ....++|++++|   .|..|..+++.+|+.++|++++..+..        ....+|++++...+|..+
T Consensus       269 ~~~~~~~~~---~~v~gkivl~~~---~~~~~~~~~~~~Ga~gvi~~~~~~~~~--------~~~~lP~~~v~~~~g~~i  334 (621)
T 3vta_A          269 FCTDKSVNP---NLLKGKIVVCEA---SFGPHEFFKSLDGAAGVLMTSNTRDYA--------DSYPLPSSVLDPNDLLAT  334 (621)
T ss_dssp             TTCTTCSCG---GGTTTSEEECSS---CCCHHHHHHHHTTCSEEEEECSCCSSC--------CCCSSSEEEECHHHHHHH
T ss_pred             ccccccccc---ccccceEEEEec---CCChhHHhhhhcceeEEEEEecCCCcc--------cccccceEEECHHHHHHH
Confidence            465543322   345799999865   466899999999999999998765421        234688999999988887


Q ss_pred             hhh
Q 013394          141 KQY  143 (444)
Q Consensus       141 ~~~  143 (444)
                      +.+
T Consensus       335 ~~~  337 (621)
T 3vta_A          335 LRY  337 (621)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.60  E-value=0.17  Score=36.62  Aligned_cols=46  Identities=26%  Similarity=0.593  Sum_probs=31.5

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCcccc
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKR  275 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~  275 (444)
                      .++..|.||.+.   ++-+..-.|...||..|+++-|..   ..-.||.|+.
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            346889999874   443443348899999999865543   2335988864

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=81.48  E-value=1.3  Score=37.79  Aligned_cols=48  Identities=23%  Similarity=0.504  Sum_probs=31.6

Q ss_pred             ccCCCccccccccccccCceeEEeccCCeecHhHHHHHH------h----cCCCCCCcccc
Q 013394          225 DNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWL------T----SWRTFCPVCKR  275 (444)
Q Consensus       225 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl------~----~~~~~CP~CR~  275 (444)
                      ++..++.|.||.+.   ++-+..=.|...||..||++=+      +    ...-.|++|+.
T Consensus        53 ~Dg~~~~C~vC~dG---G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           53 SDGMDEQCRWCAEG---GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             TTSCBSSCTTTCCC---SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCCCCcCeecCCC---CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            34456889999864   3322222388999999999742      1    23456999954

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=81.46  E-value=0.41  Score=39.47  Aligned_cols=47  Identities=26%  Similarity=0.599  Sum_probs=31.0

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCK  274 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR  274 (444)
                      +++.|.||.+.=...+-+.--.|...||..|++.++..   ....||.|+
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            46889999876322222444558999999999887642   233466553

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=81.32  E-value=0.56  Score=32.98  Aligned_cols=45  Identities=24%  Similarity=0.571  Sum_probs=29.3

Q ss_pred             cccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCcccc
Q 013394          231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKR  275 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~  275 (444)
                      .|.||.+.-..++-+..-.|...||..|+++=|..   ..-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            48899865333333333348899999999764443   2345999964

---

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	444
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	9e-14
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-12
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	9e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-10
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	5e-09
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	3e-08
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	4e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	4e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	8e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-04

>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 = 63.4 bits (154), Expect = 9e-14
 Identities = 24/47 (51%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 231 TCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            CA+CL +   GE+ R LP C H FHA CVD WL S  T CP+C+  
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLT 52

>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 = 58.9 bits (142), Expect = 6e-12
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 3/58 (5%)

Query: 223 VEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS 280
            E   T + C IC E+    + ++I PC H     C+ SW  S    CP C+ + + +
Sbjct: 17  CEMGSTFQLCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT 71

>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 = 56.3 bits (135), Expect = 4e-11
 Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 2/51 (3%)

Query: 230 RTCAICLEDYSVGEKLRIL--PCRHKFHAFCVDSWLTSWRTFCPVCKRDAR 278
           + C  C         L+++   C H     CVD         CP C    R
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR 54

>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 = 54.7 bits (131), Expect = 9e-11
 Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 1/46 (2%)

Query: 232 CAICLEDYSVGEK-LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
           C +C+E   + +       C ++   FC     T     CP C++ 
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 48

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRD 276
            +  C ICLED S       LPC H F   C+  W+    T CP+CK  
Sbjct: 4   VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPT-CPLCKVP 49

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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]

 Score = 50.9 bits (121), Expect = 5e-09
 Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 16/66 (24%)

Query: 226 NCTSRTCAICLEDY---------------SVGEKLRILPCRHKFHAFCVDSWLTSWRTFC 270
           +     CAIC                   S    +    C H FH  C+  WL + +  C
Sbjct: 18  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-C 76

Query: 271 PVCKRD 276
           P+  R+
Sbjct: 77  PLDNRE 82

>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 = 48.7 bits (116), Expect = 1e-08
 Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 7/54 (12%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEP 284
            C  C  +    +  ++LPC H   + C+++        CP+C+         P
Sbjct: 8   RCQQCQAEA---KCPKLLPCLHTLCSGCLEASGMQ----CPICQAPWPLGADTP 54

>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 = 47.9 bits (113), Expect = 3e-08
 Identities = 13/53 (24%), Positives = 17/53 (32%), Gaps = 3/53 (5%)

Query: 230 RTCAICLEDYSVGEKL--RILPCRHKFHAFCVDSWLTS-WRTFCPVCKRDART 279
             C IC E+                  H  C+ +WLT    T C +C     T
Sbjct: 7   PVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT 59

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

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]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 7/53 (13%)

Query: 229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS-------WRTFCPVCK 274
           S  C +CL +Y V +   I  C+  F   C+  ++             CP   
Sbjct: 5   SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

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]

 Score = 43.5 bits (101), Expect = 4e-06
 Identities = 21/94 (22%), Positives = 30/94 (31%), Gaps = 20/94 (21%)

Query: 225 DNCTSRTCAICLEDYSV---------------GEKLRILPCRHKFHAFCVDSWLTS---- 265
                  C IC+E  +V                   R+  C H FH  C+ +   +    
Sbjct: 21  KVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD 80

Query: 266 WRTFCPVCKRDARTSTGEPPASESTPLLSSSPAS 299
               CP CK      TG  P  +   +  S P+S
Sbjct: 81  GSLQCPSCKTIYGEKTGTQPWGKME-VFRSGPSS 113

>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 = 42.6 bits (100), Expect = 4e-06
 Identities = 15/71 (21%), Positives = 23/71 (32%), Gaps = 3/71 (4%)

Query: 216 SLIFTAVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKR 275
            L+          S +C IC              C+H F   C+   L    ++CP C+ 
Sbjct: 10  KLLAVDFPAHFVKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRY 66

Query: 276 DARTSTGEPPA 286
               +  E P 
Sbjct: 67  PCFPTDLESPV 77

>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 = 42.4 bits (99), Expect = 8e-06
 Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 5/48 (10%)

Query: 231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRT--FCPVCKRD 276
            C ICLE     ++     C H F  FC+   L   +    CP+CK D
Sbjct: 23  ECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

>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 = 37.5 bits (86), Expect = 4e-04
 Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 4/60 (6%)

Query: 221 AVVEDNCTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFC--PVCKRDAR 278
           A ++       C+ C           +  C H F + CV   + +    C  P   +D +
Sbjct: 14  AALDRLEKLLRCSRCTNILREPV--CLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLK 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	444
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.59
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.44
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.42
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.41
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.36
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.35
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.33
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.2
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.13
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.1
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.01
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.96
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.93
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.91
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.8
d1de4c2	193	Transferrin receptor ectodomain, apical domain {Hu	98.65
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.5
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.43
d3bi1a2	233	Glutamate carboxypeptidase II {Human (Homo sapiens	98.13
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	90.67
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	89.97
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	87.82
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	86.63
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	85.12
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	82.6
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	81.83

>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=99.59  E-value=2.6e-16  Score=114.99  Aligned_cols=49  Identities=47%  Similarity=1.023  Sum_probs=44.1

Q ss_pred             CccccccccccccCceeEEec-cCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      +.+|+||+++|..+++++.++ |+|.||..||++||++++ +||+||++|.
T Consensus         5 ~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~-~CP~CR~~i~   54 (55)
T d1iyma_           5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV   54 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCC-SCSSSCCCSC
T ss_pred             CCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCC-cCCCCCCEeE
Confidence            468999999999999998886 999999999999999855 5999999874

>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=99.44  E-value=8.7e-15  Score=105.54  Aligned_cols=49  Identities=20%  Similarity=0.569  Sum_probs=42.3

Q ss_pred             cccccccccccCce-eEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          231 TCAICLEDYSVGEK-LRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       231 ~C~ICle~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      +|+||+++|..++. ++.++|+|.||..||++|++.++..||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            69999999987764 45668999999999999999766679999998865

>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=99.42  E-value=5.1e-14  Score=107.09  Aligned_cols=48  Identities=38%  Similarity=0.825  Sum_probs=41.6

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      .++|+||++.|...  ++.+||+|.||..||.+|++.++ +||+||+++..
T Consensus         5 ~d~C~IC~~~~~~~--~~~~~C~H~Fc~~Ci~~w~~~~~-~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPSNY--SMALPCLHAFCYVCITRWIRQNP-TCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCSC--EEETTTTEEESTTHHHHHHHHSC-STTTTCCCCCC
T ss_pred             CCCCccCCcCccCC--cEEeCCCCcCcHHHHHHHHHhCC-cCCCCCcchHh
Confidence            47899999998654  67899999999999999999865 49999998754

>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=99.41  E-value=1.7e-13  Score=114.36  Aligned_cols=59  Identities=31%  Similarity=0.588  Sum_probs=46.2

Q ss_pred             Ccccccccccccc---------------CceeEEeccCCeecHhHHHHHHhcCC----CCCCccccCCcCCCCCCCCC
Q 013394          229 SRTCAICLEDYSV---------------GEKLRILPCRHKFHAFCVDSWLTSWR----TFCPVCKRDARTSTGEPPAS  287 (444)
Q Consensus       229 ~~~C~ICle~~~~---------------~~~~~~lpC~H~FH~~Ci~~Wl~~~~----~~CP~CR~~i~~~~~~~~~~  287 (444)
                      ++.|+||+++|..               .+.+++++|+|+||..||+.||+..+    .+||+||..+....+..|..
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~qP~~  102 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWG  102 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCCCCC
Confidence            4689999999864               23467788999999999999998642    35999999887766655443

>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=99.36  E-value=1.6e-13  Score=103.29  Aligned_cols=53  Identities=26%  Similarity=0.467  Sum_probs=42.8

Q ss_pred             CCccccccccccccCc--eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGE--KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~--~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ++.+|+||++++..++  .+.+++|+|.||..||++|+...+..||+||+++...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            3589999999875443  4567789999999999999987555699999988653

>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=99.35  E-value=3.3e-13  Score=105.56  Aligned_cols=51  Identities=29%  Similarity=0.673  Sum_probs=43.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      ...|+||++.+..   .+++||||.||..||+.||..+...||+||.+|.....
T Consensus        23 ~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            3579999998765   58899999999999999998655569999999976544

>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=99.33  E-value=3.7e-13  Score=107.42  Aligned_cols=50  Identities=28%  Similarity=0.626  Sum_probs=41.6

Q ss_pred             CCccccccccccccCc---------------eeEEeccCCeecHhHHHHHHhcCCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGE---------------KLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~---------------~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~  278 (444)
                      .++.|+||++.+....               .+..++|+|+||..||++||+.+++ ||+||++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~-CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSB-CSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCc-CCCCCCccc
Confidence            3567999999886532               3678899999999999999999655 999999864

>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=99.20  E-value=3.1e-12  Score=101.37  Aligned_cols=52  Identities=25%  Similarity=0.527  Sum_probs=44.0

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGE  283 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~  283 (444)
                      ...|+||++.|.+.   .+++|||.||..||.+|++.++..||+||.++.+....
T Consensus        23 ~l~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          23 SISCQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CcCCccCCcchhcc---eecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            36899999998764   78999999999999999987666699999988765443

>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=99.13  E-value=3.2e-12  Score=93.20  Aligned_cols=49  Identities=22%  Similarity=0.602  Sum_probs=40.3

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCCCCCC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTGEP  284 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~~~  284 (444)
                      ..+|+||++.|.++   +++||||.||..||++|    +..||+||+++....+.+
T Consensus         6 ~l~C~IC~~~~~~p---~~lpCgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~~~~   54 (56)
T d1bora_           6 FLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGADTP   54 (56)
T ss_dssp             CSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCSSCC
T ss_pred             CCCCcccCcccCCC---EEecCCCHHhHHHHHcC----CCcCcCCCCcccCCCCCC
Confidence            46899999999775   67899999999999876    445999999997655443

>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=99.10  E-value=1e-11  Score=90.41  Aligned_cols=48  Identities=15%  Similarity=0.164  Sum_probs=40.4

Q ss_pred             cccccccccccCceeEEec-cCCeecHhHHHHHHhcCCCCCCccccCCcCCCC
Q 013394          231 TCAICLEDYSVGEKLRILP-CRHKFHAFCVDSWLTSWRTFCPVCKRDARTSTG  282 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~~~  282 (444)
                      .|+||++.|+++   .+++ |||+||.+||.+||++++. ||+||+++...+.
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~-CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGN-DPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSB-CTTTCCBCCGGGC
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccC-CCccCCcCCHHhc
Confidence            599999998765   5564 9999999999999998665 9999998876543

>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=99.01  E-value=5.9e-11  Score=96.99  Aligned_cols=47  Identities=34%  Similarity=0.690  Sum_probs=40.2

Q ss_pred             ccccccccccccCceeEEeccCCeecHhHHHHHHhcCC--CCCCccccCCcC
Q 013394          230 RTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWR--TFCPVCKRDART  279 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~--~~CP~CR~~i~~  279 (444)
                      ..|+||++.|.++   ..++|||.||..||..|+...+  ..||+||.++..
T Consensus        22 l~CpIC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          22 LECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             TSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCCCccCchhCCe---EEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            6799999999776   5689999999999999998743  369999998854

>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=98.96  E-value=1e-10  Score=86.13  Aligned_cols=48  Identities=27%  Similarity=0.527  Sum_probs=37.7

Q ss_pred             CCccccccccccccCceeEEec-----cCCeecHhHHHHHHhc-CCCCCCccccCCc
Q 013394          228 TSRTCAICLEDYSVGEKLRILP-----CRHKFHAFCVDSWLTS-WRTFCPVCKRDAR  278 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lp-----C~H~FH~~Ci~~Wl~~-~~~~CP~CR~~i~  278 (444)
                      +...|.||++++...   .+.|     |+|.||..||++|+.. ++.+||+||+++.
T Consensus         5 d~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           5 DVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            458899999998654   2334     4599999999999965 4556999998764

>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=98.93  E-value=1.9e-10  Score=89.54  Aligned_cols=50  Identities=16%  Similarity=0.133  Sum_probs=43.5

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ++..|+||++-|.++   .+++|||.|+..||.+|+.+.+..||+||.++...
T Consensus         6 ~~l~CpIc~~l~~dP---v~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           6 DYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             STTBCTTTCSBCSSE---EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             ccccCcCcCchhhhh---cccCCcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            358999999999886   67899999999999999988666799999987643

>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=98.91  E-value=2.8e-10  Score=88.13  Aligned_cols=50  Identities=18%  Similarity=0.337  Sum_probs=43.5

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ++..|+||++.|.++   .+++|||.|+..||.+|+..+...||.||.++...
T Consensus         7 ~~l~CpIc~~~m~dP---V~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           7 EYFRCPISLELMKDP---VIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSSE---EEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCcCcCchhhCc---eEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            458999999999876   67899999999999999988666699999987653

>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=98.80  E-value=4.1e-10  Score=90.85  Aligned_cols=46  Identities=26%  Similarity=0.503  Sum_probs=38.3

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcCCCCCCccccCCcC
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDART  279 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~  279 (444)
                      ...|+||++.|..+  +...+|||.||..||.+|+..   .||+||.++..
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~CgH~fC~~Ci~~~~~~---~CP~Cr~~~~~   67 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGGCEHIFCSNCVSDCIGT---GCPVCYTPAWI   67 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCSSSCCBCTTTGGGGTTT---BCSSSCCBCSC
T ss_pred             cCCCccCCchhhcC--ceeCCCCCchhHHHHHHHHhc---cccccCCcCch
Confidence            36899999999776  444589999999999999854   39999988754

>d1de4c2 c.8.4.1 (C:190-382) Transferrin receptor ectodomain, apical domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: PA domain
family: PA domain
domain: Transferrin receptor ectodomain, apical domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=1.3e-08  Score=91.58  Aligned_cols=125  Identities=18%  Similarity=0.210  Sum_probs=78.9

Q ss_pred             cceEEEEEeCceeeEee-ccccccCCCCCCCCceEEEEecCCcCCCCCCCCCCcccCCCcceEEEEecCCCCHHHHHHHH
Q 013394           18 ASANVVLIGNNVTLSFD-DIEANFAPAIRGSGDCGVLYVAEPLDACSNLTSKVEKVSNMSSAFVLTIRGGCSFEDKVRNA   96 (444)
Q Consensus        18 ~~a~v~~~~~~~~~~f~-~~~A~Fg~~~~~~~~~G~L~~~~p~~aC~~l~~~~~~~~~~~~~ivLV~RG~CsF~~Kv~~A   96 (444)
                      ....+.+.+.+..+.|. ..+..|-.-.+...++|.|+.+.-   +...+... -..++.++||||+||+|.|.+|+++|
T Consensus         7 ~~n~~~~~d~~g~~~~~~~~p~~~~ays~~G~v~g~lVy~n~---G~~~Df~~-L~~~v~GkI~l~r~G~~~~~~Kv~~A   82 (193)
T d1de4c2           7 AQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANF---GTKKDFED-LYTPVNGSIVIVRAGKITFAEKVANA   82 (193)
T ss_dssp             SCCEEEEEETTTTEECCCBCCSCCEETCCCEEEEECEEECST---TCHHHHHT-CSSCCTTSEEEEESCSSCHHHHHHHH
T ss_pred             CcceEEEEcCCCCEEeccCCCCceeccCCCCceeEEEEEccC---CCHHHHHH-hccccCceEEEEeCCCCCHHHHHHHH
Confidence            34556666655433332 234445444444568898887632   22111100 01356799999999999999999999


Q ss_pred             HHcCCeEEEEeccCCCcc-------eee----ecCCC-------------------CCceEEEEEEeccccchhhhhcCc
Q 013394           97 QKAGFEAAIVYDNEDDGV-------LVA----MAGNS-------------------AGIKIHAVFVSKASGEKLKQYAGS  146 (444)
Q Consensus        97 q~aGA~avII~n~~~~~~-------~~~----~~g~~-------------------~~i~Ip~v~Is~~~G~~L~~~l~~  146 (444)
                      |++||+|||||.+..+..       ...    ..|+.                   .--.||+.-|+..|++.|++.++.
T Consensus        83 ~~~GA~gviiysDp~d~~~~~~~~~~~g~~~~~~GDPlTPg~ps~~~~~~~~~~~~~lP~IP~~PIS~~dA~~lL~~L~G  162 (193)
T d1de4c2          83 ESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEG  162 (193)
T ss_dssp             HHTTCCCEEEECCTTTSCCSCTTCCCCEECCSSSSCTTSTTSCCCGGGTCCSCCCTTSCSSCEEECCHHHHHHHHTTBCS
T ss_pred             HHcCceEEEEecCccccCCcCcccccccccccCCCCCCCCCcccccccccCccccCCCCcCCeeeCCHHHHHHHHHHcCC
Confidence            999999999998633210       000    11110                   122599999999999999887753

>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=98.50  E-value=2.9e-08  Score=79.97  Aligned_cols=49  Identities=12%  Similarity=-0.023  Sum_probs=41.6

Q ss_pred             CCccccccccccccCceeEEeccC-CeecHhHHHHHHhcCCCCCCccccCCcCC
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCR-HKFHAFCVDSWLTSWRTFCPVCKRDARTS  280 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~-H~FH~~Ci~~Wl~~~~~~CP~CR~~i~~~  280 (444)
                      ++..|+||++-|.++   .+++|+ |.|+..||..||..+. .||+||+++...
T Consensus        21 ~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~-~~P~~~~~l~~~   70 (98)
T d1wgma_          21 DEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQ-TDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSC-BCTTTCSBCCTT
T ss_pred             HHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcC-Ccccccccccch
Confidence            358999999999887   788866 5899999999998855 499999988654

>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=98.43  E-value=3.4e-08  Score=78.60  Aligned_cols=48  Identities=25%  Similarity=0.614  Sum_probs=38.6

Q ss_pred             CCccccccccccccCceeEEeccCCeecHhHHHHHHhcC-------CCCCCcccc
Q 013394          228 TSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW-------RTFCPVCKR  275 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-------~~~CP~CR~  275 (444)
                      ...+|+||++++...+.++.++|+|.||.+|+..|++..       ...||.|+-
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            457899999999877777777899999999999999742       124998643

>d3bi1a2 c.8.4.1 (A:118-350) Glutamate carboxypeptidase II {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: PA domain
family: PA domain
domain: Glutamate carboxypeptidase II
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=1.5e-06  Score=80.03  Aligned_cols=60  Identities=25%  Similarity=0.197  Sum_probs=45.3

Q ss_pred             CCceEEEEecCCcCCCCCCCCCC---cccCCCcceEEEEecCCCCHHHHHHHHHHcCCeEEEEecc
Q 013394           47 SGDCGVLYVAEPLDACSNLTSKV---EKVSNMSSAFVLTIRGGCSFEDKVRNAQKAGFEAAIVYDN  109 (444)
Q Consensus        47 ~~~~G~L~~~~p~~aC~~l~~~~---~~~~~~~~~ivLV~RG~CsF~~Kv~~Aq~aGA~avII~n~  109 (444)
                      ..++|.||.+.-   |...+...   ...-+++++|||+++|++.|.+|+++||++||+|||||++
T Consensus        51 G~v~g~~Vyvny---G~~~Df~~L~~~~gi~~~gkIvl~ryG~~~~~~Kv~~A~~~GA~GviiysD  113 (233)
T d3bi1a2          51 GMPEGDLVYVNY---ARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSD  113 (233)
T ss_dssp             BCCEECEEECTT---CCHHHHHHHHHTSCCCCTTCEEEEECCSSCHHHHHHHHHHTTCSEEEEECC
T ss_pred             CceeEEEEEecC---CcHHHHHHHHHhcCCcccceEEEEeCCCCchhHHHHHHHHcCceEEEEecC
Confidence            347888877642   33222211   1133678999999999999999999999999999999986

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.67  E-value=0.041  Score=37.32  Aligned_cols=45  Identities=24%  Similarity=0.581  Sum_probs=29.9

Q ss_pred             cccccccccccCceeEEeccCCeecHhHHHHHHhcC---CCCCCcccc
Q 013394          231 TCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW---RTFCPVCKR  275 (444)
Q Consensus       231 ~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~~~CP~CR~  275 (444)
                      .|.||...-..++.+.-=.|...||..|++.-+...   .-.||.||.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            488897654333323222389999999999876542   235999974

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=89.97  E-value=0.043  Score=39.05  Aligned_cols=49  Identities=29%  Similarity=0.499  Sum_probs=34.0

Q ss_pred             CCccccccccccccCceeE-EeccCCeecHhHHHHH---Hhc-CCCCCCccccC
Q 013394          228 TSRTCAICLEDYSVGEKLR-ILPCRHKFHAFCVDSW---LTS-WRTFCPVCKRD  276 (444)
Q Consensus       228 ~~~~C~ICle~~~~~~~~~-~lpC~H~FH~~Ci~~W---l~~-~~~~CP~CR~~  276 (444)
                      .+..|.||.+....++.++ .-.|+..||..|+..=   ... ..-.||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            4578999998877766543 3349999999998632   111 23469999753

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.82  E-value=0.12  Score=38.62  Aligned_cols=35  Identities=20%  Similarity=0.532  Sum_probs=26.0

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHH
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSW  262 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~W  262 (444)
                      .++..|.|| +.|...+..-.--|+-+||..|+++-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CcCcccccc-CcccccceecceeecchhhHHHHHHh
Confidence            457899999 88877743311127899999999987

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.63  E-value=0.055  Score=38.19  Aligned_cols=48  Identities=27%  Similarity=0.593  Sum_probs=32.3

Q ss_pred             CCCccccccccccccCceeEEeccCCeecHhHHHHHHhc---CCCCCCccccCC
Q 013394          227 CTSRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTS---WRTFCPVCKRDA  277 (444)
Q Consensus       227 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~~~CP~CR~~i  277 (444)
                      ..++.|.||.+.   ++-+..=.|.-.||..|++..+..   ..-.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            445789999853   433333338899999999866653   234699997543

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.12  E-value=0.12  Score=38.17  Aligned_cols=46  Identities=17%  Similarity=0.380  Sum_probs=29.4

Q ss_pred             ccccccccccccCceeEEec---cCCeecHhHHHH----HHhc----CCCCCCccccCC
Q 013394          230 RTCAICLEDYSVGEKLRILP---CRHKFHAFCVDS----WLTS----WRTFCPVCKRDA  277 (444)
Q Consensus       230 ~~C~ICle~~~~~~~~~~lp---C~H~FH~~Ci~~----Wl~~----~~~~CP~CR~~i  277 (444)
                      ..| ||.+....++ .....   |...||..|+.-    ....    .+-.||.|+..-
T Consensus        17 ~~C-~C~~~~~~~~-~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          17 VRC-VCGNSLETDS-MIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCC-SSCCCCCCSC-EEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             cEe-ECCCccCCCc-EEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            567 9998776544 34453   889999999842    1110    124699997643

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.60  E-value=0.12  Score=38.90  Aligned_cols=50  Identities=20%  Similarity=0.511  Sum_probs=31.3

Q ss_pred             CccccccccccccCc-eeE-EeccCCeecHhHHHHHHh-----c--CCCCCCccccCCc
Q 013394          229 SRTCAICLEDYSVGE-KLR-ILPCRHKFHAFCVDSWLT-----S--WRTFCPVCKRDAR  278 (444)
Q Consensus       229 ~~~C~ICle~~~~~~-~~~-~lpC~H~FH~~Ci~~Wl~-----~--~~~~CP~CR~~i~  278 (444)
                      ...|.||........ .+. .=-|...||..|+.+.+.     .  ..-.||.|+....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            367999987544322 222 223889999999875432     1  1346999976443

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.83  E-value=0.28  Score=35.35  Aligned_cols=44  Identities=23%  Similarity=0.502  Sum_probs=29.9

Q ss_pred             CccccccccccccCceeEEeccCCeecHhHHHHHHhcC---CCCCCcccc
Q 013394          229 SRTCAICLEDYSVGEKLRILPCRHKFHAFCVDSWLTSW---RTFCPVCKR  275 (444)
Q Consensus       229 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~~~CP~CR~  275 (444)
                      ...|.||.+.   ++.+..=.|...||..|+.+.+...   .-.||.|+.
T Consensus         7 c~~C~~C~~~---~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~   53 (70)
T d1fp0a1           7 ATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHV   53 (70)
T ss_dssp             SSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCC
T ss_pred             CCCCCCCCCc---CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcC
Confidence            4567777643   4433333489999999999887542   345999964