Citrus Sinensis ID: 018364

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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-------
Protein Sequence
MVPYYYISTSRGWGWGWGWRWGWGWGRRWHKGANSSGVYSREALDAPFCSSEICSNSQRAEGAKQESKMREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESNEVGV
Secondary Structure (PSIPRED)
cccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccEEEEEEEccEEEEccccccccccccccccEEEEEEccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHccccEEEEEEcccccccccccccccccEEEEEEEcHHHHHHHHHHHccccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHccccEEEEccccccccccccccEEccccccccEEEEEccccccccccHHHHHccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEccccccccccccccccccccccccccccccccHHHccccccccHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHEHcccccEccccccccccccccccccEEEEEEccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHccccEEEEEEccccccEEEccccccccEEEEEEEccccHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHcccEEEEEcccccccccccEEEEEEcccccccEEEEEccccHHHHHcccHHHHHccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MVPYYYIStsrgwgwgwgwrwgwgwgrrwhkganssgvysrealdapfcsseicsnsqraegakQESKMREKFLMKFLIIYLNLCFVVSLSSAtlvwkplslhfpdlpakfavdvnssgtcgalhvadpadacsplsnpvasndadhiNFVLIVRGQCIFEDKIRNAQAAGYRAAIVyndrekgslVSMTASHEGVKVHAIFVSLETGvylkehargetgeccifpesnrgsWSVLMVSVFSLIVVFALFAVAfitprpwrpwpgqnqplsrrldskvvealpcflfssasssqchggetcaicledyqdgeklkvlsckhefhASCVDSWltkwgtfcpvckhdmrnnsesnevgv
Flexible Loop (DISEMBL)
MVPYYYIStsrgwgwgwGWRWGWGWGRRWHKGANSSGVYSREALDAPFCSseicsnsqraegakqesKMREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFitprpwrpwpGQNQPLSRRLDSKVVEALPCFLfssasssqchGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPvckhdmrnnsesnevgv
Low Complexity Region (SEG)
MVPYYYISTSrgwgwgwgwrwgwgwgrrwHKGANSSGVYSREALDAPFCSSEICSNSQRAEGAKQESKMREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESNEVGV
Disordered region (IsUnstruct)
**PYYYISTSRGWGWGWGWRWGWGWGRRWHKGANSSGVYSREALDAPFC**********************KFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH*************
Disordered Region (DISOPRED)
*VPYYYISTSRGWGWGWGWRWGWGWGRRW*****************************************EKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQ**********VEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVC***************
Disordered Region (DISEMBL)
MVPYYYISTSRGWGWGWGWRWGWGWGRRWHKGANSSGVYSREALDAPFCSSEIC*************KMREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN********
Disordered Region (DISPRO)
MVPYYYISTSRGWGWGWGWRWGWGWGRRWHKGANSSGVYSREALDAPFCSSEICSNSQRAEGAKQESKMREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR**********
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVPYYYISTSRGWGWGWGWRWGWGWGRRWHKGANSSGVYSREALDAPFCSSEICSNSQRAEGAKQESKMREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESNEVGV
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	357	2.2.26 [Sep-21-2011]
Q0VD51	380	E3 ubiquitin-protein liga	yes	no	0.649	0.610	0.297	2e-26
Q90972	381	E3 ubiquitin-protein liga	yes	no	0.647	0.606	0.317	2e-26
O54965	381	E3 ubiquitin-protein liga	yes	no	0.649	0.608	0.302	3e-26
Q66HG0	380	E3 ubiquitin-protein liga	yes	no	0.649	0.610	0.302	3e-26
Q5RCV8	381	E3 ubiquitin-protein liga	yes	no	0.649	0.608	0.297	6e-26
O43567	381	E3 ubiquitin-protein liga	yes	no	0.649	0.608	0.297	6e-26
Q91XF4	347	E3 ubiquitin-protein liga	no	no	0.658	0.677	0.289	2e-25
Q9H6Y7	350	E3 ubiquitin-protein liga	no	no	0.655	0.668	0.297	2e-23
Q5XIL0	349	E3 ubiquitin-protein liga	no	no	0.658	0.673	0.302	1e-22
Q8WWF5	429	Zinc/RING finger protein	no	no	0.677	0.564	0.309	2e-20

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

 Score =  120 bits (301), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 120/245 (48%), Gaps = 13/245 (5%)

Query: 104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
           F DLPA+F   + + G  G L  + P +AC P+  P   +++     VLI R  C F++K
Sbjct: 48  FDDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPVRDNSSGTFIVLIRRLDCNFDEK 107

Query: 164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
           + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LK+    E 
Sbjct: 108 VLNAQRAGYKAAIVHN-VDSDDLISMGSNDIEVLKKIDIPSVFIGESSANSLKDEFTYEK 166

Query: 220 GECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVV 279
           G   I            ++    ++ +  +  V F+  +  +      +   R+     +
Sbjct: 167 GGHIILVPEFSLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRARRNRLRK---DQL 223

Query: 280 EALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFC 339
           + LP   F           + CAICL++Y+DG+KL++L C H +H  CVD WLTK    C
Sbjct: 224 KKLPVHKFKKGDEY-----DVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 340 PVCKH 344
           PVCK 
Sbjct: 279 PVCKQ 283

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.
Bos taurus (taxid: 9913)
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 =  120 bits (300), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 125/246 (50%), Gaps = 15/246 (6%)

Query: 104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
           F DLPA+F   + + G  G L  + P +AC P++ P   +++     VLI R +C F+ K
Sbjct: 48  FDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLRDNSSTAFIVLIRRLECNFDIK 107

Query: 164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
           + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LKE    E 
Sbjct: 108 VLNAQRAGYKAAIVHN-VDSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKEEFTYEK 166

Query: 220 G-ECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKV 278
           G    + PE +      L+  +  + +   L  +  IT    +    +++    RL    
Sbjct: 167 GGHVVLIPEFSLPLEYYLIPFLIIVGICLILIVIFMIT----KFVQDRHRARRNRLRKDQ 222

Query: 279 VEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTF 338
           ++ LP   F           + CAICL++Y+DG+KL++L C H +H  CVD WLTK    
Sbjct: 223 LKKLPVHKFKKGDEY-----DVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKT 277

Query: 339 CPVCKH 344
           CPVCK 
Sbjct: 278 CPVCKQ 283

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

 Score =  119 bits (298), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 119/245 (48%), Gaps = 13/245 (5%)

Query: 104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
           F DLPA+F   + + G  G L  + P +AC P+  P   +++     VLI R  C F+ K
Sbjct: 48  FEDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPLKDNSSGTFIVLIRRLDCNFDIK 107

Query: 164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
           + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LK+    E 
Sbjct: 108 VLNAQRAGYKAAIVHN-VDSDDLISMGSNDIDTLKKIDIPSVFIGESSANSLKDEFTYEK 166

Query: 220 GECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVV 279
           G   I            ++    ++ +  +  V F+  +  +      +   R+     +
Sbjct: 167 GGHIILVPELSLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRNRRNRLRK---DQL 223

Query: 280 EALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFC 339
           + LP   F           + CAICLE+Y+DG+KL++L C H +H  CVD WLTK    C
Sbjct: 224 KKLPVHKFKKGDEY-----DVCAICLEEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 340 PVCKH 344
           PVCK 
Sbjct: 279 PVCKQ 283

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 =  119 bits (298), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 119/245 (48%), Gaps = 13/245 (5%)

Query: 104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
           F DLPA+F   + + G  G L  + P +AC P+  P   +++     VLI R  C F+ K
Sbjct: 48  FEDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPLKDNSSGTFIVLIRRLDCNFDIK 107

Query: 164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
           + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LK+    E 
Sbjct: 108 VLNAQRAGYKAAIVHN-VDSDDLISMGSNDIDILKKIDIPSVFIGESSANSLKDEFTYEK 166

Query: 220 GECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVV 279
           G   I            ++    ++ +  +  V F+  +  +      +   R+     +
Sbjct: 167 GGHVILVPELSLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRNRRNRLRK---DQL 223

Query: 280 EALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFC 339
           + LP   F           + CAICLE+Y+DG+KL++L C H +H  CVD WLTK    C
Sbjct: 224 KKLPVHKFKKGDEY-----DVCAICLEEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 340 PVCKH 344
           PVCK 
Sbjct: 279 PVCKQ 283

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 =  118 bits (296), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 13/245 (5%)

Query: 104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
           F DLPA+F   + + G  G L  + P +AC P+  P   +++     VLI R  C F+ K
Sbjct: 48  FDDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPVKDNSSGTFIVLIRRLDCNFDIK 107

Query: 164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
           + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LK+    E 
Sbjct: 108 VLNAQRAGYKAAIVHN-VDSDDLISMGSNDIEVLKKIDIPSVFIGESSANSLKDEFTYEK 166

Query: 220 GECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVV 279
           G   I            ++    ++ +  +  V F+  +  +      +   R+     +
Sbjct: 167 GGHLILVPEFSLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRARRNRLRK---DQL 223

Query: 280 EALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFC 339
           + LP   F           + CAICL++Y+DG+KL++L C H +H  CVD WLTK    C
Sbjct: 224 KKLPVHKFKKGDEY-----DVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 340 PVCKH 344
           PVCK 
Sbjct: 279 PVCKQ 283

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 =  118 bits (296), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 13/245 (5%)

Query: 104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
           F DLPA+F   + + G  G L  + P +AC P+  P   +++     VLI R  C F+ K
Sbjct: 48  FDDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPVKDNSSGTFIVLIRRLDCNFDIK 107

Query: 164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
           + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LK+    E 
Sbjct: 108 VLNAQRAGYKAAIVHN-VDSDDLISMGSNDIEVLKKIDIPSVFIGESSANSLKDEFTYEK 166

Query: 220 GECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVV 279
           G   I            ++    ++ +  +  V F+  +  +      +   R+     +
Sbjct: 167 GGHLILVPEFSLPLEYYLIPFLIIVGICLILIVIFMITKFVQDRHRARRNRLRK---DQL 223

Query: 280 EALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFC 339
           + LP   F           + CAICL++Y+DG+KL++L C H +H  CVD WLTK    C
Sbjct: 224 KKLPVHKFKKGDEY-----DVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 340 PVCKH 344
           PVCK 
Sbjct: 279 PVCKQ 283

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

 Score =  116 bits (291), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 123/252 (48%), Gaps = 17/252 (6%)

Query: 101 SLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIF 160
           S+ F DLPA F   ++  G  G L  A P +AC P++ P ++     +   L+ R  C F
Sbjct: 35  SMDFADLPALFGATLSDEGLQGFLVEAHPENACGPIAPPPSAPVNGSVFIALLRRFDCNF 94

Query: 161 EDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVK----VHAIFVSLETGVYLKEHAR 216
           + K+ NAQ AGY AA+V+N      L++M  + E ++    + ++F+   +  YL+    
Sbjct: 95  DLKVLNAQKAGYGAAVVHN-VNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRALFV 153

Query: 217 GETGECCIFPESNRGSWSVLMVSVFSLI--VVFALFAVAFITPRPWRPWPGQNQPLSRRL 274
            E G   +    N       ++    ++  +V A+  V  +     R    +N     RL
Sbjct: 154 YEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLAMGTVLIVRCIQHRKRLQRN-----RL 208

Query: 275 DSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK 334
             + ++ +P   +           + CAICL++Y+DG+KL+VL C H +H+ CVD WLT+
Sbjct: 209 TKEQLKQIPTHDYQKGDEY-----DVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQ 263

Query: 335 WGTFCPVCKHDM 346
               CP+CK  +
Sbjct: 264 TRKTCPICKQPV 275

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

 Score =  110 bits (275), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 122/249 (48%), Gaps = 15/249 (6%)

Query: 101 SLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIF 160
           S+ F DLPA F   ++  G  G L  A P +ACSP++ P  +     +   L+ R  C F
Sbjct: 35  SMDFADLPALFGATLSQEGLQGFLVEAHPDNACSPIAPPPPAPVNGSVFIALLRRFDCNF 94

Query: 161 EDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVK----VHAIFVSLETGVYLKEHAR 216
           + K+ NAQ AGY AA+V+N      L++M  + E ++    + ++F+   +  YL+    
Sbjct: 95  DLKVLNAQKAGYGAAVVHN-VNSNELLNMVWNSEEIQQQIWIPSVFIGERSSEYLRALFV 153

Query: 217 GETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSR-RLD 275
            E G   +    N       ++    ++ +  L   A +  R  +      + L R RL 
Sbjct: 154 YEKGARVLLVPDNTFPLGYYLIPFTGIVGLLVLAMGAVMIARCIQ----HRKRLQRNRLT 209

Query: 276 SKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW 335
            + ++ +P   +           + CAICL++Y+DG+KL+VL C H +H+ CVD WLT+ 
Sbjct: 210 KEQLKQIPTHDYQKGDQY-----DVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQT 264

Query: 336 GTFCPVCKH 344
              CP+CK 
Sbjct: 265 RKTCPICKQ 273

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: 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 =  107 bits (267), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 123/248 (49%), Gaps = 13/248 (5%)

Query: 101 SLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIF 160
           S+ F DLPA F   ++  G  G L  A P +ACSP++ P ++     +   L+ R  C F
Sbjct: 35  SMDFADLPALFGATLSDEGLQGFLVEAHPENACSPIAPPPSAPVNGSVFIALLRRFDCNF 94

Query: 161 EDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVK----VHAIFVSLETGVYLKEHAR 216
           + K+ NAQ AGY AA+V+N      L++M  + E ++    + ++F+   +  YL+    
Sbjct: 95  DLKVLNAQKAGYGAAVVHN-VNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRALFV 153

Query: 217 GETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDS 276
            E G   +    N       ++  F+ IV   L  +A  T    R    + +    RL  
Sbjct: 154 YEKGARVLLVPDNSFPLGYYLIP-FTGIV--GLLVLAMGTVLIVRCIQHRKRLQRNRLTK 210

Query: 277 KVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG 336
           + ++ +P   +           + CAICL++Y+DG+KL++L C H +H+ CVD WLT+  
Sbjct: 211 EQLKQIPTHDYQKGDEY-----DVCAICLDEYEDGDKLRILPCAHAYHSRCVDPWLTQTR 265

Query: 337 TFCPVCKH 344
             CP+CK 
Sbjct: 266 KTCPICKQ 273

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

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 81/262 (30%), Positives = 121/262 (46%), Gaps = 20/262 (7%)

Query: 101 SLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIF 160
           S+ F DLPA F V +   G  G L    PA+AC P+  P   N +     VLI R  C F
Sbjct: 110 SVDFADLPALFGVPLAPEGIRGYLMEVKPANACHPIEAPRLGNRSLG-AIVLIRRYDCTF 168

Query: 161 EDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVK----VHAIFVSLETGVYLKE-HA 215
           + K+ NAQ AG+ AAIV+N      LVSMT  +E ++    + ++FVS      L+    
Sbjct: 169 DLKVLNAQRAGFEAAIVHN-VHSDDLVSMTHVYEDLRGQIAIPSVFVSEAASQDLRVILG 227

Query: 216 RGETGECCIFPES----NRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLS 271
             ++    + P+     + G   VL VS + L    AL   AF        W        
Sbjct: 228 CNKSAHALLLPDDPPCHDLGCHPVLTVS-WVLGCTLALVVSAFFVLNHLWLWAQACCSHR 286

Query: 272 RRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSW 331
           R + +   +      F+          + CAICL++Y++G++LK+L C H +H  C+D W
Sbjct: 287 RPVKTSTCQKAQVRTFT-------WHNDLCAICLDEYEEGDQLKILPCSHTYHCKCIDPW 339

Query: 332 LTKWG-TFCPVCKHDMRNNSES 352
            ++     CPVCK  +    +S
Sbjct: 340 FSQAPRRSCPVCKQSVAATEDS 361

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	357
224133660	311	predicted protein [Populus trichocarpa]	0.775	0.890	0.546	7e-86
297734999	352	unnamed protein product [Vitis vinifera]	0.756	0.767	0.521	2e-75
225431110	294	PREDICTED: E3 ubiquitin-protein ligase R	0.759	0.921	0.519	2e-75
297797773	308	hypothetical protein ARALYDRAFT_497000 [	0.745	0.863	0.479	3e-71
15239276	310	receptor homology-transmembrane-ring H2	0.745	0.858	0.479	5e-70
42573810	290	receptor homology-transmembrane-ring H2	0.745	0.917	0.479	7e-70
225470792	446	PREDICTED: E3 ubiquitin-protein ligase R	0.787	0.630	0.431	3e-60
255577542	577	zinc finger protein, putative [Ricinus c	0.711	0.440	0.477	1e-58
255586465	434	zinc finger protein, putative [Ricinus c	0.764	0.629	0.417	1e-58
296081075	424	unnamed protein product [Vitis vinifera]	0.733	0.617	0.439	1e-57

>gi|224133660|ref|XP_002327649.1| predicted protein [Populus trichocarpa] gi|222836734|gb|EEE75127.1| predicted protein [Populus trichocarpa]

 Score =  323 bits (828), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 154/282 (54%), Positives = 203/282 (71%), Gaps = 5/282 (1%)

Query: 69  MREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVAD 128
           MRE   +   + Y  +  ++  SSAT++ KP S+ FPDLPAK A+ +N S  CG+LHVA+
Sbjct: 1   MREGLFLILSLFYAIM--IIEGSSATVLIKPSSISFPDLPAKSALSLNGSSVCGSLHVAN 58

Query: 129 PADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVS 188
           P DACSPL N    N++    F LIVRG+C FEDKI+NAQ+AG+RAAIV++D++  +L+ 
Sbjct: 59  PLDACSPLRNRFEFNESG--RFALIVRGECAFEDKIKNAQSAGFRAAIVFDDKDNRNLIY 116

Query: 189 MTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFA 248
           M  + EG+KVHA+FV+   G  LK+ ARG+ GECCI+      +W+VL +S+ S++V+  
Sbjct: 117 MMVNPEGIKVHAVFVTKYAGEILKDRARGKEGECCIYSSRTDAAWTVLAISLISVVVILG 176

Query: 249 LFAVAFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDY 308
           L  + F+TPR W  W   N    + +DSK+VEALPCF F +AS SQCH GETCAICLEDY
Sbjct: 177 LLILVFVTPRHWLHWQRTNNR-CKSVDSKMVEALPCFTFRNASLSQCHVGETCAICLEDY 235

Query: 309 QDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
           +DGE LKVL C HEFH++CVDSWLTKWGTFCPVCK DM++ S
Sbjct: 236 KDGEVLKVLPCHHEFHSTCVDSWLTKWGTFCPVCKLDMKDKS 277

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734999|emb|CBI17361.3| unnamed protein product [Vitis vinifera]

 Score =  289 bits (739), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 146/280 (52%), Positives = 194/280 (69%), Gaps = 10/280 (3%)

Query: 80  IYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNP 139
           I + + + V L+ A +  K LS  F D PA+FAV VNS+G CGALH+ADP +ACS L N 
Sbjct: 70  ILVFVSYSVRLTYAIVHLKSLSASFIDAPARFAVSVNSTGICGALHLADPLEACSSLLNR 129

Query: 140 VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVH 199
             S + D I F LI+RG+C FEDK+RNAQ AG+ A IVY+DR+KG+LVSM  + +G+ V 
Sbjct: 130 FRSQEIDTIKFALIIRGKCAFEDKVRNAQDAGFHAVIVYDDRDKGNLVSMIGNSQGIWVP 189

Query: 200 AIFVSLETGVYLKEHARGETGECCI----FPESNRGSWSVLMVSVFSLIVVFALFAVAFI 255
           A+FVS   G  LK +A+G+ GECCI    FPES   +W+V+++S  SL+V+ A   + F 
Sbjct: 190 AVFVSKAAGETLKIYAQGQEGECCIINPSFPES---AWTVMVISFISLLVI-ATVVLTFF 245

Query: 256 TPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLK 315
             R  R       P    +D+K+VE LPCF FS A   +C  G+TC+ICLEDY+DGE+L+
Sbjct: 246 LTRNRRLNQRGTNPHRPSVDAKLVEVLPCFTFSQA--CECRVGDTCSICLEDYKDGERLR 303

Query: 316 VLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESNEV 355
           VL C+HEFHASCVDSWLTKWGTFCPVCK+D+  ++  ++V
Sbjct: 304 VLPCQHEFHASCVDSWLTKWGTFCPVCKYDLSTDATCSKV 343

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431110|ref|XP_002265670.1| PREDICTED: E3 ubiquitin-protein ligase RNF167 [Vitis vinifera]

 Score =  288 bits (738), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 146/281 (51%), Positives = 195/281 (69%), Gaps = 10/281 (3%)

Query: 80  IYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNP 139
           I + + + V L+ A +  K LS  F D PA+FAV VNS+G CGALH+ADP +ACS L N 
Sbjct: 12  ILVFVSYSVRLTYAIVHLKSLSASFIDAPARFAVSVNSTGICGALHLADPLEACSSLLNR 71

Query: 140 VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVH 199
             S + D I F LI+RG+C FEDK+RNAQ AG+ A IVY+DR+KG+LVSM  + +G+ V 
Sbjct: 72  FRSQEIDTIKFALIIRGKCAFEDKVRNAQDAGFHAVIVYDDRDKGNLVSMIGNSQGIWVP 131

Query: 200 AIFVSLETGVYLKEHARGETGECCI----FPESNRGSWSVLMVSVFSLIVVFALFAVAFI 255
           A+FVS   G  LK +A+G+ GECCI    FPES   +W+V+++S  SL+V+  +    F+
Sbjct: 132 AVFVSKAAGETLKIYAQGQEGECCIINPSFPES---AWTVMVISFISLLVIATVVLTFFL 188

Query: 256 TPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLK 315
           T        G N P    +D+K+VE LPCF FS A   +C  G+TC+ICLEDY+DGE+L+
Sbjct: 189 TRNRRLNQRGTN-PHRPSVDAKLVEVLPCFTFSQA--CECRVGDTCSICLEDYKDGERLR 245

Query: 316 VLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESNEVG 356
           VL C+HEFHASCVDSWLTKWGTFCPVCK+D+  ++  ++V 
Sbjct: 246 VLPCQHEFHASCVDSWLTKWGTFCPVCKYDLSTDATCSKVN 286

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297797773|ref|XP_002866771.1| hypothetical protein ARALYDRAFT_497000 [Arabidopsis lyrata subsp. lyrata] gi|297312606|gb|EFH43030.1| hypothetical protein ARALYDRAFT_497000 [Arabidopsis lyrata subsp. lyrata]

 Score =  275 bits (702), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 130/271 (47%), Positives = 182/271 (67%), Gaps = 5/271 (1%)

Query: 87  VVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASN--D 144
           ++ +S AT+V   +S  F DLPAKF   V  +G CGAL+VADP D CSPL +  ASN   
Sbjct: 19  LLQVSLATVVLNSISASFADLPAKFDGSVTKNGICGALYVADPLDGCSPLLHAAASNWTQ 78

Query: 145 ADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVS 204
                F LI+RG+C FEDK+ NAQ +G++A IVY++ +   L+ M  + + + V A+FVS
Sbjct: 79  QSTTKFALIIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVS 138

Query: 205 LETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWP 264
              G  L+++ARG  GECC++P +   +W+VL +S FSL+++     +AF  PR W  W 
Sbjct: 139 NVAGEILRKYARGRDGECCLYPPTKGSAWTVLAISFFSLLLIVTFLLIAFFAPRHWTQWR 198

Query: 265 GQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFH 324
           G++   + RLD+K+V  LPCF F+ ++  +   GETCAICLEDY+ GE L++L C+H FH
Sbjct: 199 GRHNR-TIRLDAKLVHTLPCFTFTDSAHHK--AGETCAICLEDYRFGESLRLLPCQHAFH 255

Query: 325 ASCVDSWLTKWGTFCPVCKHDMRNNSESNEV 355
            SC+DSWLTKWGT CPVCKHD+R  + S+EV
Sbjct: 256 LSCIDSWLTKWGTSCPVCKHDIRTETMSSEV 286

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239276|ref|NP_201417.1| receptor homology-transmembrane-ring H2 domain protein 1 [Arabidopsis thaliana] gi|6942147|gb|AAF32325.1|AF218807_1 ReMembR-H2 protein JR700 [Arabidopsis thaliana] gi|10177131|dbj|BAB10421.1| ReMembR-H2 protein JR700 [Arabidopsis thaliana] gi|14334832|gb|AAK59594.1| putative ReMembR-H2 protein JR700 [Arabidopsis thaliana] gi|15293205|gb|AAK93713.1| putative ReMembR-H2 protein JR700 [Arabidopsis thaliana] gi|332010784|gb|AED98167.1| receptor homology-transmembrane-ring H2 domain protein 1 [Arabidopsis thaliana]

 Score =  271 bits (692), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 130/271 (47%), Positives = 181/271 (66%), Gaps = 5/271 (1%)

Query: 87  VVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDAD 146
           ++ +S AT+V   +S  F DLPAKF   V  +G CGAL+VADP D CSPL +  ASN   
Sbjct: 19  LLRVSLATVVLNSISASFADLPAKFDGSVTKNGICGALYVADPLDGCSPLLHAAASNWTQ 78

Query: 147 H--INFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVS 204
           H    F LI+RG+C FEDK+ NAQ +G++A IVY++ +   L+ M  + + + V A+FVS
Sbjct: 79  HRTTKFALIIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVS 138

Query: 205 LETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWP 264
              G  L+++ARG  GECC+ P     +W+VL +S FSL+++     +AF  PR W  W 
Sbjct: 139 NVAGEILRKYARGRDGECCLNPPDRGSAWTVLAISFFSLLLIVTFLLIAFFAPRHWTQWR 198

Query: 265 GQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFH 324
           G++   + RLD+K+V  LPCF F+ ++  +   GETCAICLEDY+ GE L++L C+H FH
Sbjct: 199 GRHTR-TIRLDAKLVHTLPCFTFTDSAHHK--AGETCAICLEDYRFGESLRLLPCQHAFH 255

Query: 325 ASCVDSWLTKWGTFCPVCKHDMRNNSESNEV 355
            +C+DSWLTKWGT CPVCKHD+R  + S+EV
Sbjct: 256 LNCIDSWLTKWGTSCPVCKHDIRTETMSSEV 286

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42573810|ref|NP_975001.1| receptor homology-transmembrane-ring H2 domain protein 1 [Arabidopsis thaliana] gi|332010783|gb|AED98166.1| receptor homology-transmembrane-ring H2 domain protein 1 [Arabidopsis thaliana]

 Score =  270 bits (690), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 130/271 (47%), Positives = 181/271 (66%), Gaps = 5/271 (1%)

Query: 87  VVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDAD 146
           ++ +S AT+V   +S  F DLPAKF   V  +G CGAL+VADP D CSPL +  ASN   
Sbjct: 19  LLRVSLATVVLNSISASFADLPAKFDGSVTKNGICGALYVADPLDGCSPLLHAAASNWTQ 78

Query: 147 H--INFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVS 204
           H    F LI+RG+C FEDK+ NAQ +G++A IVY++ +   L+ M  + + + V A+FVS
Sbjct: 79  HRTTKFALIIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVS 138

Query: 205 LETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWP 264
              G  L+++ARG  GECC+ P     +W+VL +S FSL+++     +AF  PR W  W 
Sbjct: 139 NVAGEILRKYARGRDGECCLNPPDRGSAWTVLAISFFSLLLIVTFLLIAFFAPRHWTQWR 198

Query: 265 GQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFH 324
           G++   + RLD+K+V  LPCF F+ ++  +   GETCAICLEDY+ GE L++L C+H FH
Sbjct: 199 GRHTR-TIRLDAKLVHTLPCFTFTDSAHHK--AGETCAICLEDYRFGESLRLLPCQHAFH 255

Query: 325 ASCVDSWLTKWGTFCPVCKHDMRNNSESNEV 355
            +C+DSWLTKWGT CPVCKHD+R  + S+EV
Sbjct: 256 LNCIDSWLTKWGTSCPVCKHDIRTETMSSEV 286

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  238 bits (607), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 123/285 (43%), Positives = 171/285 (60%), Gaps = 4/285 (1%)

Query: 69  MREKFLMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVAD 128
           MR   L+     +LNL   V+ ++  L+   ++L F D+ A FA  V  SG CG L+VA+
Sbjct: 1   MRSMNLVLLFCAFLNLMASVAFANVVLIGNNVTLSFDDIQANFAKPVKGSGECGILYVAE 60

Query: 129 PADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVS 188
           P DACSPL+N V   +     FVLIVRG C FEDK+RNAQ AG+ AAIVY++ + G LV+
Sbjct: 61  PLDACSPLTNAVEKVEGASSPFVLIVRGGCGFEDKVRNAQKAGFAAAIVYDNEDGGVLVA 120

Query: 189 MTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFA 248
           M  +  G+K+HA+FVS  +G+ L+ +A     E  I P     +WS++ +S  SL+ + A
Sbjct: 121 MAGNSAGIKIHAVFVSKASGMVLQTYAGSPDMELWIIPSFENSAWSIMAISFISLLAMSA 180

Query: 249 LFAVAFITPRPWRPWPGQNQPLSRR---LDSKVVEALPCFLFSSASSSQCHGGETCAICL 305
           + A  F   R             R    + S++V+A+P  +F++     C    TCAICL
Sbjct: 181 VLATCFFVRRHRIRRQRPRVSRVREFHGMSSRLVKAMPSLIFTTVLEDNC-TSRTCAICL 239

Query: 306 EDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
           EDY  GEKL++L C+H+FHA CVDSWLT W TFCPVCK D R ++
Sbjct: 240 EDYNVGEKLRILPCRHKFHAFCVDSWLTSWRTFCPVCKRDARTST 284

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255577542|ref|XP_002529649.1| zinc finger protein, putative [Ricinus communis] gi|223530875|gb|EEF32736.1| zinc finger protein, putative [Ricinus communis]

 Score =  233 bits (594), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 125/262 (47%), Positives = 166/262 (63%), Gaps = 8/262 (3%)

Query: 85  CFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSN---PVA 141
           C+   L S+T+V KP    FPDLPAK A  +N SG CGALHVA+P DACS + N    + 
Sbjct: 18  CYFTQLISSTVVLKPYFFSFPDLPAKSAAGLNKSGICGALHVANPLDACSWIRNNGFEMN 77

Query: 142 SNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAI 201
             +   + F LI RG C FEDKIRN Q  G+ AAIV++DR+K +LV M  + EG+KVHA+
Sbjct: 78  ETEKGVVRFALIERGGCSFEDKIRNVQNGGFTAAIVFDDRDKRNLVYMMMNPEGIKVHAV 137

Query: 202 FVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWR 261
           FVS   G  LKEHARGE GECCI+P  +  +W+VL +S  SL+++ A   +AFI PR W 
Sbjct: 138 FVSKIAGEILKEHARGEEGECCIYPSHSDTAWTVLAISFLSLLLILAFIMIAFILPRHWL 197

Query: 262 PWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKH 321
            W G N   +  +  +++E  P F F SA  ++ H GETCAICLEDY++GE LKVL C+H
Sbjct: 198 YWQGTNFHCN-SVGVRMLEGFPRFTFPSAHLNRSHSGETCAICLEDYKEGETLKVLPCQH 256

Query: 322 EFHAS----CVDSWLTKWGTFC 339
            +  S     ++    +W  +C
Sbjct: 257 GYRVSSAIDVLEQLCKQWHLYC 278

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586465|ref|XP_002533876.1| zinc finger protein, putative [Ricinus communis] gi|223526177|gb|EEF28507.1| zinc finger protein, putative [Ricinus communis]

 Score =  233 bits (593), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 116/278 (41%), Positives = 173/278 (62%), Gaps = 5/278 (1%)

Query: 77  FLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPL 136
            L+ YL+ C  ++L++  L+ + ++L F D+ A FA  V SSG CG L++A+P DACS L
Sbjct: 10  ILLFYLSACCSMTLANVVLIGRNVTLSFDDVEATFAPAVKSSGECGQLYLAEPVDACSEL 69

Query: 137 SNPVASNDADHIN-FVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEG 195
           +N V    ++  + FVL++RG C FEDK+R AQ AG++AAIVY++ + G LVSM  +  G
Sbjct: 70  TNKVVKPTSNVTSPFVLVIRGGCSFEDKVRRAQRAGFKAAIVYDNEDDGVLVSMAGNSAG 129

Query: 196 VKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFI 255
           +K+HA+F+S  +G  LK++      E  + P     +WS++ +S  SL+ + A+ A  F 
Sbjct: 130 IKIHAVFISKSSGETLKKYVGLSEMELWLIPSFENSAWSIMAISFISLLAMSAVLATCFF 189

Query: 256 TPRPWRPWPGQNQPLSRR---LDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGE 312
             R             R    + S++V+A+P  +F++     C   +TCAICLEDY  GE
Sbjct: 190 VRRHRIRRGRPRSSRVREFHGMSSRLVKAMPSLIFTAVVEDNC-TSQTCAICLEDYSVGE 248

Query: 313 KLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
           KL++L C+H+FHA CVDSWLT W TFCPVCK D R ++
Sbjct: 249 KLRILPCRHKFHALCVDSWLTSWRTFCPVCKRDARTST 286

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  229 bits (585), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 117/266 (43%), Positives = 163/266 (61%), Gaps = 4/266 (1%)

Query: 88  VSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADH 147
           V+ ++  L+   ++L F D+ A FA  V  SG CG L+VA+P DACSPL+N V   +   
Sbjct: 4   VAFANVVLIGNNVTLSFDDIQANFAKPVKGSGECGILYVAEPLDACSPLTNAVEKVEGAS 63

Query: 148 INFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLET 207
             FVLIVRG C FEDK+RNAQ AG+ AAIVY++ + G LV+M  +  G+K+HA+FVS  +
Sbjct: 64  SPFVLIVRGGCGFEDKVRNAQKAGFAAAIVYDNEDGGVLVAMAGNSAGIKIHAVFVSKAS 123

Query: 208 GVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQN 267
           G+ L+ +A     E  I P     +WS++ +S  SL+ + A+ A  F   R         
Sbjct: 124 GMVLQTYAGSPDMELWIIPSFENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRRQRPR 183

Query: 268 QPLSRR---LDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFH 324
               R    + S++V+A+P  +F++     C    TCAICLEDY  GEKL++L C+H+FH
Sbjct: 184 VSRVREFHGMSSRLVKAMPSLIFTTVLEDNC-TSRTCAICLEDYNVGEKLRILPCRHKFH 242

Query: 325 ASCVDSWLTKWGTFCPVCKHDMRNNS 350
           A CVDSWLT W TFCPVCK D R ++
Sbjct: 243 AFCVDSWLTSWRTFCPVCKRDARTST 268

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	357
TAIR|locus:2156872	310	RMR1 "receptor homology region	0.753	0.867	0.478	1.4e-69
TAIR|locus:2016044	448	AT1G71980 [Arabidopsis thalian	0.761	0.607	0.399	5.5e-54
TAIR|locus:2014726	318	AT1G35630 [Arabidopsis thalian	0.759	0.852	0.371	3.8e-46
TAIR|locus:2133697	448	AT4G09560 [Arabidopsis thalian	0.770	0.613	0.389	6.2e-46
TAIR|locus:2199665	422	AT1G22670 [Arabidopsis thalian	0.764	0.646	0.370	1.2e-42
UNIPROTKB|F1MFJ1	350	F1MFJ1 "Uncharacterized protei	0.691	0.705	0.316	3.4e-29
UNIPROTKB|Q0VD51	380	RNF13 "E3 ubiquitin-protein li	0.714	0.671	0.313	2.4e-28
UNIPROTKB|I3LG86	381	RNF13 "Ring finger protein 13"	0.714	0.669	0.313	2.4e-28
UNIPROTKB|F1NA38	380	RNF13 "E3 ubiquitin-protein li	0.644	0.605	0.318	3.9e-28
UNIPROTKB|F1NUJ3	272	RNF13 "E3 ubiquitin-protein li	0.644	0.845	0.318	3.9e-28

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

 Score = 705 (253.2 bits), Expect = 1.4e-69, P = 1.4e-69
 Identities = 131/274 (47%), Positives = 182/274 (66%)

Query:    84 LCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASN 143
             L  ++ +S AT+V   +S  F DLPAKF   V  +G CGAL+VADP D CSPL +  ASN
Sbjct:    16 LSSLLRVSLATVVLNSISASFADLPAKFDGSVTKNGICGALYVADPLDGCSPLLHAAASN 75

Query:   144 DADH--INFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAI 201
                H    F LI+RG+C FEDK+ NAQ +G++A IVY++ +   L+ M  + + + V A+
Sbjct:    76 WTQHRTTKFALIIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAV 135

Query:   202 FVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWR 261
             FVS   G  L+++ARG  GECC+ P     +W+VL +S FSL+++     +AF  PR W 
Sbjct:   136 FVSNVAGEILRKYARGRDGECCLNPPDRGSAWTVLAISFFSLLLIVTFLLIAFFAPRHWT 195

Query:   262 PWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKH 321
              W G++   + RLD+K+V  LPCF F+ ++  +   GETCAICLEDY+ GE L++L C+H
Sbjct:   196 QWRGRHTR-TIRLDAKLVHTLPCFTFTDSAHHKA--GETCAICLEDYRFGESLRLLPCQH 252

Query:   322 EFHASCVDSWLTKWGTFCPVCKHDMRNNSESNEV 355
              FH +C+DSWLTKWGT CPVCKHD+R  + S+EV
Sbjct:   253 AFHLNCIDSWLTKWGTSCPVCKHDIRTETMSSEV 286

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:2016044 AT1G71980 [Arabidopsis thaliana (taxid:3702)]

 Score = 558 (201.5 bits), Expect = 5.5e-54, P = 5.5e-54
 Identities = 111/278 (39%), Positives = 170/278 (61%)

Query:    78 LIIYLNLCFVVSLSSATLVW--KPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSP 135
             L++ L +C V  L+S+ ++     ++L F D+ A FA  V  +G  G ++VA+P DAC  
Sbjct:     5 LVLLLYVCTVSCLASSKVILMRNNITLSFDDIEANFAPSVKGTGEIGVVYVAEPLDACQN 64

Query:   136 LSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEG 195
             L N    +  +   FVLIVRG C FE+K+R AQ AG++AAI+Y++ ++G+L++M  +  G
Sbjct:    65 LMNKPEQSSNETSPFVLIVRGGCSFEEKVRKAQRAGFKAAIIYDNEDRGTLIAMAGNSGG 124

Query:   196 VKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFI 255
             +++HA+FV+ ETG  LKE+A     +  + P     +WS++ VS  SL+ + A+ A  F 
Sbjct:   125 IRIHAVFVTKETGEVLKEYAGFPDTKVWLIPSFENSAWSIMAVSFISLLAMSAVLATCFF 184

Query:   256 TPRPW-RPWPGQNQPLSR--RLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGE 312
               R   R    ++  +     +  ++V+A+P  +FSS          TCAICLEDY  G+
Sbjct:   185 VRRHRIRRRTSRSSRVREFHGMSRRLVKAMPSLIFSSFHEDNTTAF-TCAICLEDYTVGD 243

Query:   313 KLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
             KL++L C H+FHA+CVDSWLT W TFCPVCK D R ++
Sbjct:   244 KLRLLPCCHKFHAACVDSWLTSWRTFCPVCKRDARTST 281

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 = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 104/280 (37%), Positives = 159/280 (56%)

Query:    79 IIYLNLCFVVSLSSA--TLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPL 136
             I  ++L  +  L+SA   L+ K   L F D+ A F   V +SG CG L+VA+P +ACS +
Sbjct:     6 ITIMSLLVICKLASAKVVLIGKNTILSFDDVEATFTPIVRNSGECGILYVAEPLEACSDI 65

Query:   137 SNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGV 196
             +N          ++VLIV G C FE+K+R AQ AGY+AAIVYND     LV M  +  GV
Sbjct:    66 TNMAEKRSKYRSSYVLIVLGGCSFEEKVRKAQKAGYKAAIVYNDGYDELLVPMAGNSSGV 125

Query:   197 KVHAIFVSLETGVYLKEHARGETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFIT 256
              +H + V+  +G  LK +A  +  +  + P     SWS++ ++  SL+ + A+ A  F+ 
Sbjct:   126 DIHGLLVTRASGEVLKGYADQDEMKLWLIPGFGISSWSIMGITFISLLAMSAILATCFVV 185

Query:   257 PRPW-----RPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDG 311
              R       R  P   Q LS  +   +++++P  ++S     +     TCAIC++DY  G
Sbjct:   186 RRHQIRQSVRDLPHGGQGLSC-MPRDLLQSMPTEVYSGVLE-ESSTSVTCAICIDDYCVG 243

Query:   312 EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE 351
             EKL++L CKH++HA C+DSWL +  +FCPVCK + R  ++
Sbjct:   244 EKLRILPCKHKYHAVCIDSWLGRCRSFCPVCKQNPRTGND 283

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 = 482 (174.7 bits), Expect = 6.2e-46, P = 6.2e-46
 Identities = 111/285 (38%), Positives = 159/285 (55%)

Query:    74 LMKFLIIYLNLCFVVSLSSAT--LVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPAD 131
             +++  I+ L+L  +  L SA   L+    SL F D+ A F   +  S   G L+VA+P D
Sbjct:     1 MIRSSIVILSLLLISHLVSAKVLLIGNSTSLSFDDVEATFTPMIKRSDQGGVLYVAEPLD 60

Query:   132 ACSPLSNPVASNDADHIN--FVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSM 189
             ACS L N V   +   ++  +VLI+RG C FEDKIRNAQ AGY+AAIVY+  + G LVSM
Sbjct:    61 ACSDLVNTVNVKNGTTVSPPYVLIIRGGCSFEDKIRNAQKAGYKAAIVYDYEDFGFLVSM 120

Query:   190 TASHEGVKVHAIFVSLETGVYLKEHARGETG-ECCIFPESNRGSWSVLMVSVFSLIVVFA 248
               +  GV ++  FVS  TG  LKE+A G T  E  + P     +WS++ +S  SL+ + A
Sbjct:   121 AGNPSGVLIYGTFVSKATGEVLKEYA-GRTDFEVWLMPSFETSAWSIMAISFISLLAMSA 179

Query:   249 LFAVAFITPRPW---RPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICL 305
             + A  F   R     R     N     R+   ++  +P  +F+     +      C ICL
Sbjct:   180 VLATCFFVRRHRVRRRRILALNGNDFHRMPKSMIIRMPTTIFNGICD-EATTSILCCICL 238

Query:   306 EDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
             E+Y+ G+KL++L C H+FH +CVD WL +  +FCPVCK D R+ S
Sbjct:   239 ENYEKGDKLRILPCHHKFHVACVDLWLGQRKSFCPVCKRDARSIS 283

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 = 451 (163.8 bits), Expect = 1.2e-42, P = 1.2e-42
 Identities = 104/281 (37%), Positives = 157/281 (55%)

Query:    74 LMKFLIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADAC 133
             L+  L++++ + +VV      LV   ++  F D+ A F+  V +  T G ++VA+P +AC
Sbjct:     7 LILTLLLFI-VSYVVDAGQVILVDSNITRSFVDMEADFSPSVTTVET-GVVYVAEPLNAC 64

Query:   134 SPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASH 193
               L N    +       VLI+RG C FE K+RNAQ +G++AAIVY++ ++  L +M    
Sbjct:    65 RNLRNKPEQSPYGTSPLVLIIRGGCSFEYKVRNAQRSGFKAAIVYDNVDRNFLSAMGGDS 124

Query:   194 EGVKVHAIFVSLETGVYLKEHARGETGECCIFPESNRGS-WSVLMVSVFSLIVVFALFAV 252
             +G+K+ A+FV    G  LK++A  E  E  + P +   S WS L  S+ +LI+  A+F V
Sbjct:   125 DGIKIQAVFVMKRAGEMLKKYAGSEEMEVMLVPPNTEDSVWS-LYASI-ALILSLAIFCV 182

Query:   253 AFITPRPWRPWPGQNQPLSR--RLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQD 310
                    +R         S+   +  + V+A+P   F+ A      G  +CAICLEDY  
Sbjct:   183 MVTCVFFYRYCSTIRNSTSQFNGMCRRTVKAMPSVTFTCAKIDNTTGF-SCAICLEDYIV 241

Query:   311 GEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE 351
             G+KL+VL C H+FH +CVDSWL  W TFCPVCK D R  ++
Sbjct:   242 GDKLRVLPCSHKFHVACVDSWLISWRTFCPVCKRDARTTAD 282

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

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

UNIPROTKB|F1MFJ1 F1MFJ1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 83/262 (31%), Positives = 129/262 (49%)

Query:   101 SLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIF 160
             S+ F DLPA F   ++  G  G L  A PA+ACSP++ P  +     +   L+ R  C F
Sbjct:    35 SMEFADLPALFGAALSPEGLKGFLVEAQPANACSPIAPPPPAQANGSVFIALLRRFDCKF 94

Query:   161 EDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVK----VHAIFVSLETGVYLKEHAR 216
             + K+ +AQ AGY AA+V+N      L++M  S+E V+    + ++F+S ++  YL+    
Sbjct:    95 DLKVLHAQKAGYGAAVVHNVNSN-ELLNMVGSNEEVQQQIWIPSVFISEKSSQYLRAFFI 153

Query:   217 GETGECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDS 276
              + G   +    N G  S     +F  I+   +     I    W  +  Q Q     L  
Sbjct:   154 YQQGAQVLLVPDN-GFLSTYFFILFYGILAMLILGTGAIVIVHWIHF--QKQRWRNLLTK 210

Query:   277 KVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG 336
             + ++ +P   +           + CAICL++Y+DG+KL+VL C H +H  CVD WLT+  
Sbjct:   211 EQLKQIPTHDYRRGDRY-----DVCAICLDEYEDGDKLRVLPCAHAYHCRCVDPWLTQTK 265

Query:   337 TFCPVCKHDM-RN-NSESNEVG 356
               CP+CK  + RN   E  E G
Sbjct:   266 KTCPICKQPVCRNLGEEEQEEG 287

GO:0045786 "negative regulation of cell cycle" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0000209 "protein polyubiquitination" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q0VD51 RNF13 "E3 ubiquitin-protein ligase RNF13" [Bos taurus (taxid:9913)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 85/271 (31%), Positives = 134/271 (49%)

Query:    78 LIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLS 137
             L  +LNL   V        ++  S  F DLPA+F   + + G  G L  + P +AC P+ 
Sbjct:    23 LFAFLNL-LPVEADILAYNFENASQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIV 81

Query:   138 NPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASH-EGV 196
              P   +++     VLI R  C F++K+ NAQ AGY+AAIV+N  +   L+SM ++  E +
Sbjct:    82 PPPVRDNSSGTFIVLIRRLDCNFDEKVLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEVL 140

Query:   197 K---VHAIFVSLETGVYLKEHARGETG-ECCIFPESNRGSWSVLMVSVFSLIVVFALFAV 252
             K   + ++F+   +   LK+    E G    + PE +      L+  +  + +   L  +
Sbjct:   141 KKIDIPSVFIGESSANSLKDEFTYEKGGHIILVPEFSLPLEYYLIPFLIIVGICLILIVI 200

Query:   253 AFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGE 312
               IT    +    +++    RL    ++ LP   F           + CAICL++Y+DG+
Sbjct:   201 FMIT----KFVQDRHRARRNRLRKDQLKKLPVHKFKKGDEY-----DVCAICLDEYEDGD 251

Query:   313 KLKVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
             KL++L C H +H  CVD WLTK    CPVCK
Sbjct:   252 KLRILPCSHAYHCKCVDPWLTKTKKTCPVCK 282

GO:0031902 "late endosome membrane" evidence=ISS

GO:0005765 "lysosomal membrane" evidence=ISS

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

GO:0051865 "protein autoubiquitination" evidence=ISS

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0005637 "nuclear inner membrane" evidence=IEA

GO:0000139 "Golgi membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|I3LG86 RNF13 "Ring finger protein 13" [Sus scrofa (taxid:9823)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 85/271 (31%), Positives = 134/271 (49%)

Query:    78 LIIYLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLS 137
             L  +LNL   V        ++  S  F DLPA+F   + + G  G L  + P +AC P+ 
Sbjct:    23 LFAFLNL-LPVEADVLAYNFENASQTFDDLPARFGYRLPAEGLKGFLINSKPENACEPIV 81

Query:   138 NPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASH-EGV 196
              P   +++     VLI R  C F++K+ NAQ AGY+AAIV+N  +   L+SM ++  E +
Sbjct:    82 PPPLKDNSSGTFIVLIRRLDCNFDEKVLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEVL 140

Query:   197 K---VHAIFVSLETGVYLKEHARGETG-ECCIFPESNRGSWSVLMVSVFSLIVVFALFAV 252
             K   + ++F+   +   LK+    E G    + PE +      L+  +  + +   L  +
Sbjct:   141 KKIDIPSVFIGESSANSLKDEFTYEKGGHIILVPEFSLPLEYYLIPFLIIVGICLILIVI 200

Query:   253 AFITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGE 312
               IT    +    +++    RL    ++ LP   F           + CAICL++Y+DG+
Sbjct:   201 FMIT----KFVQDRHRARRNRLRKDQLKKLPIHKFKKGDEY-----DVCAICLDEYEDGD 251

Query:   313 KLKVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
             KL++L C H +H  CVD WLTK    CPVCK
Sbjct:   252 KLRILPCSHAYHCKCVDPWLTKTKKTCPVCK 282

GO:0051865 "protein autoubiquitination" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0005765 "lysosomal membrane" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 78/245 (31%), Positives = 125/245 (51%)

Query:   104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
             F DLPA+F   + + G  G L  + P +AC P++ P   +++     VLI R +C F+ K
Sbjct:    47 FDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLRDNSSTAFIVLIRRLECNFDIK 106

Query:   164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
             + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LKE    E 
Sbjct:   107 VLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKEEFTYEK 165

Query:   220 G-ECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKV 278
             G    + PE +      L+  +  + +   L  +  IT    +    +++    RL    
Sbjct:   166 GGHVVLIPEFSLPLEYYLIPFLIIVGICLILIVIFMIT----KFVQDRHRARRNRLRKDQ 221

Query:   279 VEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTF 338
             ++ LP   F           + CAICL++Y+DG+KL++L C H +H  CVD WLTK    
Sbjct:   222 LKKLPVHKFKKGDEY-----DVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKT 276

Query:   339 CPVCK 343
             CPVCK
Sbjct:   277 CPVCK 281

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 = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 78/245 (31%), Positives = 125/245 (51%)

Query:   104 FPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDK 163
             F DLPA+F   + + G  G L  + P +AC P++ P   +++     VLI R +C F+ K
Sbjct:     6 FDDLPARFGYRLPAEGLKGFLINSKPENACEPIAPPPLRDNSSTAFIVLIRRLECNFDIK 65

Query:   164 IRNAQAAGYRAAIVYNDREKGSLVSMTASH----EGVKVHAIFVSLETGVYLKEHARGET 219
             + NAQ AGY+AAIV+N  +   L+SM ++     + + + ++F+   +   LKE    E 
Sbjct:    66 VLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEILKKIDIPSVFIGEASANSLKEEFTYEK 124

Query:   220 G-ECCIFPESNRGSWSVLMVSVFSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKV 278
             G    + PE +      L+  +  + +   L  +  IT    +    +++    RL    
Sbjct:   125 GGHVVLIPEFSLPLEYYLIPFLIIVGICLILIVIFMIT----KFVQDRHRARRNRLRKDQ 180

Query:   279 VEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTF 338
             ++ LP   F           + CAICL++Y+DG+KL++L C H +H  CVD WLTK    
Sbjct:   181 LKKLPVHKFKKGDEY-----DVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKT 235

Query:   339 CPVCK 343
             CPVCK
Sbjct:   236 CPVCK 240

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00570065 hypothetical protein (311 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	357
cd02123	153	cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-a	2e-40
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-16
cd04818	118	cd04818, PA_subtilisin_1, PA_subtilisin_1: Proteas	6e-16
cd00538	126	cd00538, PA, PA: Protease-associated (PA) domain	4e-15
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	4e-13
cd02133	143	cd02133, PA_C5a_like, PA_C5a_like: Protease-associ	2e-11
pfam02225	96	pfam02225, PA, PA domain	6e-11
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-10
cd02127	118	cd02127, PA_hPAP21_like, PA_hPAP21_like: Protease-	5e-10
cd04813	117	cd04813, PA_1, PA_1: Protease-associated (PA) doma	2e-09
cd02126	126	cd02126, PA_EDEM3_like, PA_EDEM3_like: protease as	7e-09
cd02122	138	cd02122, PA_GRAIL_like, PA _GRAIL_like: Protease-a	8e-09
cd02132	139	cd02132, PA_GO-like, PA_GO-like: Protease-associat	9e-09
cd02130	122	cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-as	4e-08
smart00184	40	smart00184, RING, Ring finger	5e-08
cd02124	129	cd02124, PA_PoS1_like, PA_PoS1_like: Protease-asso	8e-08
cd04816	122	cd04816, PA_SaNapH_like, PA_SaNapH_like: Protease-	2e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	4e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	3e-05
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	6e-04
cd02125	127	cd02125, PA_VSR, PA_VSR: Protease-associated (PA)	0.001
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	0.001

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

 Score =  139 bits (352), Expect = 2e-40
 Identities = 59/128 (46%), Positives = 78/128 (60%), Gaps = 4/128 (3%)

Query: 100 LSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCI 159
           L+  F DLPA F      SG  G L VA+P +ACSP+ NP  +++A     VLI RG C 
Sbjct: 20  LTDEFDDLPANFGPIPPGSGLKGVLVVAEPLNACSPIENPPLNSNASGSFIVLIRRGNCS 79

Query: 160 FEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHE---GVKVHAIFVSLETGVYLKEHAR 216
           FE K+RNAQ AGY+AAIVYND E   L+SM+ + +   G+ + ++FV   TG  LK++A 
Sbjct: 80  FETKVRNAQRAGYKAAIVYND-ESNDLISMSGNDQEIKGIDIPSVFVGKSTGEILKKYAS 138

Query: 217 GETGECCI 224
            E G   I
Sbjct: 139 YEKGVILI 146

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

 Score = 78.9 bits (194), Expect = 3e-16
 Identities = 53/235 (22%), Positives = 83/235 (35%), Gaps = 36/235 (15%)

Query: 140 VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGS--LVSMTASHEGV- 196
           V S +  ++      RG    ED  R  +   ++  I  ++R   +  L  M A  +   
Sbjct: 139 VPSVEERNLVDRCNRRGNETEEDPTRERRRTRFKGVIRGSERNGETFRLHYMVAPDKVDP 198

Query: 197 -KVHAIFVSLETGVYL---------------KEHARGETGECCIFPESNRGSWSVLMVSV 240
                      T                      A+ ETG+   +P  +R   S     V
Sbjct: 199 RSEGVEDPVTLTTSINVTWDGLGNTYQAPSQSAEAQDETGDM-FWPRLSRFVGSRGFRVV 257

Query: 241 FSLIVVFALFAVAFITPRPWRPWPGQNQPLSRRLDSKVV-----EALPCFL-------FS 288
           F  I    L  +     +  R     N  L  +++  V      EA+P           S
Sbjct: 258 FPRIPSQELRFLFLTQSKGSR----FNIILEIQINFDVGFYSSSEAIPTTTTKGSLKPLS 313

Query: 289 SASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
              + +   G  CAIC+ ++   ++L+VL C H FH  CVD WL  +   CPVC+
Sbjct: 314 IERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

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

 Score = 72.7 bits (179), Expect = 6e-16
 Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 4/87 (4%)

Query: 127 ADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSL 186
           A   D C+  +N  A          LI RG C F  K+ NAQ AG  A IV N+   G+ 
Sbjct: 24  ASNTDGCTAFTNAAAFAG----KIALIDRGTCNFTVKVLNAQNAGAIAVIVANNVAGGAP 79

Query: 187 VSMTASHEGVKVHAIFVSLETGVYLKE 213
           ++M      + + A+ +S   G  LK 
Sbjct: 80  ITMGGDDPDITIPAVMISQADGDALKA 106

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

 Score = 71.0 bits (174), Expect = 4e-15
 Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 123 ALHVADPADACSPLSNPVASNDADHINFVLIV-RGQCIFEDKIRNAQAAGYRAAIVYNDR 181
              VA P   C   +   +  D      +++V RG C F +K++NAQ AG +A I+YN+ 
Sbjct: 23  VGVVAGPLVGCGYGTTDDSGADVK--GKIVLVRRGGCSFSEKVKNAQKAGAKAVIIYNN- 79

Query: 182 EKGSLVSMTASHEGVKVHAI---FVSLETGVYLKE 213
                  M +        +I    +S   G  L  
Sbjct: 80  GDDPGPQMGSVGLESTDPSIPTVGISYADGEALLS 114

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|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 62.8 bits (153), Expect = 4e-13
 Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           + C ICL++++ GE++ VL C H FH  C+D WL    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 = 60.8 bits (148), Expect = 2e-11
 Identities = 25/63 (39%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 151 VLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVY 210
            LI RG+  F +KI NA+AAG    I+YN+ +   L+  T   E V +  +F+S E G  
Sbjct: 51  ALIQRGEITFVEKIANAKAAGAVGVIIYNNVD--GLIPGTLG-EAVFIPVVFISKEDGEA 107

Query: 211 LKE 213
           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|216938 pfam02225, PA, PA domain

 Score = 58.3 bits (141), Expect = 6e-11
 Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 5/89 (5%)

Query: 123 ALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDRE 182
             +  D    C                 VL+ RG C F +K  NAQ AG    I+YN+  
Sbjct: 13  VGNGDDAGGCCPEDLADSDVKG----KIVLVRRGGCSFVEKAENAQRAGAAGVIIYNNDT 68

Query: 183 KGSLVSMTASHEGVKVHAIFVSLETGVYL 211
            G   ++      V +  +F+S E G  L
Sbjct: 69  GGLGGTVGDP-SDVTIPVVFISYEDGEAL 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|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 = 55.9 bits (135), Expect = 1e-10
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
            C ICLE++++   + +L C H F  SC+D WL      CP+C+  
Sbjct: 1   ECPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44

Length = 45

>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 = 5e-10
 Identities = 30/93 (32%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 127 ADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGS- 185
           ADP +AC  L N    N     N  LI RG C F  K  NAQ AG  A I+  D    S 
Sbjct: 18  ADPLEACEELRNIHDING----NIALIERGGCSFLTKAINAQKAGALAVIIT-DVNNDSD 72

Query: 186 --LVSMTASHEGVKVH--AIFVSLETGVYLKEH 214
              V M       +    A F+  + G  +++ 
Sbjct: 73  EYYVEMIQDDSSRRADIPAAFLLGKNGYMIRKT 105

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 = 54.3 bits (131), Expect = 2e-09
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 129 PADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVS 188
           P DACS   +   +     +   L++RG C F DK+  AQ  G +A IV +D     L++
Sbjct: 26  PTDACSLQEH---AEIDGKV--ALVLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRGLIT 80

Query: 189 MTASHE--GVKVHAIFVSLETGVYLK 212
           M ++ +   V + A+F 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|239041 cd02126, PA_EDEM3_like, PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins

 Score = 53.1 bits (128), Expect = 7e-09
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 7/80 (8%)

Query: 108 PAKFAVDV--NSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIR 165
           PA+F +D+  + +G  G +  A P  ACS ++N     +       ++ RG C+F +K R
Sbjct: 4   PAQFGMDLTGDKAGV-GRVVKAKPYRACSEITNA----EEVKGKIAIMERGDCMFVEKAR 58

Query: 166 NAQAAGYRAAIVYNDREKGS 185
             Q AG    IV ++ E  S
Sbjct: 59  RVQKAGAIGGIVIDNNEGSS 78

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

 Score = 53.5 bits (129), Expect = 8e-09
 Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 126 VADPAD--ACSPLSNPVASNDADH-INFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDRE 182
              P D   C P +      + +  I   LI RG C FE+KI+ A      A ++YN+  
Sbjct: 38  PDPPNDHYGCDPDTRFPIPPNGEPWI--ALIQRGNCTFEEKIKLAAERNASAVVIYNNPG 95

Query: 183 KGS-LVSMTASHEGVK 197
            G+  V M  SH G  
Sbjct: 96  TGNETVKM--SHPGTG 109

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

 Score = 53.2 bits (128), Expect = 9e-09
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 8/64 (12%)

Query: 126 VADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGS 185
           +A+P D CSP ++ ++      I   L+ RG+C F +K + A+A G  A ++ ND+E+  
Sbjct: 44  LANPLDCCSPSTSKLS----GSI--ALVERGECAFTEKAKIAEAGGASALLIINDQEE-- 95

Query: 186 LVSM 189
           L  M
Sbjct: 96  LYKM 99

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

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 20/38 (52%), Positives = 23/38 (60%)

Query: 149 NFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSL 186
           N  LI RG+C F DK   A AAG  AAI+YN+   G L
Sbjct: 46  NIALIERGECPFGDKSALAGAAGAAAAIIYNNVPAGGL 83

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|214546 smart00184, RING, Ring finger

 Score = 48.3 bits (115), Expect = 5e-08
 Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVC 342
           C ICLE+Y   +   +L C H F  SC+  WL      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|239039 cd02124, PA_PoS1_like, PA_PoS1_like: Protease-associated (PA) domain PoS1-like

 Score = 50.4 bits (121), Expect = 8e-08
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 5/55 (9%)

Query: 127 ADPADACSPLSNPVASNDADHINF-VLIVRGQCIFEDKIRNAQAAGYRAAIVYND 180
           +   DAC PL      +  D   + VL+ RG C F  K  NA A G +  ++YN+
Sbjct: 38  SVADDACQPLP----DDTPDLSGYIVLVRRGTCTFATKAANAAAKGAKYVLIYNN 88

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|240120 cd04816, PA_SaNapH_like, PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH)

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 151 VLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLV-SMTASHEGVKVHAIFVSLETGV 209
           VL+ RG C F DK + A A G  A IV N+ + G    ++ A +  +KV    ++   G 
Sbjct: 47  VLVDRGGCPFADKQKVAAARGAVAVIVVNNSDGGGTAGTLGAPNIDLKVPVGVITKAAGA 106

Query: 210 YLKEHARGETGE 221
            L+   R   GE
Sbjct: 107 ALR--RRLGAGE 116

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

 Score = 48.5 bits (115), Expect = 4e-06
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 7/95 (7%)

Query: 254  FITPRPWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEK 313
              +   W+ W    Q    + +   ++ L   L+      +  G E CAIC       ++
Sbjct: 1427 GTSEIGWKSWINLRQNEMIKKNGSFMDLL--GLWKKNIDEKFSGHEECAICYSVLDMVDR 1484

Query: 314  L----KVLSCKHEFHASCVDSWLTKWG-TFCPVCK 343
                 +  +CK++FH  C+  W      + CP+C+
Sbjct: 1485 SLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519

Length = 1525

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

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVC 342
           C ICLE+ +D   + +L C H F + C+ SWL      CP+C
Sbjct: 1   CPICLEEPKD--PVTILPCGHLFCSKCILSWLESGNVTCPLC 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|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH 344
            C ICL+  +D   + +  C H F   C+  +L K  + CP+C+ 
Sbjct: 4   ECPICLDLLRD--PVVLTPCGHVFCRECILRYLKK-KSKCPICRT 45

Length = 45

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

 Score = 41.1 bits (96), Expect = 6e-04
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 11/69 (15%)

Query: 297 GGETCAICLED--YQDGEKL--------KVLSCKHEFHASCVDSWLTKWGTFCPVCKHDM 346
              TC IC+++  + D E L        K L C H  H  C+ +WL +  T CP+C+  +
Sbjct: 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQT-CPICRRPV 344

Query: 347 RNNSESNEV 355
             +  S   
Sbjct: 345 IFDQSSPTP 353

Length = 491

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

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 149 NFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHE 194
             +L+ RG C F  K  NAQ AG  A +V ++ ++  L++M    E
Sbjct: 44  VILLLDRGGCFFTLKAWNAQQAGAAAVLVADNVDE-PLLTMDTPEE 88

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|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 11/55 (20%)

Query: 299 ETCAICLEDYQD--------GE--KLKVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
           + CAIC   +          G+   +    C H FH  C+  WL      CP+C+
Sbjct: 20  DVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKT-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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	357
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
cd02123	153	PA_C_RZF_like PA_C-RZF_ like: Protease-associated	99.9
cd02125	127	PA_VSR PA_VSR: Protease-associated (PA) domain-con	99.89
cd02126	126	PA_EDEM3_like PA_EDEM3_like: protease associated d	99.89
cd02127	118	PA_hPAP21_like PA_hPAP21_like: Protease-associated	99.88
cd02122	138	PA_GRAIL_like PA _GRAIL_like: Protease-associated	99.86
cd02132	139	PA_GO-like PA_GO-like: Protease-associated domain	99.84
cd04813	117	PA_1 PA_1: Protease-associated (PA) domain subgrou	99.83
cd02129	120	PA_hSPPL_like PA_hSPPL_like: Protease-associated d	99.8
cd04818	118	PA_subtilisin_1 PA_subtilisin_1: Protease-associat	99.77
cd04816	122	PA_SaNapH_like PA_SaNapH_like: Protease-associated	99.74
cd02130	122	PA_ScAPY_like PA_ScAPY_like: Protease-associated d	99.71
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.71
KOG3920	193	consensus Uncharacterized conserved protein, conta	99.66
cd04817	139	PA_VapT_like PA_VapT_like: Protease-associated dom	99.65
cd02124	129	PA_PoS1_like PA_PoS1_like: Protease-associated (PA	99.59
PF02225	101	PA: PA domain; InterPro: IPR003137 The PA (Proteas	99.59
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.58
KOG2442	541	consensus Uncharacterized conserved protein, conta	99.41
cd00538	126	PA PA: Protease-associated (PA) domain. The PA dom	99.4
cd02133	143	PA_C5a_like PA_C5a_like: Protease-associated domai	99.36
PHA02929	238	N1R/p28-like protein; Provisional	99.34
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.31
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.25
cd04819	127	PA_2 PA_2: Protease-associated (PA) domain subgrou	99.21
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.07
cd04815	134	PA_M28_2 PA_M28_2: Protease-associated (PA) domain	99.03
cd02120	126	PA_subtilisin_like PA_subtilisin_like: Protease-as	98.98
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.98
cd02128	183	PA_TfR PA_TfR: Protease-associated domain containi	98.96
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.95
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.93
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.92
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.88
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.88
PF14634	44	zf-RING_5: zinc-RING finger domain	98.84
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.84
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.8
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.8
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.78
PHA02926	242	zinc finger-like protein; Provisional	98.76
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.69
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.58
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.54
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.54
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.44
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.42
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.39
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.39
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.36
cd02121	220	PA_GCPII_like PA_GCPII_like: Protease-associated d	98.35
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.29
cd04822	151	PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) do	98.24
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.19
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.12
cd04814	142	PA_M28_1 PA_M28_1: Protease-associated (PA) domain	98.11
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.09
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.08
cd04820	137	PA_M28_1_1 PA_M28_1_1: Protease-associated (PA) do	98.08
cd02131	153	PA_hNAALADL2_like PA_hNAALADL2_like: Protease-asso	98.06
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.05
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.01
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.96
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.89
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.87
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.85
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.69
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.69
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	97.68
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.56
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.52
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.46
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.41
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.39
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.38
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.26
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.17
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.17
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	96.97
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	96.92
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.89
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.8
PHA02862	156	5L protein; Provisional	96.77
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.76
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.7
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.69
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.41
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.37
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.34
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.18
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.06
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.89
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.64
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.28
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.21
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.16
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.16
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.15
PHA03096	284	p28-like protein; Provisional	94.97
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.89
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	94.77
KOG2660	331	consensus Locus-specific chromosome binding protei	94.66
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.6
KOG1940	276	consensus Zn-finger protein [General function pred	94.46
COG5152	259	Uncharacterized conserved protein, contains RING a	94.31
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	93.81
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	93.63
cd04821	157	PA_M28_1_2 PA_M28_1_2: Protease-associated (PA) do	93.6
PF04641	260	Rtf2: Rtf2 RING-finger	93.55
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.41
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	93.26
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.23
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	93.0
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	92.74
KOG1001	674	consensus Helicase-like transcription factor HLTF/	92.6
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	92.53
KOG3053	293	consensus Uncharacterized conserved protein [Funct	92.23
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	92.19
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	91.44
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	89.79
KOG1609	323	consensus Protein involved in mRNA turnover and st	89.61
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	88.62
KOG3002	299	consensus Zn finger protein [General function pred	87.99
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	87.79
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	87.72
KOG0298	1394	consensus DEAD box-containing helicase-like transc	86.25
KOG1829	580	consensus Uncharacterized conserved protein, conta	86.16
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	85.54
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	84.5
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	83.79
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	82.36
KOG0825	1134	consensus PHD Zn-finger protein [General function	81.35
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	80.95
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	80.08

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

Probab=100.00  E-value=4.7e-53  Score=402.56  Aligned_cols=252  Identities=41%  Similarity=0.743  Sum_probs=216.3

Q ss_pred             ccceecccccccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEec
Q 018364          100 LSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYN  179 (357)
Q Consensus       100 ~~~~~~~~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~  179 (357)
                      .+.+|.+.+|+||+.+..++..|.++.++|.|||+++.+.+........+++||+||+|+|++|+++||++|++|+||||
T Consensus        32 ~S~sf~d~~a~f~~s~~~e~~~G~l~~~ep~~aC~~i~~~p~~~~~~~~~laLI~Rg~CsFe~Kv~~AQ~aGfkaaIVyn  111 (348)
T KOG4628|consen   32 TSLSFADLPALFGPSLPSEGNLGVLVVAEPLNACNPITNFPEHSTRSTSFLALIRRGGCSFEDKVLNAQRAGFKAAIVYN  111 (348)
T ss_pred             ccccccCCccccCCccccccceeeeecCCCccccCccccCccCCCCCcceEEEEEccCCchHHHHhhcccccCceEEEec
Confidence            67789999999999999999999999999999999998744434456789999999999999999999999999999999


Q ss_pred             ccCcccccccccCCCcceeeEEEeehhhhhhhhhhcccCCceeeecC-CCCCcccccceeeeehhhHHHHhhhhccccCC
Q 018364          180 DREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGETGECCIFP-ESNRGSWSVLMVSVFSLIVVFALFAVAFITPR  258 (357)
Q Consensus       180 ~~~~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~l~~~~~~v~I~p-~~s~~~~~im~IsfI~llvi~~vlli~~~~~r  258 (357)
                      |.+.++++.|..+..++.|+++||+...|+.|.++.......+...+ ....+.|.++.++++.++++..++++.+++++
T Consensus       112 n~~~~~lv~~~~~~~~v~i~~~~vs~~~ge~l~~~~~~~~~~~~~~~~~~~~~~ws~~~~~~i~~l~v~~il~~~f~i~~  191 (348)
T KOG4628|consen  112 NVGSEDLVAMASNPSKVDIHIVFVSVFSGELLSSYAGRTEFECLLIPLGFDTSPWSILAISLISLLTVVAILVTCFFIYR  191 (348)
T ss_pred             CCCCchheeeccCCccceeEEEEEeeehHHHHHHhhcccceeeeeccccccCCcchhhhhhhhhHHHHHHHHHHHHHHHH
Confidence            98888899999999999999999999999999997655555555444 78888999999888888888888877776666


Q ss_pred             CCCCCCCCCCccccccchhHHhhccccccccCCCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCC
Q 018364          259 PWRPWPGQNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTF  338 (357)
Q Consensus       259 ~r~~~~~~~~~~~~~l~~~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~  338 (357)
                      .+...+.++..+.+++.++.++++|...|+..+++...  +.|+||||+|++||+||+|||+|.||..|||+||.++++.
T Consensus       192 ~~~~~~~r~~~~~~r~~k~~l~~~p~~~f~~~~~~~~~--~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~  269 (348)
T KOG4628|consen  192 IRRLIRARNRLRRNRLIKRLLKKLPVRTFTKGDDEDAT--DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTF  269 (348)
T ss_pred             HHHHHHHHhHhhhhhhHHHHHhhCCcEEeccccccCCC--ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCcc
Confidence            55444333334567899999999999999996665222  7999999999999999999999999999999999999888


Q ss_pred             CCcccccCcCCCCCC
Q 018364          339 CPVCKHDMRNNSESN  353 (357)
Q Consensus       339 CPlCR~~i~~~~~~~  353 (357)
                      ||+||+++......+
T Consensus       270 CPvCK~di~~~~~~~  284 (348)
T KOG4628|consen  270 CPVCKRDIRTDSGSE  284 (348)
T ss_pred             CCCCCCcCCCCCCCC
Confidence            999999997765544

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

Probab=99.90  E-value=5.7e-23  Score=178.49  Aligned_cols=119  Identities=47%  Similarity=0.745  Sum_probs=102.2

Q ss_pred             cceecccccccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecc
Q 018364          101 SLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYND  180 (357)
Q Consensus       101 ~~~~~~~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~  180 (357)
                      +.+|+..+|.||.+.+++++.|.|+.++|.+||+++++++.......++|+||+||+|+|.+|++|||++||++|||||+
T Consensus        21 ~~~~~~~~A~FG~~~~~~~~~g~lv~~~p~~gC~~~~~~~~~~~~~~g~IvLV~RG~CtF~~Kv~nAq~aGA~avII~n~  100 (153)
T cd02123          21 TDEFDDLPANFGPIPPGSGLKGVLVVAEPLNACSPIENPPLNSNASGSFIVLIRRGNCSFETKVRNAQRAGYKAAIVYND  100 (153)
T ss_pred             cceEeeecccCCCCCCCCceEEEEEeCCccccCCCCcccccccccCCCeEEEEECCCCCHHHHHHHHHHCCCCEEEEEEC
Confidence            46788899999999999999999999999999999986431123457899999999999999999999999999999998


Q ss_pred             cCcccccccccCCC---cceeeEEEeehhhhhhhhhhcccCCc
Q 018364          181 REKGSLVSMTASHE---GVKVHAIFVSLETGVYLKEHARGETG  220 (357)
Q Consensus       181 ~~~~~~~~m~~~~~---~i~Ip~v~is~~~G~~L~~~l~~~~~  220 (357)
                      .+ +.+..|.+++.   .++||+++|++++|+.|++.++....
T Consensus       101 ~~-~~~~~m~~~~~~~~~v~IP~v~Is~~dg~~L~~~l~~~~~  142 (153)
T cd02123         101 ES-NDLISMSGNDQEIKGIDIPSVFVGKSTGEILKKYASYEKG  142 (153)
T ss_pred             CC-CcceeccCCCCCCcCCEEEEEEeeHHHHHHHHHHHhcCCc
Confidence            76 45667776554   68999999999999999998877655

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

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

Probab=99.89  E-value=6.4e-23  Score=172.61  Aligned_cols=109  Identities=20%  Similarity=0.313  Sum_probs=90.2

Q ss_pred             ccccccCCCCeEEEEeeC-CCCCCCCCCCCCCCCC---CCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCccc
Q 018364          110 KFAVDVNSSGTCGALHVA-DPADACSPLSNPVASN---DADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGS  185 (357)
Q Consensus       110 ~Fg~~~~~~~~~g~l~~~-~p~~aC~~~~~~~~~~---~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~  185 (357)
                      +||.++|++.+.|.|+++ ++.+||+++++...+.   ....++||||+||+|+|.+|++|||++||++|||||+.+ ++
T Consensus         1 ~FG~~~yg~~~~G~l~~~~~~~~gC~~~~~~~~~~~~~~~~~~~IvLv~RG~C~F~~K~~~Aq~aGA~avII~n~~~-~~   79 (127)
T cd02125           1 NFGLPQYGGTLTGVVVYPKENRTGCKEFDVFFKPKKSEPGRRPVILLLDRGGCFFTLKAWNAQQAGAAAVLVADNVD-EP   79 (127)
T ss_pred             CCCCCCcCCeeEEEEEecCCccccCCCCcccccccccccCCCceEEEEECCCcCHHHHHHHHHHCCCcEEEEEECCC-Cc
Confidence            699999999999999877 6789999997632121   135689999999999999999999999999999999875 34


Q ss_pred             cccccc--------CCCcceeeEEEeehhhhhhhhhhcccCC
Q 018364          186 LVSMTA--------SHEGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       186 ~~~m~~--------~~~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      ++.|..        ..++++||+++|++++|+.|++.+..+.
T Consensus        80 ~~~m~~~~~~~~~~~~~~i~IP~v~Is~~~G~~L~~~l~~g~  121 (127)
T cd02125          80 LLTMDTPEESGSADYIEKITIPSALITKAFGEKLKKAISNGE  121 (127)
T ss_pred             cccccCcccccccccCCCceEeEEEECHHHHHHHHHHHhcCC
Confidence            556643        2345789999999999999999887654

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

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

Probab=99.89  E-value=1.4e-22  Score=170.64  Aligned_cols=109  Identities=26%  Similarity=0.465  Sum_probs=92.3

Q ss_pred             ccccccccccCCC-CeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcc
Q 018364          106 DLPAKFAVDVNSS-GTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKG  184 (357)
Q Consensus       106 ~~~a~Fg~~~~~~-~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~  184 (357)
                      ..||+||.+++.. ++.|.|+.++|.+||++..++.    ...++|+||+||+|+|.+|+++||++||+|||||||.+++
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            3689999999874 7899999999999999887532    2468999999999999999999999999999999886542


Q ss_pred             -----cccccccCC---CcceeeEEEeehhhhhhhhhhcccC
Q 018364          185 -----SLVSMTASH---EGVKVHAIFVSLETGVYLKEHARGE  218 (357)
Q Consensus       185 -----~~~~m~~~~---~~i~Ip~v~is~~~G~~L~~~l~~~  218 (357)
                           .++.|.++.   +.++||+++|++++|+.|++.++.+
T Consensus        78 ~~~~~~~~~m~~~~~~~~~~~IP~v~I~~~dG~~L~~~l~~~  119 (126)
T cd02126          78 SSDTAPMFAMSGDGDSTDDVTIPVVFLFSKEGSKLLAAIKEH  119 (126)
T ss_pred             cccccceeEeecCCCCCCCCeEEEEEEEHHHHHHHHHHHHhC
Confidence                 355666654   3689999999999999999988764

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

>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=99.88  E-value=2.9e-22  Score=166.57  Aligned_cols=108  Identities=28%  Similarity=0.302  Sum_probs=91.6

Q ss_pred             ccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCc--cccc
Q 018364          110 KFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREK--GSLV  187 (357)
Q Consensus       110 ~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~--~~~~  187 (357)
                      .||.+++.+...|.|+.++|.+||++..+..    +.+++|+||+||+|+|.+|+++||++||+||||||+.++  ...+
T Consensus         1 ~~~~~~~~~~~~~~lv~~~p~~gC~~~~~~~----~~~g~I~Lv~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~~~   76 (118)
T cd02127           1 DFGTIFNTRYKHVPLVPADPLEACEELRNIH----DINGNIALIERGGCSFLTKAINAQKAGALAVIITDVNNDSDEYYV   76 (118)
T ss_pred             CCCccccccccceEEEECCccccCCCCCCcc----ccCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccce
Confidence            4899999999999999999999999876432    247899999999999999999999999999999998653  3445


Q ss_pred             ccccC--CCcceeeEEEeehhhhhhhhhhcccCCce
Q 018364          188 SMTAS--HEGVKVHAIFVSLETGVYLKEHARGETGE  221 (357)
Q Consensus       188 ~m~~~--~~~i~Ip~v~is~~~G~~L~~~l~~~~~~  221 (357)
                      .|.++  ...++||+++|++++|+.|++.++.+...
T Consensus        77 ~m~~~~~~~~i~IP~v~Is~~dG~~L~~~l~~g~~~  112 (118)
T cd02127          77 EMIQDDSSRRADIPAAFLLGKNGYMIRKTLERLGLP  112 (118)
T ss_pred             EecCCCCCCCceEEEEEecHHHHHHHHHHHHcCCce
Confidence            56665  35689999999999999999988776543

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.

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

Probab=99.86  E-value=3e-21  Score=164.72  Aligned_cols=111  Identities=21%  Similarity=0.302  Sum_probs=91.5

Q ss_pred             cccccccccCCCCeEEEEeeC---CCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccC-
Q 018364          107 LPAKFAVDVNSSGTCGALHVA---DPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDRE-  182 (357)
Q Consensus       107 ~~a~Fg~~~~~~~~~g~l~~~---~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~-  182 (357)
                      .+|+||.+++..++.|.|+.+   ++.+||+++++... ..+..++||||+||+|+|.+|++|||++||++|||||+.+ 
T Consensus        18 ~~a~fg~~~~~~~~~G~l~~~~~~~~~~gC~~~~~~~~-~~~~~g~IaLV~RG~C~F~~K~~nA~~aGA~aVIIyn~~~~   96 (138)
T cd02122          18 ESGRYGEHSPKEEAKGLVVVPDPPNDHYGCDPDTRFPI-PPNGEPWIALIQRGNCTFEEKIKLAAERNASAVVIYNNPGT   96 (138)
T ss_pred             cccccCCCCCCCccEEEEecCCCCCCcCCCCCCccccC-CccCCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCC
Confidence            489999999999999998644   45899999975211 1235789999999999999999999999999999999976 


Q ss_pred             cccccccccCCCcceeeEEEeehhhhhhhhhhcccCC
Q 018364          183 KGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       183 ~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      ...++.|..+.. ..||+++|++++|+.|++.++.+.
T Consensus        97 ~~~~~~m~~~~~-~~ip~v~Is~~~G~~l~~~l~~G~  132 (138)
T cd02122          97 GNETVKMSHPGT-GDIVAIMITNPKGMEILELLERGI  132 (138)
T ss_pred             CCceeeccCCCC-CcceEEEEcHHHHHHHHHHHHcCC
Confidence            344666655443 489999999999999999887653

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

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

Probab=99.84  E-value=1.2e-20  Score=161.34  Aligned_cols=112  Identities=23%  Similarity=0.402  Sum_probs=93.5

Q ss_pred             ccceecccccccccccCC---CCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEE
Q 018364          100 LSLHFPDLPAKFAVDVNS---SGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAI  176 (357)
Q Consensus       100 ~~~~~~~~~a~Fg~~~~~---~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avI  176 (357)
                      ...+|.+.+|.||..++.   .+..+.|+.++|.+||+++++      +..++|+||+||+|+|.+|++|||++||++||
T Consensus        15 ~~~~~~~~~a~FG~~~p~~~~~~~~~~lv~~~~~~gC~~~~~------~~~g~IvLV~RG~C~F~~K~~nA~~aGA~avI   88 (139)
T cd02132          15 EGDELVGVTARFGASLPSKEDNANKTRAVLANPLDCCSPSTS------KLSGSIALVERGECAFTEKAKIAEAGGASALL   88 (139)
T ss_pred             cccEEEeeccccCCCCCCcccCccEEEEEECCcccccCCCCc------ccCCeEEEEECCCCCHHHHHHHHHHcCCcEEE
Confidence            456799999999998765   467889999999999999863      23689999999999999999999999999999


Q ss_pred             EecccCcccccccccC----CCcceeeEEEeehhhhhhhhhhcccCC
Q 018364          177 VYNDREKGSLVSMTAS----HEGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       177 v~~~~~~~~~~~m~~~----~~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      |||+.+.  +..|...    ...+.||+++|++++|+.|++.++.+.
T Consensus        89 v~n~~~~--~~~~~~~~~~~~~~~~IP~v~Is~~~G~~L~~~l~~g~  133 (139)
T cd02132          89 IINDQEE--LYKMVCEDNDTSLNISIPVVMIPQSAGDALNKSLDQGK  133 (139)
T ss_pred             EEECCCc--ccccccCCCCCCCCCcEeEEEecHHHHHHHHHHHHcCC
Confidence            9998653  4455432    124799999999999999999887654

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.

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

Probab=99.83  E-value=2.1e-20  Score=155.07  Aligned_cols=104  Identities=28%  Similarity=0.326  Sum_probs=83.8

Q ss_pred             cccccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccc
Q 018364          107 LPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSL  186 (357)
Q Consensus       107 ~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~  186 (357)
                      ..|.||++++.+--. . +.++|.+||++++.     .+.+++||||+||+|+|.+|++|||++||++|||||+.+.+.+
T Consensus         6 ~~~~~~~~~~~~~~~-~-~~~~p~~gC~~~~~-----~~l~gkIvLV~RG~CsF~~K~~nAq~aGA~avII~n~~~~~~~   78 (117)
T cd04813           6 RYASFSPILNPHLRG-S-YKVSPTDACSLQEH-----AEIDGKVALVLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRGL   78 (117)
T ss_pred             cccccCCccCccccc-c-ccCCCCCCCCCCCc-----CCcCCeEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCCcccc
Confidence            468899998877322 2 23789999998832     1347899999999999999999999999999999998765555


Q ss_pred             ccccc--CCCcceeeEEEeehhhhhhhhhhccc
Q 018364          187 VSMTA--SHEGVKVHAIFVSLETGVYLKEHARG  217 (357)
Q Consensus       187 ~~m~~--~~~~i~Ip~v~is~~~G~~L~~~l~~  217 (357)
                      +.|..  +...++||+++|++++|+.|+.++..
T Consensus        79 ~~m~~~~~~~~v~IPav~Is~~~g~~L~~l~~~  111 (117)
T cd04813          79 ITMFSNGDTDNVTIPAMFTSRTSYHLLSSLLPK  111 (117)
T ss_pred             eecccCCCCCCcEEEEEEEcHHHHHHHHHhccc
Confidence            56653  34568999999999999999987654

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

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

Probab=99.80  E-value=2.2e-19  Score=148.93  Aligned_cols=93  Identities=17%  Similarity=0.226  Sum_probs=74.2

Q ss_pred             EEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcceeeEE
Q 018364          122 GALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAI  201 (357)
Q Consensus       122 g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i~Ip~v  201 (357)
                      -.|+.++|..||++.+....   +.+++|+||+||+|+|.+|++|||++||+|||||||.+........++...++||++
T Consensus        22 ~~~~~~~~~~gC~~~~~~~~---~l~gkIaLV~RG~CsF~~K~~~Aq~aGA~aVII~nn~~~~~~~~~~~~~~~v~IP~v   98 (120)
T cd02129          22 LPLRNLTSSVLCSASDVPPG---GLKGKAVVVMRGNCTFYEKARLAQSLGAEGLLIVSRERLVPPSGNRSEYEKIDIPVA   98 (120)
T ss_pred             eeeecCCCcCCCCccccCcc---ccCCeEEEEECCCcCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCcCCcccEE
Confidence            35778899999998764321   247899999999999999999999999999999998653221111222356899999


Q ss_pred             Eeehhhhhhhhhhccc
Q 018364          202 FVSLETGVYLKEHARG  217 (357)
Q Consensus       202 ~is~~~G~~L~~~l~~  217 (357)
                      ||++++|+.|++.+..
T Consensus        99 ~Is~~dG~~i~~~l~~  114 (120)
T cd02129          99 LLSYKDMLDIQQTFGD  114 (120)
T ss_pred             EEeHHHHHHHHHHhcc
Confidence            9999999999998764

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=99.77  E-value=2.8e-18  Score=142.63  Aligned_cols=107  Identities=28%  Similarity=0.373  Sum_probs=90.9

Q ss_pred             ccccccccCC---CCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcc
Q 018364          108 PAKFAVDVNS---SGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKG  184 (357)
Q Consensus       108 ~a~Fg~~~~~---~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~  184 (357)
                      +|.||+.++.   ..+.|.|+.++|.++|++.....    +..++|+|++||+|+|.+|+++|+++||+++||||+.+..
T Consensus         2 ~a~fg~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~----~v~GkIvL~~rg~c~f~~k~~~a~~aGA~gvIi~~~~~~~   77 (118)
T cd04818           2 SAGFGPALTNVTADVVLAGAAPASNTDGCTAFTNAA----AFAGKIALIDRGTCNFTVKVLNAQNAGAIAVIVANNVAGG   77 (118)
T ss_pred             CcccCCcCccccccceeEEEecCCcccccCCCCcCC----CCCCEEEEEECCCCCHHHHHHHHHHCCCeEEEEEECCCCC
Confidence            7999998875   66889999999999999887422    2578999999999999999999999999999999987654


Q ss_pred             cccccccCCCcceeeEEEeehhhhhhhhhhcccC
Q 018364          185 SLVSMTASHEGVKVHAIFVSLETGVYLKEHARGE  218 (357)
Q Consensus       185 ~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~l~~~  218 (357)
                      ..+.|..+.....||+++|++++|+.|+++++.+
T Consensus        78 ~~~~~~~~~~~~~iP~v~V~~~~g~~l~~~l~~g  111 (118)
T cd04818          78 APITMGGDDPDITIPAVMISQADGDALKAALAAG  111 (118)
T ss_pred             cceeccCCCCCCEEeEEEecHHHHHHHHHHHhcC
Confidence            4455655554578999999999999999998754

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=99.74  E-value=2.2e-17  Score=138.12  Aligned_cols=109  Identities=23%  Similarity=0.310  Sum_probs=86.3

Q ss_pred             ccccccccCCCCeEEEEeeCCC--CCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCccc
Q 018364          108 PAKFAVDVNSSGTCGALHVADP--ADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGS  185 (357)
Q Consensus       108 ~a~Fg~~~~~~~~~g~l~~~~p--~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~  185 (357)
                      ...|++..+..+++|.|++.++  .+||++.+.+.   .+.+++||||+||+|+|.+|+++||++||+++||||+.+...
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            3568888888999999988765  58999875432   235789999999999999999999999999999999866322


Q ss_pred             ccccccC-CCcceeeEEEeehhhhhhhhhhcccCC
Q 018364          186 LVSMTAS-HEGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       186 ~~~m~~~-~~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      ...+..+ .....||+++|++++|+.|+++++.+.
T Consensus        82 ~~~~~~~~~~~~~iP~~~Is~~~G~~l~~~l~~g~  116 (122)
T cd04816          82 TAGTLGAPNIDLKVPVGVITKAAGAALRRRLGAGE  116 (122)
T ss_pred             ccccccCCCCCCeeeEEEEcHHHHHHHHHHHcCCC
Confidence            2222222 245789999999999999999987654

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=99.71  E-value=7.9e-17  Score=134.78  Aligned_cols=109  Identities=30%  Similarity=0.396  Sum_probs=81.6

Q ss_pred             eecccccccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccC
Q 018364          103 HFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDRE  182 (357)
Q Consensus       103 ~~~~~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~  182 (357)
                      .|+.....|++.   .+.+|+|++. +.+||++.+.+.    +..++||||+||+|+|.+|+++||++||++|||||+..
T Consensus         8 ~~~~~~~~~~~~---~~~~g~lv~~-~~~gC~~~~~~~----~~~gkIvlv~rg~c~f~~K~~~A~~aGA~~vIv~n~~~   79 (122)
T cd02130           8 AIPTTAFTYSPA---GEVTGPLVVV-PNLGCDAADYPA----SVAGNIALIERGECPFGDKSALAGAAGAAAAIIYNNVP   79 (122)
T ss_pred             EEeeeecccCCC---CCcEEEEEEe-CCCCCCcccCCc----CCCCEEEEEECCCCCHHHHHHHHHHCCCcEEEEEECCC
Confidence            344444444433   5557999885 457999865431    35789999999999999999999999999999999873


Q ss_pred             cccccccccCCCcceeeEEEeehhhhhhhhhhcccCC
Q 018364          183 KGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       183 ~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      ......+.++..+..||+++|++++|+.|++.++.++
T Consensus        80 ~~~~~~~~~~~~~~~Ip~v~Is~~~G~~L~~~l~~g~  116 (122)
T cd02130          80 AGGLSGTLGEPSGPYVPTVGISQEDGKALVAALANGG  116 (122)
T ss_pred             CcccccccCCCCCCEeeEEEecHHHHHHHHHHHhcCC
Confidence            2322223334445789999999999999999887653

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=99.71  E-value=1.2e-18  Score=161.19  Aligned_cols=54  Identities=39%  Similarity=1.042  Sum_probs=49.0

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ...+.+|+|||++|-++|++++|||.|.||..|+++|+.-++..||+||.++++
T Consensus       320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            344579999999999999999999999999999999999766679999999876

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

Probab=99.66  E-value=4.9e-17  Score=137.41  Aligned_cols=119  Identities=29%  Similarity=0.421  Sum_probs=96.7

Q ss_pred             eEEEcc--ccceecccccc-cccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHc
Q 018364           94 TLVWKP--LSLHFPDLPAK-FAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAA  170 (357)
Q Consensus        94 ~vv~~~--~~~~~~~~~a~-Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~a  170 (357)
                      |.|+.|  ..++|...+|. ||..++..--.-.|+.++|..||+.+.|.-..    .+.|+|++||+|+|..|.+++|++
T Consensus        35 F~vlsP~~l~Yty~~~pAkdfG~~F~~r~e~~~lV~adPp~aC~elrN~~f~----~d~vaL~eRGeCSFl~Ktl~~e~a  110 (193)
T KOG3920|consen   35 FTVLSPYTLAYTYQMKPAKDFGVHFPDRFENLELVLADPPHACEELRNEIFA----PDSVALMERGECSFLVKTLNGEKA  110 (193)
T ss_pred             EEecCcccEEEEEEecchhhhccccchhhcCcceeecCChhHHHHHhhcccC----CCcEEEEecCCceeeehhhhhhhc
Confidence            446677  67788888887 99988876555578999999999999875543    458999999999999999999999


Q ss_pred             CCcEEEEecccCccc----ccccccCC--CcceeeEEEeehhhhhhhhhhcc
Q 018364          171 GYRAAIVYNDREKGS----LVSMTASH--EGVKVHAIFVSLETGVYLKEHAR  216 (357)
Q Consensus       171 GA~avIv~~~~~~~~----~~~m~~~~--~~i~Ip~v~is~~~G~~L~~~l~  216 (357)
                      ||.|+||.|+..++.    .+.|..|+  .+.+||++++-..+|..+..-++
T Consensus       111 Ga~aiiitd~~~~~~sf~~YveMI~D~sq~~AniPa~fllg~~Gy~ir~sL~  162 (193)
T KOG3920|consen  111 GATAIIITDSQNYEYSFHQYVEMIPDESQDRANIPAVFLLGVTGYYIRVSLK  162 (193)
T ss_pred             CceEEEEecCCCCchhHHHHHHhcCcccccccCCceEEEeccceEEEehhHH
Confidence            999999999865543    45676553  35799999999999988776553

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

Probab=99.65  E-value=1.6e-15  Score=129.20  Aligned_cols=101  Identities=21%  Similarity=0.197  Sum_probs=75.9

Q ss_pred             ccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCC-----hHHHHHHHHHcCCcEEEEecccCcc
Q 018364          110 KFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCI-----FEDKIRNAQAAGYRAAIVYNDREKG  184 (357)
Q Consensus       110 ~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~Cs-----F~~K~~~Aq~aGA~avIv~~~~~~~  184 (357)
                      .|-...+...++|.|+..... +|+-..      .+..++|+||+||+|+     |.+|+++||++||+|||||||.++.
T Consensus        26 ~~~s~~~~g~~tg~lv~~g~~-g~d~~~------~d~~GkIaLI~RG~c~~~~~~f~~Kv~~A~~aGA~avIIyNn~~~~   98 (139)
T cd04817          26 SYASMPVTGSATGSLYYCGTS-GGSYIC------GGMAGKICLIERGGNSKSVYPEIDKVKACQNAGAIAAIVYSNAALA   98 (139)
T ss_pred             cccccccCCcceEEEEEccCC-CccccC------CCcCccEEEEECCCCCCCcccHHHHHHHHHHCCCeEEEEEeCCCCC
Confidence            344455566788888876653 473211      1246899999999999     9999999999999999999997433


Q ss_pred             c-ccccccCCC-cceeeEEEeehhhhhhhhhhccc
Q 018364          185 S-LVSMTASHE-GVKVHAIFVSLETGVYLKEHARG  217 (357)
Q Consensus       185 ~-~~~m~~~~~-~i~Ip~v~is~~~G~~L~~~l~~  217 (357)
                      . +..+.++.. .++||+++|++++|+.|++.+..
T Consensus        99 g~~~~~lg~~~~~~~IP~v~is~~dG~~L~~~l~~  133 (139)
T cd04817          99 GLQNPFLVDTNNDTTIPSVSVDRADGQALLAALGQ  133 (139)
T ss_pred             CcccccccCCCCCceEeEEEeeHHHHHHHHHHhcC
Confidence            3 223434433 68999999999999999998754

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.

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

Probab=99.59  E-value=7.3e-15  Score=124.02  Aligned_cols=90  Identities=26%  Similarity=0.381  Sum_probs=68.4

Q ss_pred             EEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcceeeEEE
Q 018364          123 ALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIF  202 (357)
Q Consensus       123 ~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i~Ip~v~  202 (357)
                      .+..+++.+||++++... +  +.+++||||+||+|+|.+|++|||++||++|||||+.+. . ..+...+. ..+|.++
T Consensus        34 ~~~~~~~~~gC~~~~~~~-~--~~~g~IaLv~rg~c~f~~K~~nA~~aGA~aviiyn~~~~-~-~~~~~~~~-~~~~~~~  107 (129)
T cd02124          34 SLDTSVADDACQPLPDDT-P--DLSGYIVLVRRGTCTFATKAANAAAKGAKYVLIYNNGSG-P-TDQVGSDA-DSIIAAV  107 (129)
T ss_pred             ecccCCCcccCcCCCccc-c--cccCeEEEEECCCCCHHHHHHHHHHcCCcEEEEEECCCC-c-ccccCCCC-cceeeEE
Confidence            344567889999986432 2  347899999999999999999999999999999998753 2 23333332 3456666


Q ss_pred             eehhhhhhhhhhcccCC
Q 018364          203 VSLETGVYLKEHARGET  219 (357)
Q Consensus       203 is~~~G~~L~~~l~~~~  219 (357)
                      + +++|+.|++.++.+.
T Consensus       108 ~-~~~G~~l~~~l~~G~  123 (129)
T cd02124         108 T-PEDGEAWIDALAAGS  123 (129)
T ss_pred             e-HHHHHHHHHHHhcCC
Confidence            6 999999999887653

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.

>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=99.59  E-value=1.1e-15  Score=122.84  Aligned_cols=95  Identities=28%  Similarity=0.469  Sum_probs=65.5

Q ss_pred             CCeEEEEeeCCCC---CCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCC
Q 018364          118 SGTCGALHVADPA---DACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHE  194 (357)
Q Consensus       118 ~~~~g~l~~~~p~---~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~  194 (357)
                      ....|+|+.+.+.   ..|.+.+..   ....+++|||++||+|+|.+|+++||++||+||||+|+.+.........+..
T Consensus         4 ~~~~~~lV~~~~~~~~~~~~~~~~~---~~~~~gkIvlv~rg~~~~~~k~~~a~~~GA~gvIi~~~~~~~~~~~~~~~~~   80 (101)
T PF02225_consen    4 GTVTGPLVPAGNGIDEGDCCPSDYN---GSDVKGKIVLVERGSCSFDDKVRNAQKAGAKGVIIYNPPPNNGSMIDSEDPD   80 (101)
T ss_dssp             EEEEEEEEEETTEEECCHHHHHHTS---TSTCTTSEEEEESTSSCHHHHHHHHHHTTESEEEEE-TSCSCTTTTCEBTTT
T ss_pred             CCEEEEEEEecCCCCcccccccccC---CccccceEEEEecCCCCHHHHHHHHHHcCCEEEEEEeCCccccCcccccCCC
Confidence            4466778744332   233332211   2235789999999999999999999999999999999322222222333445


Q ss_pred             cceeeEEEeehhhhhhhhhhc
Q 018364          195 GVKVHAIFVSLETGVYLKEHA  215 (357)
Q Consensus       195 ~i~Ip~v~is~~~G~~L~~~l  215 (357)
                      ...||+++|++++|+.|++++
T Consensus        81 ~~~iP~v~I~~~~g~~L~~~i  101 (101)
T PF02225_consen   81 PIDIPVVFISYEDGEALLAYI  101 (101)
T ss_dssp             STBSEEEEE-HHHHHHHHHHH
T ss_pred             CcEEEEEEeCHHHHhhhhccC
Confidence            589999999999999999863

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 ....

>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=99.58  E-value=5.9e-16  Score=106.21  Aligned_cols=44  Identities=50%  Similarity=1.241  Sum_probs=40.1

Q ss_pred             cccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCccc
Q 018364          299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK  343 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR  343 (357)
                      ++|+||+++|..++.+..|+|+|.||.+||.+|+++++ +||+||
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            57999999999999999999999999999999999976 699998

...

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

Probab=99.41  E-value=4.6e-13  Score=131.39  Aligned_cols=138  Identities=25%  Similarity=0.409  Sum_probs=94.6

Q ss_pred             ecccccccccccCCCCeEE---EEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecc
Q 018364          104 FPDLPAKFAVDVNSSGTCG---ALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYND  180 (357)
Q Consensus       104 ~~~~~a~Fg~~~~~~~~~g---~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~  180 (357)
                      +....+.||..++...-..   .+...+|.|-|++.+++-      ++++++|.||+|+|.+|+++||++||.|++|.||
T Consensus        55 ~a~~~~~~~~t~~~~~~~a~~~~~a~~~pld~cs~~~~kl------~~~~~~v~RGnC~Ft~Ka~~Aq~aGAsaLliin~  128 (541)
T KOG2442|consen   55 FAGMLARFGITLPSKCKAADIPHLAQVDPLDSCSTLQSKL------SGKVALVFRGNCSFTEKAKLAQAAGASALLIINN  128 (541)
T ss_pred             hhhhhhhcCCcCCCCccccccchhhhcCCccccCCCCccc------cceeEEEecccceeehhhhhhhhcCceEEEEEcC
Confidence            4456788988655433222   233568999999876432      5699999999999999999999999999999998


Q ss_pred             cCcccccccccC----CCcceeeEEEeehhhhhhhhhhccc-CCceeeecCCCCCcccccceeeeehhhHHHHhhh
Q 018364          181 REKGSLVSMTAS----HEGVKVHAIFVSLETGVYLKEHARG-ETGECCIFPESNRGSWSVLMVSVFSLIVVFALFA  251 (357)
Q Consensus       181 ~~~~~~~~m~~~----~~~i~Ip~v~is~~~G~~L~~~l~~-~~~~v~I~p~~s~~~~~im~IsfI~llvi~~vll  251 (357)
                      ..  ++.-|...    ..+++||++||++++|+.+.+.... .++++.+..+..  +-..+.+.|+.++.+..+.+
T Consensus       129 ~~--d~~~~~~~~~~~~~dv~IPv~mi~~~~~~~l~~~~~~~~~V~~~lYaPk~--P~vD~~~v~iwlmAVgTVa~  200 (541)
T KOG2442|consen  129 KK--DLLFMPCGNKETSLDVTIPVAMISYSDGRDLNKSTRSNDNVELALYAPKR--PAVDYAMVFIWLMAVGTVAC  200 (541)
T ss_pred             ch--hhccCCCCCCCccccccceEEEEEhhhHHHHHhhhccCCeEEEEEECCCC--CCccHHHHHHHHHHHhHhhc
Confidence            65  33334332    2358999999999999999985443 345555544433  22334444555555555443

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

Probab=99.40  E-value=9.6e-13  Score=109.62  Aligned_cols=92  Identities=26%  Similarity=0.371  Sum_probs=69.2

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccc-cccccC-CCcceeeEEEe
Q 018364          126 VADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSL-VSMTAS-HEGVKVHAIFV  203 (357)
Q Consensus       126 ~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~-~~m~~~-~~~i~Ip~v~i  203 (357)
                      ...+.++|++... ........++|+|++||+|+|.+|+++||++||+++||+|+.+.... ..+.++ .....||+++|
T Consensus        26 ~~~~~~~C~~~~~-~~~~~~~~GkIvl~~~g~~~~~~k~~~a~~~GA~gvii~~~~~~~~~~~~~~~~~~~~~~iP~~~i  104 (126)
T cd00538          26 VAGPLVGCGYGTT-DDSGADVKGKIVLVRRGGCSFSEKVKNAQKAGAKAVIIYNNGDDPGPQMGSVGLESTDPSIPTVGI  104 (126)
T ss_pred             cccceEEEecCcc-cccCCCccceEEEEECCCcCHHHHHHHHHHCCCEEEEEEECCCCcccccccccCCCCCCcEeEEEe
Confidence            3457789988752 11112357999999999999999999999999999999998753211 112111 23468999999


Q ss_pred             ehhhhhhhhhhcccC
Q 018364          204 SLETGVYLKEHARGE  218 (357)
Q Consensus       204 s~~~G~~L~~~l~~~  218 (357)
                      ++++|+.|+++++.+
T Consensus       105 s~~~g~~l~~~~~~~  119 (126)
T cd00538         105 SYADGEALLSLLEAG  119 (126)
T ss_pred             CHHHHHHHHHHHhcC
Confidence            999999999988754

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=99.36  E-value=7.4e-12  Score=107.57  Aligned_cols=100  Identities=28%  Similarity=0.283  Sum_probs=74.1

Q ss_pred             cccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccc
Q 018364          109 AKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVS  188 (357)
Q Consensus       109 a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~  188 (357)
                      ..++.+.+.....+.|++...   |.+-+..   ..+.+++|+|++||+|+|.+|+++||++||++|||||+.+..  ..
T Consensus        15 ~~~~~~~~~~~~~~~lv~~g~---g~~~d~~---~~dv~GkIvL~~rg~c~~~~K~~~a~~aGA~gvIi~n~~~~~--~~   86 (143)
T cd02133          15 AFSGNPTDLLGKTYELVDAGL---GTPEDFE---GKDVKGKIALIQRGEITFVEKIANAKAAGAVGVIIYNNVDGL--IP   86 (143)
T ss_pred             ccCCCcCCCCCcEEEEEEccC---CchhccC---CCCccceEEEEECCCCCHHHHHHHHHHCCCeEEEEeecCCCc--cc
Confidence            456666666778888886532   2222111   123578999999999999999999999999999999987532  22


Q ss_pred             cccCCCcceeeEEEeehhhhhhhhhhccc
Q 018364          189 MTASHEGVKVHAIFVSLETGVYLKEHARG  217 (357)
Q Consensus       189 m~~~~~~i~Ip~v~is~~~G~~L~~~l~~  217 (357)
                      +..+. ...||+++|++++|+.|+++++.
T Consensus        87 ~~~~~-~~~iP~v~Is~~dG~~L~~~l~~  114 (143)
T cd02133          87 GTLGE-AVFIPVVFISKEDGEALKAALES  114 (143)
T ss_pred             ccCCC-CCeEeEEEecHHHHHHHHHHHhC
Confidence            32222 35799999999999999998876

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=99.34  E-value=7e-13  Score=122.18  Aligned_cols=75  Identities=27%  Similarity=0.582  Sum_probs=55.4

Q ss_pred             cccchhHHhhccccccccCCCCCCCCCcccccccccccCCC----ceEE-eCCCCccchhHHHHHHhcCCCCCCcccccC
Q 018364          272 RRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGE----KLKV-LSCKHEFHASCVDSWLTKWGTFCPVCKHDM  346 (357)
Q Consensus       272 ~~l~~~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~----~vr~-LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i  346 (357)
                      .+..+..++.+|....+-........+.+|+||++++.+.+    .+.+ ++|+|.||.+||.+|+..+. +||+||..+
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            34467777888877654332223455789999999987653    1234 46999999999999999866 599999887


Q ss_pred             c
Q 018364          347 R  347 (357)
Q Consensus       347 ~  347 (357)
                      .
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=99.31  E-value=1.3e-12  Score=99.38  Aligned_cols=46  Identities=35%  Similarity=0.859  Sum_probs=36.4

Q ss_pred             CCcccccccccccCC----------CceEEeCCCCccchhHHHHHHhcCCCCCCccc
Q 018364          297 GGETCAICLEDYQDG----------EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK  343 (357)
Q Consensus       297 ~~~~CaICLe~f~~~----------~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR  343 (357)
                      .++.|+||+++|.+.          -.+...+|+|.||..||.+||+.++ +||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN-TCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS-B-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC-cCCCCC
Confidence            356799999999322          2456668999999999999999987 599998

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 ....

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

Probab=99.25  E-value=3.8e-12  Score=121.06  Aligned_cols=70  Identities=24%  Similarity=0.636  Sum_probs=53.2

Q ss_pred             cchhHHhhccccccccCCCCCCCCCccccccccc-ccCCC---------ceEEeCCCCccchhHHHHHHhcCCCCCCccc
Q 018364          274 LDSKVVEALPCFLFSSASSSQCHGGETCAICLED-YQDGE---------KLKVLSCKHEFHASCVDSWLTKWGTFCPVCK  343 (357)
Q Consensus       274 l~~~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~-f~~~~---------~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR  343 (357)
                      ..++.-+.+|+...++.    ..++..|.||+|+ |+.+.         +-+.|||||+||-+|++.|++++++ ||+||
T Consensus       267 ~~kdl~~~~~t~t~eql----~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQT-CPICr  341 (491)
T COG5243         267 ATKDLNAMYPTATEEQL----TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQT-CPICR  341 (491)
T ss_pred             HhhHHHhhcchhhhhhh----cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccC-CCccc
Confidence            34455555666655553    3457799999999 55541         3478999999999999999999995 99999


Q ss_pred             ccCcC
Q 018364          344 HDMRN  348 (357)
Q Consensus       344 ~~i~~  348 (357)
                      +++.-
T Consensus       342 ~p~if  346 (491)
T COG5243         342 RPVIF  346 (491)
T ss_pred             Ccccc
Confidence            99543

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

Probab=99.21  E-value=1.1e-10  Score=98.42  Aligned_cols=98  Identities=20%  Similarity=0.045  Sum_probs=70.2

Q ss_pred             CCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCC--ChHHHHHHHHHcCCcEEEEecccCccccccc-ccC-
Q 018364          117 SSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQC--IFEDKIRNAQAAGYRAAIVYNDREKGSLVSM-TAS-  192 (357)
Q Consensus       117 ~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~C--sF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m-~~~-  192 (357)
                      .....|+|++...  | .+-+..   ..+..++||||+||.|  +|.+|+++|+++||+||||||+.++....+. .+. 
T Consensus        20 ~~~~~~~lV~~g~--G-~~~d~~---~~~v~GkIvlv~~g~~~~~~~~k~~~A~~~GA~avi~~~~~~g~~~~~~~~~~~   93 (127)
T cd04819          20 SGEAKGEPVDAGY--G-LPKDFD---GLDLEGKIAVVKRDDPDVDRKEKYAKAVAAGAAAFVVVNTVPGVLPATGDEGTE   93 (127)
T ss_pred             CCCeeEEEEEeCC--C-CHHHcC---CCCCCCeEEEEEcCCCchhHHHHHHHHHHCCCEEEEEEeCCCCcCccccccccc
Confidence            3456888887542  2 111111   1235789999999999  9999999999999999999987654322111 111 


Q ss_pred             -CCcceeeEEEeehhhhhhhhhhcccCCc
Q 018364          193 -HEGVKVHAIFVSLETGVYLKEHARGETG  220 (357)
Q Consensus       193 -~~~i~Ip~v~is~~~G~~L~~~l~~~~~  220 (357)
                       .....||++.|+.+||+.|+++++.++.
T Consensus        94 ~~~~~~IP~v~Is~edg~~L~~~l~~g~~  122 (127)
T cd04819          94 DGPPSPIPAASVSGEDGLRLARVAERNDT  122 (127)
T ss_pred             CCCCCCCCEEEEeHHHHHHHHHHHhcCCc
Confidence             2336899999999999999999887553

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

>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=99.07  E-value=1.2e-10  Score=78.81  Aligned_cols=45  Identities=40%  Similarity=1.038  Sum_probs=37.5

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccC
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDM  346 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i  346 (357)
                      +|+||++.+  .+.+..++|+|.||..|++.|++..+..||+||..+
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  345666679999999999999998444699999764

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

Probab=99.03  E-value=5e-10  Score=95.24  Aligned_cols=105  Identities=17%  Similarity=0.107  Sum_probs=75.0

Q ss_pred             ccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCC------ChHHH-------HHHHHHcCCcEEE
Q 018364          110 KFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQC------IFEDK-------IRNAQAAGYRAAI  176 (357)
Q Consensus       110 ~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~C------sF~~K-------~~~Aq~aGA~avI  176 (357)
                      .|++..++.+++|+++.....+   .+..  .+..+..+|||||+||.|      +|..|       ..+|+++||.|+|
T Consensus         7 ~~s~~t~~~gvta~vv~v~~~~---~~~~--~~~~~v~GKIvlv~~~~~~~~~~~~~~~k~~~r~~~~~~A~~~GA~avI   81 (134)
T cd04815           7 GGSVATPPEGITAEVVVVKSFD---ELKA--APAGAVKGKIVFFNQPMVRTQTGSGYGPTVAYRRRGAVEAAKKGAVAVL   81 (134)
T ss_pred             CCCCCCCCCCcEEEEEEECCHH---HHHh--cchhhcCCeEEEecCCccccCchhhcCchhhhhhHHHHHHHhCCCEEEE
Confidence            3555566677999988655322   2211  111235799999999999      99999       7999999999999


Q ss_pred             EecccCccc--c-cccccC-CCcceeeEEEeehhhhhhhhhhcccCC
Q 018364          177 VYNDREKGS--L-VSMTAS-HEGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       177 v~~~~~~~~--~-~~m~~~-~~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      |+|+.+...  . ..+.+. +....||++.|+.++|+.|.++++.++
T Consensus        82 v~s~~~~~~~~~~~G~~~~~~~~~~IP~v~is~ed~~~L~r~l~~g~  128 (134)
T cd04815          82 IRSIGTDSHRSPHTGMMSYDDGVPKIPAAAISVEDADMLERLAARGK  128 (134)
T ss_pred             EEecCcccCCCCcCCccccCCCCCCCCEEEechhcHHHHHHHHhCCC
Confidence            999753321  1 122222 334689999999999999999887764

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

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

Probab=98.98  E-value=1.8e-09  Score=90.25  Aligned_cols=84  Identities=25%  Similarity=0.225  Sum_probs=66.0

Q ss_pred             CCCCCCCCCCCCCCCCCCcceEEEEEcCCC-ChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcceeeEEEeehhh
Q 018364          129 PADACSPLSNPVASNDADHINFVLIVRGQC-IFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLET  207 (357)
Q Consensus       129 p~~aC~~~~~~~~~~~~~~~~I~LV~RG~C-sF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i~Ip~v~is~~~  207 (357)
                      ....|++.....   ....++|||.+||.| +|.+|+.+|+++||.++|++|+..+.  ..+...  ...||+++|++++
T Consensus        36 ~~~~C~~~~~~~---~~v~GkIVlc~~~~~~~~~~k~~~~~~~GA~gvI~~~~~~~~--~~~~~~--~~~iP~v~I~~~~  108 (126)
T cd02120          36 DASLCLPGSLDP---SKVKGKIVLCDRGGNTSRVAKGDAVKAAGGAGMILANDPTDG--LDVVAD--AHVLPAVHVDYED  108 (126)
T ss_pred             ccccCCCCCCCh---hhccccEEEEeCCCCccHHHHHHHHHHcCCcEEEEEecCCCC--ceeccc--ccccceEEECHHH
Confidence            346898765332   235789999999999 99999999999999999999986532  222221  3579999999999


Q ss_pred             hhhhhhhcccCC
Q 018364          208 GVYLKEHARGET  219 (357)
Q Consensus       208 G~~L~~~l~~~~  219 (357)
                      |+.|+++++...
T Consensus       109 g~~l~~y~~~~~  120 (126)
T cd02120         109 GTAILSYINSTS  120 (126)
T ss_pred             HHHHHHHHHcCC
Confidence            999999987653

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

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.98  E-value=3.9e-10  Score=100.19  Aligned_cols=52  Identities=35%  Similarity=0.731  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc---------------CCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK---------------WGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~---------------~~~~CPlCR~~i~~~  349 (357)
                      ..+..+|+||++.+++.   .+++|||.||..||..|+..               ++..||+||.++...
T Consensus        15 ~~~~~~CpICld~~~dP---VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         15 SGGDFDCNICLDQVRDP---VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CCCccCCccCCCcCCCc---EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            34567999999998664   56899999999999999863               124699999998653

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

Probab=98.96  E-value=1.5e-09  Score=96.34  Aligned_cols=110  Identities=17%  Similarity=0.166  Sum_probs=75.1

Q ss_pred             cccccccccCCCCeEEEEeeCCCCCCCCCCCCC--CCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcc
Q 018364          107 LPAKFAVDVNSSGTCGALHVADPADACSPLSNP--VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKG  184 (357)
Q Consensus       107 ~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~--~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~  184 (357)
                      .+..|.+--+...++|.|+++..  | .+.+..  .....+..++||||+||+|+|.+|+++||++||+|||||+|..+.
T Consensus        16 ~~~~f~~~s~~G~v~g~lVyvn~--G-~~~Df~~L~~~gv~v~GkIvLvr~G~~~~~~Kv~~A~~~GA~gvIiy~Dp~d~   92 (183)
T cd02128          16 NPGGYVAYSAAGTVTGKLVYANY--G-RKKDFEDLQSVGVSVNGSVVLVRAGKISFAEKVANAEKLGAVGVLIYPDPADF   92 (183)
T ss_pred             ccccccCCCCCCceEEEEEEcCC--C-CHHHHHHHHhcCCCCCCeEEEEECCCCCHHHHHHHHHHCCCEEEEEecCHHHc
Confidence            34456665566778999988732  3 222111  001124578999999999999999999999999999999984221


Q ss_pred             ccc----------c-cccC----------------C---CcceeeEEEeehhhhhhhhhhcccCC
Q 018364          185 SLV----------S-MTAS----------------H---EGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       185 ~~~----------~-m~~~----------------~---~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                      ...          . ..+|                .   .--.||++-|+.++++.|++.+.+..
T Consensus        93 ~~~~~~~~~~g~~~~~~GDplTPG~ps~~~~~~~~~~~~~lP~IPs~PIS~~da~~lL~~l~G~~  157 (183)
T cd02128          93 PIDPSETALFGHVHLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPAQTISAAAAAKLLSKMGGPV  157 (183)
T ss_pred             CcccCcceeecceeccCCCcCCCCCccccccccCcccccCCCCCCEeccCHHHHHHHHHHcCCCC
Confidence            100          0 0111                0   11479999999999999999887643

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

>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=98.95  E-value=4.7e-10  Score=74.77  Aligned_cols=39  Identities=41%  Similarity=1.048  Sum_probs=33.1

Q ss_pred             cccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcc
Q 018364          301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVC  342 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlC  342 (357)
                      |+||++++.+  .+..++|||.|+.+||.+|++.+ ..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~-~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKN-PKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCT-SB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCc-CCCcCC
Confidence            8999998777  56789999999999999999995 569998

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

Probab=98.93  E-value=1.7e-09  Score=100.56  Aligned_cols=51  Identities=25%  Similarity=0.710  Sum_probs=43.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ......|.+|||..+..   .-+||||+||..||..|+..+. .||+||....+.
T Consensus       236 ~~a~~kC~LCLe~~~~p---SaTpCGHiFCWsCI~~w~~ek~-eCPlCR~~~~ps  286 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNP---SATPCGHIFCWSCILEWCSEKA-ECPLCREKFQPS  286 (293)
T ss_pred             CCCCCceEEEecCCCCC---CcCcCcchHHHHHHHHHHcccc-CCCcccccCCCc
Confidence            44567999999997654   5789999999999999999977 599999988664

>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=98.92  E-value=6.8e-10  Score=78.10  Aligned_cols=46  Identities=33%  Similarity=0.867  Sum_probs=38.2

Q ss_pred             CcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCc
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      +..|.||+++...   +..+||||. |+.+|++.|++... .||+||++|.
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            4689999998554   678899999 99999999999766 5999999885

...

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

Probab=98.88  E-value=1.2e-09  Score=98.87  Aligned_cols=52  Identities=35%  Similarity=0.661  Sum_probs=43.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC--CCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW--GTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~--~~~CPlCR~~i~~~  349 (357)
                      .....+|.||||.-++.   .++.|||+||.-||.+||+.+  +..||+||..|..+
T Consensus        44 ~~~~FdCNICLd~akdP---VvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP---VVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             CCCceeeeeeccccCCC---EEeecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            45577999999986654   577899999999999999995  34699999988764

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

Probab=98.88  E-value=1.3e-09  Score=84.30  Aligned_cols=52  Identities=29%  Similarity=0.794  Sum_probs=40.2

Q ss_pred             CCccccccccccc--------CCCc--eEEeCCCCccchhHHHHHHhcC--CCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQ--------DGEK--LKVLSCKHEFHASCVDSWLTKW--GTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~--------~~~~--vr~LpC~H~FH~~CI~~Wl~~~--~~~CPlCR~~i~~  348 (357)
                      .++.|.||...|+        +||.  +..-.|+|.||..||.+|+.+.  +..||+||++..-
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            3789999999987        3433  3333599999999999999974  4569999997643

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.84  E-value=2.2e-09  Score=73.54  Aligned_cols=44  Identities=30%  Similarity=0.823  Sum_probs=37.9

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccc
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH  344 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~  344 (357)
                      .|.||+++|.+.+..++|+|||+|+.+|+.... .....||+||+
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            499999999777788999999999999999988 33446999985

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

Probab=98.84  E-value=1.3e-09  Score=112.96  Aligned_cols=54  Identities=39%  Similarity=0.888  Sum_probs=46.5

Q ss_pred             CCCCcccccccccccCCCc--eEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEK--LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~--vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ....+.|+||+|++..+++  .+.|||+|+||..|+..|+++.++ ||+||..+...
T Consensus       288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qt-CP~CR~~~~~~  343 (543)
T KOG0802|consen  288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQT-CPTCRTVLYDY  343 (543)
T ss_pred             hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCc-CCcchhhhhcc
Confidence            3457899999999999866  789999999999999999999774 99999955443

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

Probab=98.80  E-value=3e-09  Score=92.41  Aligned_cols=57  Identities=23%  Similarity=0.607  Sum_probs=45.4

Q ss_pred             CCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          291 SSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       291 ~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .......-..|+|||+.|.+... .-+.|||+||++||..-+....+ ||+||..|..+
T Consensus       124 ~~~~~~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~-CP~C~kkIt~k  180 (187)
T KOG0320|consen  124 DPLRKEGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNK-CPTCRKKITHK  180 (187)
T ss_pred             cccccccccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCC-CCCcccccchh
Confidence            33445566799999999888533 23679999999999999998774 99999888654

>smart00184 RING Ring finger

Probab=98.80  E-value=4.4e-09  Score=68.55  Aligned_cols=39  Identities=44%  Similarity=1.054  Sum_probs=33.1

Q ss_pred             cccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcc
Q 018364          301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVC  342 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlC  342 (357)
                      |+||++.   .+....++|+|.||.+|++.|++..+..||+|
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            7899998   34578899999999999999999544469998

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)

>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=98.78  E-value=3e-09  Score=71.45  Aligned_cols=40  Identities=40%  Similarity=1.074  Sum_probs=34.5

Q ss_pred             cccccccccCCCceEEeCCCCccchhHHHHHHh-cCCCCCCcc
Q 018364          301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLT-KWGTFCPVC  342 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~-~~~~~CPlC  342 (357)
                      |+||++.+.+.  ++.++|+|.|+..||.+|++ .....||+|
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            89999998775  36889999999999999999 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 ....

>PHA02926 zinc finger-like protein; Provisional

Probab=98.76  E-value=2.6e-09  Score=96.08  Aligned_cols=53  Identities=28%  Similarity=0.757  Sum_probs=39.7

Q ss_pred             CCCCcccccccccccCC----C-ceEEe-CCCCccchhHHHHHHhcC-----CCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDG----E-KLKVL-SCKHEFHASCVDSWLTKW-----GTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~----~-~vr~L-pC~H~FH~~CI~~Wl~~~-----~~~CPlCR~~i~  347 (357)
                      .+.+.+|+||||..-+.    + .--+| +|+|.||..||+.|...+     ...||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            45578999999986322    1 22345 599999999999999864     235999998764

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

Probab=98.69  E-value=1.2e-08  Score=69.17  Aligned_cols=39  Identities=36%  Similarity=0.855  Sum_probs=30.7

Q ss_pred             cccccccccCCCceEEeCCCCccchhHHHHHHhcCC---CCCCcc
Q 018364          301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG---TFCPVC  342 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~---~~CPlC  342 (357)
                      |+||++-|++.   ..|+|||.|+..||..|.+..+   ..||.|
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            89999999886   6799999999999999998863   359988

>smart00504 Ubox Modified RING finger domain

Probab=98.58  E-value=5.3e-08  Score=71.37  Aligned_cols=46  Identities=24%  Similarity=0.493  Sum_probs=39.6

Q ss_pred             cccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..|+||++.+++.   .++||||+|.++||.+|++.+. .||+|+..+..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~-~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHG-TDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCC-CCCCCcCCCCh
Confidence            3699999998874   5679999999999999999865 59999988854

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

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

Probab=98.54  E-value=2.5e-08  Score=98.31  Aligned_cols=53  Identities=25%  Similarity=0.735  Sum_probs=41.9

Q ss_pred             CCCcccccccccccCC---Cc-----------eEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          296 HGGETCAICLEDYQDG---EK-----------LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~---~~-----------vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ....+|+||+.+.+..   ..           ...+||+|+||..|+.+|....+..||+||+++++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3456999999986432   11           33569999999999999999777679999999874

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

Probab=98.54  E-value=6.7e-08  Score=67.68  Aligned_cols=43  Identities=28%  Similarity=0.819  Sum_probs=34.0

Q ss_pred             ccccccccccCCCceEEeCCC-----CccchhHHHHHHhcC-CCCCCccc
Q 018364          300 TCAICLEDYQDGEKLKVLSCK-----HEFHASCVDSWLTKW-GTFCPVCK  343 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~-----H~FH~~CI~~Wl~~~-~~~CPlCR  343 (357)
                      .|.||+++ ..++...++||.     |.+|.+|+++|+..+ +.+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            48999994 344455589984     999999999999886 34699995

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

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

Probab=98.44  E-value=1.5e-07  Score=71.04  Aligned_cols=51  Identities=31%  Similarity=0.765  Sum_probs=37.8

Q ss_pred             Ccccccccccc-----------cCCCceEEe--CCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDY-----------QDGEKLKVL--SCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f-----------~~~~~vr~L--pC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      -+.|+||...|           ..+++..+.  -|+|.||..||..||.+++ .||+||+...-.
T Consensus        20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~-~CPld~q~w~~~   83 (88)
T COG5194          20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKG-VCPLDRQTWVLA   83 (88)
T ss_pred             cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCC-CCCCCCceeEEe
Confidence            35666666554           456655444  4999999999999999976 599999876543

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

Probab=98.42  E-value=1.4e-07  Score=64.07  Aligned_cols=39  Identities=36%  Similarity=0.725  Sum_probs=23.1

Q ss_pred             cccccccccCCC-ceEEeCCCCccchhHHHHHHhcC---CCCCC
Q 018364          301 CAICLEDYQDGE-KLKVLSCKHEFHASCVDSWLTKW---GTFCP  340 (357)
Q Consensus       301 CaICLe~f~~~~-~vr~LpC~H~FH~~CI~~Wl~~~---~~~CP  340 (357)
                      |+||+| |...+ .-.+|+|||+|.++||+.++.+.   ...||
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 86544 45789999999999999999974   33577

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.39  E-value=1.9e-07  Score=92.35  Aligned_cols=50  Identities=24%  Similarity=0.603  Sum_probs=42.4

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ......|+||++.|...   .+++|+|.||..||..|+.... .||+||..+..
T Consensus        23 Le~~l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~~~-~CP~Cr~~~~~   72 (397)
T TIGR00599        23 LDTSLRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSNQP-KCPLCRAEDQE   72 (397)
T ss_pred             cccccCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhCCC-CCCCCCCcccc
Confidence            45567999999998764   4689999999999999998865 59999998764

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=98.39  E-value=6.3e-08  Score=89.13  Aligned_cols=54  Identities=28%  Similarity=0.607  Sum_probs=43.7

Q ss_pred             CCCCcccccccccccCCC-------ceEEeCCCCccchhHHHHHHhcC-CCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGE-------KLKVLSCKHEFHASCVDSWLTKW-GTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~-------~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPlCR~~i~~  348 (357)
                      ..++..|+||=..+...+       +.-.|.|+|+||+.||+-|.... +.+||.||..+..
T Consensus       221 hl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl  282 (328)
T KOG1734|consen  221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL  282 (328)
T ss_pred             CCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence            456779999998876554       67899999999999999998773 2359999987753

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

Probab=98.36  E-value=1.2e-07  Score=71.03  Aligned_cols=51  Identities=33%  Similarity=0.847  Sum_probs=38.5

Q ss_pred             CCcccccccccccC--------CCceEEe--CCCCccchhHHHHHHhcC--CCCCCcccccCc
Q 018364          297 GGETCAICLEDYQD--------GEKLKVL--SCKHEFHASCVDSWLTKW--GTFCPVCKHDMR  347 (357)
Q Consensus       297 ~~~~CaICLe~f~~--------~~~vr~L--pC~H~FH~~CI~~Wl~~~--~~~CPlCR~~i~  347 (357)
                      .+++|-||.-.|+.        ||..-.+  .|.|.||..||.+|+...  +..||+||+...
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            45699999998853        4433222  399999999999999984  345999998754

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

Probab=98.35  E-value=1.2e-06  Score=80.26  Aligned_cols=99  Identities=20%  Similarity=0.122  Sum_probs=68.0

Q ss_pred             CCeEEEEeeCCCCCCCCCCCCC--CCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCccc----------
Q 018364          118 SGTCGALHVADPADACSPLSNP--VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGS----------  185 (357)
Q Consensus       118 ~~~~g~l~~~~p~~aC~~~~~~--~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~----------  185 (357)
                      ..++|.|+++.   .|..-+..  .....+..++|||+++|.|.+.+|+++||++||+|||||+|..+..          
T Consensus        43 g~v~g~lVyvn---yG~~~D~~~L~~~gvdv~GKIvLvr~G~~~~~~Kv~~A~~~GA~gVIiy~Dp~d~~~~~~~~~~~y  119 (220)
T cd02121          43 GNVTAELVYAN---YGSPEDFEYLEDLGIDVKGKIVIARYGGIFRGLKVKNAQLAGAVGVIIYSDPADDGYITGENGKTY  119 (220)
T ss_pred             CCceEEEEEcC---CCcHHHHHHHhhcCCCCCCeEEEEECCCccHHHHHHHHHHcCCEEEEEEeCchhcccccccccccC
Confidence            45788988765   33332211  0112346799999999999999999999999999999999743210          


Q ss_pred             --------------ccc----cccCC--------------------CcceeeEEEeehhhhhhhhhhcccCC
Q 018364          186 --------------LVS----MTASH--------------------EGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       186 --------------~~~----m~~~~--------------------~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                                    .+.    ..+|.                    .-..||+.=|+..+++.|++.+.+..
T Consensus       120 P~g~~~~~~~vqRgsv~~~~~~~GDplTPG~ps~~~~~r~~~~~~~~lP~IPs~PIS~~da~~lL~~L~g~~  191 (220)
T cd02121         120 PDGPARPPSGVQRGSVLFMSIGPGDPLTPGYPSKPGAERRDKEESKGLPKIPSLPISYRDAQPLLKALGGPG  191 (220)
T ss_pred             CCCCCCCCCcceecceeccccCCCCCCCCCCCCCCCCcccCcccccCCCCCCcccCCHHHHHHHHHHcCCCC
Confidence                          011    01110                    01369999999999999999887643

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

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

Probab=98.29  E-value=1.6e-07  Score=98.59  Aligned_cols=54  Identities=30%  Similarity=0.815  Sum_probs=42.5

Q ss_pred             CCCCCCCcccccccccccCCCceEEeC------CCCccchhHHHHHHhcC-CCCCCcccccCc
Q 018364          292 SSQCHGGETCAICLEDYQDGEKLKVLS------CKHEFHASCVDSWLTKW-GTFCPVCKHDMR  347 (357)
Q Consensus       292 ~~~~~~~~~CaICLe~f~~~~~vr~Lp------C~H~FH~~CI~~Wl~~~-~~~CPlCR~~i~  347 (357)
                      ++..++.++|+||..-...-|  |.||      |.|.||..|+.+|+.+. +.+||+||.+++
T Consensus      1463 ~~~fsG~eECaICYsvL~~vd--r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1463 DEKFSGHEECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hhhcCCcchhhHHHHHHHHHh--ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            344677899999998766322  4444      89999999999999995 346999998875

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

Probab=98.24  E-value=1e-05  Score=70.08  Aligned_cols=93  Identities=17%  Similarity=0.038  Sum_probs=61.7

Q ss_pred             CCeEEEEeeCC---CCCCCCCCCCCCCCCCCCcceEEEEEcCC------------------CChHHHHHHHHHcCCcEEE
Q 018364          118 SGTCGALHVAD---PADACSPLSNPVASNDADHINFVLIVRGQ------------------CIFEDKIRNAQAAGYRAAI  176 (357)
Q Consensus       118 ~~~~g~l~~~~---p~~aC~~~~~~~~~~~~~~~~I~LV~RG~------------------CsF~~K~~~Aq~aGA~avI  176 (357)
                      ..++|.|+...   ..++|...++.   ..+..++||||.||.                  |+|..|+++|+++||+|||
T Consensus        18 g~vtg~lVfvGyGi~~~~~~~~Dy~---giDVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~~A~~~GA~aVI   94 (151)
T cd04822          18 GAVTAPVVFAGYGITAPELGYDDYA---GLDVKGKIVLVLRHEPQEDDANSRFNGPGLTRHAGLRYKATNARRHGAAAVI   94 (151)
T ss_pred             CCceEeEEEecCCcCccccchhhcc---CCCCCCeEEEEEcCCcccccccccccccccccccCHHHHHHHHHHCCCeEEE
Confidence            55788887653   34677654432   234689999999884                  9999999999999999999


Q ss_pred             EecccCcccccccccCCCcceeeEEEeehhhhhhhhhh
Q 018364          177 VYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEH  214 (357)
Q Consensus       177 v~~~~~~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~  214 (357)
                      ||++.+......-...... .-.++.++....+.+...
T Consensus        95 v~~d~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  131 (151)
T cd04822          95 VVNGPNSHSGDADRLPRFG-GTAPQRVDIAAADPWFTA  131 (151)
T ss_pred             EEeCCcccCcccccccccC-ccceEEechHHHHHHhhh
Confidence            9998653211000000001 112677787777777764

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

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

Probab=98.19  E-value=8.2e-07  Score=81.94  Aligned_cols=52  Identities=29%  Similarity=0.649  Sum_probs=42.1

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHH-HHhcCCCCCCcccccCcCCC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDS-WLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~-Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      ..+..|+||++..+..   ..+||||+|+..||-. |-.++--.||+||+.+.++.
T Consensus       213 ~~d~kC~lC~e~~~~p---s~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVP---SCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCc---ccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            3467999999986553   5789999999999999 87775445999999887653

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

Probab=98.12  E-value=8.9e-07  Score=86.89  Aligned_cols=50  Identities=32%  Similarity=0.773  Sum_probs=41.2

Q ss_pred             CCCCcccccccccccCC-CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDG-EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~-~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      .-+-.+|+||||.+.+. .-++...|.|.||..|+..|-..   +||+||....
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~---scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS---SCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhcccC---cChhhhhhcC
Confidence            34567999999998876 35677789999999999999655   6999998665

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

Probab=98.11  E-value=1.2e-05  Score=68.78  Aligned_cols=71  Identities=11%  Similarity=-0.006  Sum_probs=50.7

Q ss_pred             cccccccccCCCCeEEEEeeCC---CCCCCCCCCCCCCCCCCCcceEEEEEcCCC------------------ChHHHHH
Q 018364          107 LPAKFAVDVNSSGTCGALHVAD---PADACSPLSNPVASNDADHINFVLIVRGQC------------------IFEDKIR  165 (357)
Q Consensus       107 ~~a~Fg~~~~~~~~~g~l~~~~---p~~aC~~~~~~~~~~~~~~~~I~LV~RG~C------------------sF~~K~~  165 (357)
                      .+.+|+..   ..+.++|+..-   ...+|.-.+..   ..+.++|||||.||.|                  +|..|++
T Consensus        10 ~~~~~~~~---~~~~aelVfvGyGi~a~~~~~dDYa---g~DVkGKIVlv~~g~P~~~~~~~~~~~~~~~~~~~~~~K~~   83 (142)
T cd04814          10 AMLNVDAV---AIKDAPLVFVGYGIKAPELSWDDYA---GLDVKGKVVVVLRNDPQGEPGAGDFGGKAMTYYGRWTYKYE   83 (142)
T ss_pred             cccCCCCc---cccceeeEEecCCcCCCCCChhhcC---CCCCCCcEEEEEcCCCCcccccccccccccccccCHHHHHH
Confidence            34455533   34556776432   33467654432   2346899999999999                  6999999


Q ss_pred             HHHHcCCcEEEEecccCc
Q 018364          166 NAQAAGYRAAIVYNDREK  183 (357)
Q Consensus       166 ~Aq~aGA~avIv~~~~~~  183 (357)
                      +|+++||+|||++++.+.
T Consensus        84 ~A~~~GA~gvIii~~~~~  101 (142)
T cd04814          84 EAARHGAAGVLIVHELAP  101 (142)
T ss_pred             HHHHCCCcEEEEEeCCCc
Confidence            999999999999998653

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

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

Probab=98.09  E-value=6.9e-07  Score=67.36  Aligned_cols=52  Identities=27%  Similarity=0.646  Sum_probs=25.3

Q ss_pred             CcccccccccccCCCce--EEe---CCCCccchhHHHHHHhcC---C-------CCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKL--KVL---SCKHEFHASCVDSWLTKW---G-------TFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~v--r~L---pC~H~FH~~CI~~Wl~~~---~-------~~CPlCR~~i~~~  349 (357)
                      +.+|.||.+.+.+++.+  .+-   .|++.||..||.+||...   +       ..||.|+.+|.-+
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            46899999987633322  222   389999999999999862   1       1499999988643

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.08  E-value=3.2e-06  Score=80.59  Aligned_cols=53  Identities=32%  Similarity=0.686  Sum_probs=40.3

Q ss_pred             Cccccccccc-ccCCC-ceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCC
Q 018364          298 GETCAICLED-YQDGE-KLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       298 ~~~CaICLe~-f~~~~-~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      +..|+||+.+ |...+ ++.+-+|||.||..||+..+......||.|+..+..+.
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            4689999997 33332 33444899999999999977765556999998886654

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).

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

Probab=98.08  E-value=1.6e-05  Score=67.77  Aligned_cols=65  Identities=15%  Similarity=0.075  Sum_probs=49.4

Q ss_pred             CCCCeEEEEeeCC---CCCCCCCCCCCCCCCCCCcceEEEEEcCCCC------------hHHHHHHHHHcCCcEEEEecc
Q 018364          116 NSSGTCGALHVAD---PADACSPLSNPVASNDADHINFVLIVRGQCI------------FEDKIRNAQAAGYRAAIVYND  180 (357)
Q Consensus       116 ~~~~~~g~l~~~~---p~~aC~~~~~~~~~~~~~~~~I~LV~RG~Cs------------F~~K~~~Aq~aGA~avIv~~~  180 (357)
                      +...+.|.|+...   ..++|...+..   ..+..+|||||++|.|+            +..|+++|+++||+|||||++
T Consensus        18 ~~g~v~gelVfvGyG~~~~~~~~~Dy~---~iDVkGKIVlv~~g~p~~~~~~~~~~~~~~~~K~~~A~~~GA~aVIi~~d   94 (137)
T cd04820          18 PAASVEAPLVFVGYGLVAPELGHDDYA---GLDVKGKIVVVLSGGPAGIPSEEGAHAHSSNEKARYAAKAGAIGMITLTT   94 (137)
T ss_pred             CCCCceEeEEEecCCcCccCcCHhhcc---CCCCCCeEEEEEcCCCCccccccccccccHHHHHHHHHHCCCeEEEEEeC
Confidence            3456788887653   34567654432   23468999999999995            889999999999999999998


Q ss_pred             cCc
Q 018364          181 REK  183 (357)
Q Consensus       181 ~~~  183 (357)
                      ...
T Consensus        95 ~~~   97 (137)
T cd04820          95 PRS   97 (137)
T ss_pred             Ccc
Confidence            653

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

>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=98.06  E-value=7.2e-06  Score=70.44  Aligned_cols=94  Identities=13%  Similarity=0.040  Sum_probs=62.6

Q ss_pred             CCCeEEEEeeCCC---CCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCccccc------
Q 018364          117 SSGTCGALHVADP---ADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLV------  187 (357)
Q Consensus       117 ~~~~~g~l~~~~p---~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~------  187 (357)
                      ...++|++++++-   .|- +.+.+ .   -+.+++|+|++.|.-.+..|+++||++||.+||||.|..+....      
T Consensus        12 sG~Vtg~~VYvNyG~~eDf-~~L~~-~---V~v~GkIvi~RyG~~~RG~Kv~~A~~~GA~GviIYsDP~d~~~~~~~~~~   86 (153)
T cd02131          12 KGTLQAEVVDVQYGSVEDL-RRIRD-N---MNVTNQIALLKLGQAPLLYKLSLLEEAGFGGVLLYVDPCDLPKTRHTWHQ   86 (153)
T ss_pred             CCceEEEEEEecCCCHHHH-HHHHh-C---CCccceEEEEeccCcchHHHHHHHHHCCCeEEEEecChhhccCcCCCccc
Confidence            4567888887652   110 01111 1   23578999999999999999999999999999999985332100      


Q ss_pred             ----cc--ccCC-----------------CcceeeEEEeehhhhhhhhhhc
Q 018364          188 ----SM--TASH-----------------EGVKVHAIFVSLETGVYLKEHA  215 (357)
Q Consensus       188 ----~m--~~~~-----------------~~i~Ip~v~is~~~G~~L~~~l  215 (357)
                          ..  .+|.                 .--+||+.=|+..++..|++.-
T Consensus        87 v~~v~~~~~GDP~TPG~PS~~~~~R~~~~~lP~IPs~PIS~~dA~~lL~~~  137 (153)
T cd02131          87 AFMVSLNPGGDPSTPGYPSADQSCRQCRGNLTSLLVQPISAYLAKKLLSAP  137 (153)
T ss_pred             eEEEecCCCCCCCCCCCccccCcccCCcCCCCCCcccccCHHHHHHHHhCC
Confidence                00  1221                 0146888888888888877754

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.

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

Probab=98.05  E-value=2.3e-06  Score=65.00  Aligned_cols=49  Identities=22%  Similarity=0.434  Sum_probs=37.9

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||.+-+.+.   .++||||.|-+.||+.|+.++...||+|+..+...
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            46899999998885   57899999999999999999555799999988653

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 ....

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

Probab=98.01  E-value=3.1e-06  Score=84.60  Aligned_cols=48  Identities=25%  Similarity=0.587  Sum_probs=38.0

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcC----CCCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW----GTFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~----~~~CPlCR~~i~~  348 (357)
                      ...|+|||++....  + .+.|||+||..||-+.+...    -..||+||..|..
T Consensus       186 ~~~CPICL~~~~~p--~-~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP--V-RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcc--c-ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            67999999996654  2 33499999999999887774    1259999988865

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

Probab=97.96  E-value=4.9e-06  Score=80.02  Aligned_cols=49  Identities=31%  Similarity=0.794  Sum_probs=39.3

Q ss_pred             CCCcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCcC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      +...+|.|||.+-++   ..+|||.|. .|..|-+..--+++ .||+||++|.+
T Consensus       288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n-~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTN-NCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhc-CCCccccchHh
Confidence            557899999998555   579999997 88889887654545 49999999865

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

Probab=97.89  E-value=4.5e-06  Score=78.18  Aligned_cols=46  Identities=33%  Similarity=0.728  Sum_probs=40.1

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH  344 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~  344 (357)
                      ..+...|+||++.|.+.   ++|||+|.|+..||..+.. ....||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence            34567999999999997   8999999999999999988 4557999994

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

Probab=97.87  E-value=6.3e-06  Score=79.62  Aligned_cols=48  Identities=29%  Similarity=0.771  Sum_probs=35.8

Q ss_pred             CcccccccccccCC-CceEEeC-CCCccchhHHHHHHhcC--CCCCCcccccC
Q 018364          298 GETCAICLEDYQDG-EKLKVLS-CKHEFHASCVDSWLTKW--GTFCPVCKHDM  346 (357)
Q Consensus       298 ~~~CaICLe~f~~~-~~vr~Lp-C~H~FH~~CI~~Wl~~~--~~~CPlCR~~i  346 (357)
                      .-.|.|| +++.+. +.+.-+- |||+||..|+.+|+..-  +..||+||-.+
T Consensus         4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            3589999 665554 4555554 99999999999999983  22599999433

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

Probab=97.85  E-value=8.9e-06  Score=64.57  Aligned_cols=49  Identities=31%  Similarity=0.754  Sum_probs=35.7

Q ss_pred             CCcccccccccc------------cCCCceEEe--CCCCccchhHHHHHHhcCCCCCCcccccC
Q 018364          297 GGETCAICLEDY------------QDGEKLKVL--SCKHEFHASCVDSWLTKWGTFCPVCKHDM  346 (357)
Q Consensus       297 ~~~~CaICLe~f------------~~~~~vr~L--pC~H~FH~~CI~~Wl~~~~~~CPlCR~~i  346 (357)
                      .-+.|+||...+            ...+++.+.  -|+|.||..||..||++++. ||+|.++-
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~v-CPLdn~eW  107 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNV-CPLDNKEW  107 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCc-CCCcCcce
Confidence            356788886643            122334333  49999999999999999884 99997753

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

Probab=97.69  E-value=1.6e-05  Score=74.28  Aligned_cols=52  Identities=27%  Similarity=0.515  Sum_probs=42.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      .+....|-||-+-|...   ..++|||.||.-||..-|..+- .||+||.+..+..
T Consensus        22 LDs~lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~qp-~CP~Cr~~~~esr   73 (391)
T COG5432          22 LDSMLRCRICDCRISIP---CETTCGHTFCSLCIRRHLGTQP-FCPVCREDPCESR   73 (391)
T ss_pred             chhHHHhhhhhheeecc---eecccccchhHHHHHHHhcCCC-CCccccccHHhhh
Confidence            33457999999888775   5778999999999999999976 5999998876543

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

Probab=97.69  E-value=1.6e-05  Score=74.58  Aligned_cols=58  Identities=29%  Similarity=0.735  Sum_probs=47.6

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc----------------------CCCCCCcccccCcCCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK----------------------WGTFCPVCKHDMRNNSES  352 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~----------------------~~~~CPlCR~~i~~~~~~  352 (357)
                      ....-.|+|||--|..++...+++|-|.||..|+...|+.                      -+..||+||..|..+.+.
T Consensus       112 n~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~s  191 (368)
T KOG4445|consen  112 NHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENS  191 (368)
T ss_pred             CCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccc
Confidence            5567799999999999999999999999999998765543                      134699999998766543

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

Probab=97.68  E-value=1.6e-05  Score=75.66  Aligned_cols=49  Identities=24%  Similarity=0.607  Sum_probs=42.0

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .--.|-||.|-|...   .++||+|.||.-||+..|..+- .||.|+..+.+.
T Consensus        22 ~lLRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~~p-~CP~C~~~~~Es   70 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSYKP-QCPTCCVTVTES   70 (442)
T ss_pred             HHHHHhHHHHHhcCc---eeccccchHHHHHHHHHhccCC-CCCceecccchh
Confidence            346899999999886   6889999999999999998865 599999877654

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

Probab=97.56  E-value=3.5e-05  Score=72.50  Aligned_cols=51  Identities=22%  Similarity=0.469  Sum_probs=41.4

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE  351 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~  351 (357)
                      ..+|+||+.+-...   ..|+|+|.|+..||.-=.......||+||++|.+.-.
T Consensus         7 ~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~   57 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTID   57 (324)
T ss_pred             CCcceeeeccCCcC---ccccccchhhhhhhcchhhcCCCCCceecCCCCcchh
Confidence            57999999986554   6789999999999997666655569999999987543

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

Probab=97.52  E-value=1.9e-05  Score=82.12  Aligned_cols=52  Identities=29%  Similarity=0.525  Sum_probs=44.7

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      .....|++||..+.++......+|+|.||..||+.|-..-++ ||+||..+..
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqT-CPiDR~EF~~  172 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQT-CPVDRGEFGE  172 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhccc-Cchhhhhhhe
Confidence            345689999999988877777789999999999999999885 9999987654

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

Probab=97.46  E-value=1.8e-05  Score=75.83  Aligned_cols=54  Identities=22%  Similarity=0.475  Sum_probs=44.0

Q ss_pred             CCCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcCCCCCCcccccCcCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE  351 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~  351 (357)
                      ...+..|+|||+-++..   +.++ |.|.||.+||..=+...+..||.||+.+..+.+
T Consensus        40 ~~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs   94 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS   94 (381)
T ss_pred             hhhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence            44567999999988774   3333 999999999999999977789999998866543

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

Probab=97.41  E-value=5.7e-05  Score=73.18  Aligned_cols=50  Identities=32%  Similarity=0.664  Sum_probs=41.0

Q ss_pred             CcccccccccccCC-CceEEeCCCCccchhHHHHHHhcCC-CCCCcccccCc
Q 018364          298 GETCAICLEDYQDG-EKLKVLSCKHEFHASCVDSWLTKWG-TFCPVCKHDMR  347 (357)
Q Consensus       298 ~~~CaICLe~f~~~-~~vr~LpC~H~FH~~CI~~Wl~~~~-~~CPlCR~~i~  347 (357)
                      +-.|-.|=|.+-.. +.+.-|||.|+||..|+.+.|.++. .+||.||+-..
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrS  416 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRS  416 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence            45899999988554 6788999999999999999998864 35999994443

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

Probab=97.39  E-value=0.00011  Score=71.68  Aligned_cols=49  Identities=37%  Similarity=0.950  Sum_probs=38.1

Q ss_pred             CCcccccccccccCC-C-ceEEeCCCCccchhHHHHHHhcC-CCCCCccccc
Q 018364          297 GGETCAICLEDYQDG-E-KLKVLSCKHEFHASCVDSWLTKW-GTFCPVCKHD  345 (357)
Q Consensus       297 ~~~~CaICLe~f~~~-~-~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPlCR~~  345 (357)
                      ...+|+|||++|+.. | .+..|.|+|.|-.+||+.||-+. ...||.|...
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            457999999999754 3 34455699999999999999642 2459999754

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

Probab=97.38  E-value=5.1e-05  Score=79.39  Aligned_cols=48  Identities=25%  Similarity=0.647  Sum_probs=39.9

Q ss_pred             cccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      -.|+.|-...++   +.++.|+|+||.+||..=+..++..||.|...+..+
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            499999977666   245569999999999999999877899999877654

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

Probab=97.37  E-value=0.00011  Score=71.68  Aligned_cols=53  Identities=25%  Similarity=0.728  Sum_probs=39.6

Q ss_pred             CCCcccccccccccCCC----ceEEeC-CCCccchhHHHHHHhcCC------CCCCcccccCcC
Q 018364          296 HGGETCAICLEDYQDGE----KLKVLS-CKHEFHASCVDSWLTKWG------TFCPVCKHDMRN  348 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~----~vr~Lp-C~H~FH~~CI~~Wl~~~~------~~CPlCR~~i~~  348 (357)
                      ..+.+|.||+|...+.-    ...+|| |.|.|+..||+.|-..++      ..||.||.....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~  222 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF  222 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence            45789999999865432    134556 999999999999985433      469999976543

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

Probab=97.33  E-value=0.00019  Score=64.84  Aligned_cols=70  Identities=20%  Similarity=0.459  Sum_probs=52.4

Q ss_pred             cccccchhHHhhccccccccCCCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc-------CCCCCCcc
Q 018364          270 LSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK-------WGTFCPVC  342 (357)
Q Consensus       270 ~~~~l~~~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~-------~~~~CPlC  342 (357)
                      +.+-+-+..++.|..          .+....|..|-..+..||.+| |-|-|+||.+|+++|-..       ....||-|
T Consensus        32 HpkCiVQSYLqWL~D----------sDY~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~C  100 (299)
T KOG3970|consen   32 HPKCIVQSYLQWLQD----------SDYNPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCC  100 (299)
T ss_pred             CchhhHHHHHHHHhh----------cCCCCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCC
Confidence            344445555555433          233568999999999998775 789999999999999776       23469999


Q ss_pred             cccCcCCC
Q 018364          343 KHDMRNNS  350 (357)
Q Consensus       343 R~~i~~~~  350 (357)
                      ..+|.++.
T Consensus       101 s~eiFPp~  108 (299)
T KOG3970|consen  101 SQEIFPPI  108 (299)
T ss_pred             CCccCCCc
Confidence            99998764

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

Probab=97.26  E-value=8.7e-05  Score=52.22  Aligned_cols=47  Identities=30%  Similarity=0.736  Sum_probs=32.6

Q ss_pred             CCCcccccccccccCCCceEEe-CCCCc-cchhH-HHHHHhcCCCCCCcccccCc
Q 018364          296 HGGETCAICLEDYQDGEKLKVL-SCKHE-FHASC-VDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~L-pC~H~-FH~~C-I~~Wl~~~~~~CPlCR~~i~  347 (357)
                      +-+++|.||+|.-.+.    +| .|||. .+.+| ++.|-..+. .||+||++|.
T Consensus         5 ~~~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g-~CPiCRapi~   54 (62)
T KOG4172|consen    5 QWSDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHG-CCPICRAPIK   54 (62)
T ss_pred             ccccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCC-cCcchhhHHH
Confidence            3458999999984442    44 59997 56667 445544555 5999999874

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

Probab=97.17  E-value=0.00029  Score=77.41  Aligned_cols=72  Identities=24%  Similarity=0.586  Sum_probs=53.0

Q ss_pred             hhHHhhccccccccCCCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC---------CCCCCcccccC
Q 018364          276 SKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---------GTFCPVCKHDM  346 (357)
Q Consensus       276 ~~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---------~~~CPlCR~~i  346 (357)
                      +.+.+-||....++... ..+.++.|.||+.+--......+|.|+|+||-+|.+.-|+++         =..||+|+.+|
T Consensus      3465 kNEE~CLPCl~Cdks~t-kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3465 KNEEHCLPCLHCDKSAT-KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred             cchhhcccccccChhhh-hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence            34445566666444332 366788999999987666778899999999999998777663         12699999887


Q ss_pred             cC
Q 018364          347 RN  348 (357)
Q Consensus       347 ~~  348 (357)
                      ..
T Consensus      3544 nH 3545 (3738)
T KOG1428|consen 3544 NH 3545 (3738)
T ss_pred             hh
Confidence            53

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

Probab=97.17  E-value=0.00012  Score=62.85  Aligned_cols=32  Identities=31%  Similarity=0.698  Sum_probs=28.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchh
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHAS  326 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~  326 (357)
                      .++..+|.|||||++.||.+..|||-.+||+.
T Consensus       174 ~ddkGECvICLEdL~~GdtIARLPCLCIYHK~  205 (205)
T KOG0801|consen  174 KDDKGECVICLEDLEAGDTIARLPCLCIYHKQ  205 (205)
T ss_pred             cccCCcEEEEhhhccCCCceeccceEEEeecC
Confidence            34567999999999999999999999999974

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

Probab=96.97  E-value=0.00023  Score=52.12  Aligned_cols=46  Identities=26%  Similarity=0.662  Sum_probs=23.2

Q ss_pred             cccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      -.|++|.+-+++.  |....|.|+|+..||..=+..   .||+|+.+.-.+
T Consensus         8 LrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~~---~CPvC~~Paw~q   53 (65)
T PF14835_consen    8 LRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIGS---ECPVCHTPAWIQ   53 (65)
T ss_dssp             TS-SSS-S--SS---B---SSS--B-TTTGGGGTTT---B-SSS--B-S-S
T ss_pred             cCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcCC---CCCCcCChHHHH
Confidence            4799999987763  555679999999999884443   499999877544

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

Probab=96.92  E-value=0.00029  Score=68.56  Aligned_cols=50  Identities=30%  Similarity=0.771  Sum_probs=40.9

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-CCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-GTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPlCR~~i~  347 (357)
                      ....+.|-||-|.   +..|++=||||..|..|+..|-... ...||.||.+|-
T Consensus       366 gsTFeLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK  416 (563)
T KOG1785|consen  366 GSTFELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK  416 (563)
T ss_pred             cchHHHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence            4567799999886   3348889999999999999998664 335999998874

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

Probab=96.89  E-value=0.00052  Score=49.55  Aligned_cols=43  Identities=26%  Similarity=0.586  Sum_probs=29.9

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-CCCCCc
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-GTFCPV  341 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPl  341 (357)
                      ....|+|.+..|++  .|+...|+|+|-++.|.++++.+ ...||+
T Consensus        10 ~~~~CPiT~~~~~~--PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED--PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS--EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC--CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            45799999999876  68888999999999999999443 346998

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

Probab=96.80  E-value=0.00055  Score=67.05  Aligned_cols=48  Identities=31%  Similarity=0.582  Sum_probs=39.4

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-------CCCCCccc
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-------GTFCPVCK  343 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-------~~~CPlCR  343 (357)
                      .....|.||+++..-.+....|||+|+|++.|+...+..+       ...||-|+
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~  236 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK  236 (445)
T ss_pred             hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence            3457999999997666888999999999999999998873       34587664

>PHA02862 5L protein; Provisional

Probab=96.77  E-value=0.00089  Score=56.69  Aligned_cols=48  Identities=21%  Similarity=0.527  Sum_probs=36.7

Q ss_pred             CcccccccccccCCCceEEeCCC-----CccchhHHHHHHhcCC-CCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCK-----HEFHASCVDSWLTKWG-TFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~-----H~FH~~CI~~Wl~~~~-~~CPlCR~~i~~~  349 (357)
                      ++.|-||+++-++.    .-||+     ...|.+|+.+|++..+ ..||+|+.+..-+
T Consensus         2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            47899999985432    36863     5689999999998854 4699999876543

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

Probab=96.76  E-value=0.0011  Score=45.92  Aligned_cols=41  Identities=32%  Similarity=0.888  Sum_probs=28.5

Q ss_pred             cccccccccCCCceEEeCCC-----CccchhHHHHHHhcC-CCCCCcc
Q 018364          301 CAICLEDYQDGEKLKVLSCK-----HEFHASCVDSWLTKW-GTFCPVC  342 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~-----H~FH~~CI~~Wl~~~-~~~CPlC  342 (357)
                      |-||+++-.+.+ --+.||+     -..|.+|++.|+..+ +.+|++|
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            779999977766 3467863     378999999999974 3459988

>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=96.70  E-value=0.00065  Score=57.12  Aligned_cols=35  Identities=20%  Similarity=0.559  Sum_probs=31.0

Q ss_pred             CcccccccccccCCCceEEeCCC------CccchhHHHHHH
Q 018364          298 GETCAICLEDYQDGEKLKVLSCK------HEFHASCVDSWL  332 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~------H~FH~~CI~~Wl  332 (357)
                      ..+|.||++....++-|..++|+      |.||.+|+..|-
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            67999999999986678888885      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.

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

Probab=96.69  E-value=0.0011  Score=65.94  Aligned_cols=51  Identities=25%  Similarity=0.605  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...+.+|.||+..+.+.   ..+||||.|+..||+.-+.+ .+.||+||..+.+-
T Consensus        81 ~~sef~c~vc~~~l~~p---v~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   81 IRSEFECCVCSRALYPP---VVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVEL  131 (398)
T ss_pred             ccchhhhhhhHhhcCCC---ccccccccccHHHHHHHhcc-CCCCcccccccccc
Confidence            45678999999887775   56799999999999996664 55699999998763

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

Probab=96.41  E-value=0.0002  Score=69.48  Aligned_cols=54  Identities=22%  Similarity=0.546  Sum_probs=47.7

Q ss_pred             CCcccccccccccCC-CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCC
Q 018364          297 GGETCAICLEDYQDG-EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE  351 (357)
Q Consensus       297 ~~~~CaICLe~f~~~-~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~  351 (357)
                      ....|+||.++|++. +++..+-|||.+|.+||.+||.+.+ .||.|++.+.....
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~-kl~~~~rel~~~~~  249 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKR-KLPSCRRELPKNGF  249 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHH-HhHHHHhhhhhhhH
Confidence            356899999999998 8999999999999999999999966 49999999876543

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.37  E-value=0.0036  Score=54.07  Aligned_cols=51  Identities=22%  Similarity=0.585  Sum_probs=37.6

Q ss_pred             CCCCcccccccccccCCCceEEeCC--CC---ccchhHHHHHHhcCC-CCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSC--KH---EFHASCVDSWLTKWG-TFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC--~H---~FH~~CI~~Wl~~~~-~~CPlCR~~i~~~  349 (357)
                      ...+..|-||.++...  .  .-||  ..   ..|.+|++.|+...+ ..||+|+.+..-.
T Consensus         5 s~~~~~CRIC~~~~~~--~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          5 SLMDKCCWICKDEYDV--V--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCCeeEecCCCCCC--c--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            3457899999988432  2  3575  44   579999999999864 5699999876543

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

Probab=96.34  E-value=0.0024  Score=61.81  Aligned_cols=46  Identities=24%  Similarity=0.593  Sum_probs=35.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ....+.|.||+++.++   ...+||||+-+  |...-.  +...||+||+.|.
T Consensus       302 ~~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIR  347 (355)
T ss_pred             cCCCCceEEecCCccc---eeeecCCcEEE--chHHHh--hCCCCchhHHHHH
Confidence            5567899999999766   57899999955  766643  3345999999874

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

Probab=96.18  E-value=0.0029  Score=43.86  Aligned_cols=45  Identities=22%  Similarity=0.612  Sum_probs=22.0

Q ss_pred             cccccccccCCCceEEeC--CCCccchhHHHHHHhcCCCCCCcccccC
Q 018364          301 CAICLEDYQDGEKLKVLS--CKHEFHASCVDSWLTKWGTFCPVCKHDM  346 (357)
Q Consensus       301 CaICLe~f~~~~~vr~Lp--C~H~FH~~CI~~Wl~~~~~~CPlCR~~i  346 (357)
                      |++|.+++...+ ...+|  |++..+..|...-++..+..||-||++.
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            789999995543 34556  7899999998887764344699999864

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

Probab=96.06  E-value=0.0034  Score=62.70  Aligned_cols=54  Identities=28%  Similarity=0.679  Sum_probs=43.7

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE  351 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~  351 (357)
                      .+.+..|+||...+.+.  +..+.|||.|+..|+..|+..+. .||.|++.+.....
T Consensus        18 ~~~~l~C~~C~~vl~~p--~~~~~cgh~fC~~C~~~~~~~~~-~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDP--VQTTTCGHRFCAGCLLESLSNHQ-KCPVCRQELTQAEE   71 (391)
T ss_pred             CcccccCccccccccCC--CCCCCCCCcccccccchhhccCc-CCcccccccchhhc
Confidence            34567999999997775  33368999999999999999966 59999988766543

>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=95.89  E-value=0.004  Score=50.10  Aligned_cols=34  Identities=24%  Similarity=0.618  Sum_probs=28.7

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHH
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVD  329 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~  329 (357)
                      ..+...|++|-..+.. ....+.||||+||..|++
T Consensus        75 i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            4557789999999877 567788999999999975

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 [].

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

Probab=95.64  E-value=0.012  Score=54.99  Aligned_cols=52  Identities=17%  Similarity=0.363  Sum_probs=39.6

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-CCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-GTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPlCR~~i~~  348 (357)
                      .....+|++|-+.=.  ......+|+|+||.-||..=+... ..+||.|-.++.+
T Consensus       236 ~t~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             ccCCceeeccCCCCC--CCeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            566789999988733  345677899999999998755542 2469999888763

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

Probab=95.28  E-value=0.019  Score=55.30  Aligned_cols=62  Identities=23%  Similarity=0.431  Sum_probs=41.5

Q ss_pred             HHhhccccccccCCCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHH---HHhcCCCCCCccccc
Q 018364          278 VVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDS---WLTKWGTFCPVCKHD  345 (357)
Q Consensus       278 ~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~---Wl~~~~~~CPlCR~~  345 (357)
                      .+...|...-.+.++ ..++...|.||-+...-   +.++||+|..+..|--.   ...  +..||+||..
T Consensus        42 nlsaEPnlttsSadd-tDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~--~K~C~~CrTE  106 (493)
T COG5236          42 NLSAEPNLTTSSADD-TDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYM--QKGCPLCRTE  106 (493)
T ss_pred             ccccCCccccccccc-cccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHh--ccCCCccccc
Confidence            334445544333333 36778899999887554   57899999999999433   233  3359999975

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

Probab=95.21  E-value=0.0041  Score=59.43  Aligned_cols=47  Identities=30%  Similarity=0.610  Sum_probs=35.7

Q ss_pred             CCCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcCCCCCCccccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWGTFCPVCKHD  345 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~~~CPlCR~~  345 (357)
                      ..+...|++|+..-...   .+|. -|-+||..||-..+.+++. ||+=..+
T Consensus       297 ~~~~~~CpvClk~r~Np---tvl~vSGyVfCY~Ci~~Yv~~~~~-CPVT~~p  344 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNP---TVLEVSGYVFCYPCIFSYVVNYGH-CPVTGYP  344 (357)
T ss_pred             CCccccChhHHhccCCC---ceEEecceEEeHHHHHHHHHhcCC-CCccCCc
Confidence            45567999999985553   2232 4999999999999999885 9985443

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

Probab=95.16  E-value=0.013  Score=56.15  Aligned_cols=49  Identities=31%  Similarity=0.720  Sum_probs=42.1

Q ss_pred             CcccccccccccCCCc---eEEeCCCCccchhHHHHHHhcCCCCCCcccccC
Q 018364          298 GETCAICLEDYQDGEK---LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDM  346 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~---vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i  346 (357)
                      ...|-||-++|..++.   -|+|.|||.|+..|+.+-+......||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            4689999999988743   467789999999999999888777799999874

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

Probab=95.16  E-value=0.0093  Score=60.27  Aligned_cols=52  Identities=25%  Similarity=0.654  Sum_probs=40.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc----CCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK----WGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~----~~~~CPlCR~~i~~~  349 (357)
                      ..+..+|-+|-+.-++   ..+..|+|.||+-||.+++..    .+.+||.|...+.-+
T Consensus       533 nk~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             ccCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            5567799999887443   356789999999999888766    456799998877554

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.15  E-value=0.019  Score=52.88  Aligned_cols=52  Identities=17%  Similarity=0.312  Sum_probs=44.7

Q ss_pred             CCcccccccccccCCCceEEe-CCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~L-pC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ....|+||.+.+.+.-.+.+| ||||+|..+|++..+.... .||+|-.++.+.
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~-v~pv~d~plkdr  272 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDM-VDPVTDKPLKDR  272 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccc-cccCCCCcCccc
Confidence            456999999999998888888 6999999999999877755 699998877654

>PHA03096 p28-like protein; Provisional

Probab=94.97  E-value=0.012  Score=56.07  Aligned_cols=46  Identities=33%  Similarity=0.646  Sum_probs=33.7

Q ss_pred             cccccccccccCC----CceEEeC-CCCccchhHHHHHHhcCC--CCCCcccc
Q 018364          299 ETCAICLEDYQDG----EKLKVLS-CKHEFHASCVDSWLTKWG--TFCPVCKH  344 (357)
Q Consensus       299 ~~CaICLe~f~~~----~~vr~Lp-C~H~FH~~CI~~Wl~~~~--~~CPlCR~  344 (357)
                      ..|.||+|.....    ..--.|+ |.|.|+..||..|-....  ..||.||.
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            7899999986543    2344676 999999999999987742  23555543

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

Probab=94.89  E-value=0.015  Score=54.97  Aligned_cols=47  Identities=26%  Similarity=0.602  Sum_probs=35.8

Q ss_pred             cccccccccccCCCceEEeC-CCCccchhHHHHHHhcCCCCCCcc-cccCcC
Q 018364          299 ETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWGTFCPVC-KHDMRN  348 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~~~CPlC-R~~i~~  348 (357)
                      -.|+.|-.-....  ++. | |+|.|+++||..-|......||.| |++|.-
T Consensus       275 LkCplc~~Llrnp--~kT-~cC~~~fc~eci~~al~dsDf~CpnC~rkdvll  323 (427)
T COG5222         275 LKCPLCHCLLRNP--MKT-PCCGHTFCDECIGTALLDSDFKCPNCSRKDVLL  323 (427)
T ss_pred             ccCcchhhhhhCc--ccC-ccccchHHHHHHhhhhhhccccCCCcccccchh
Confidence            5899987765443  444 5 899999999998888877789999 555543

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

Probab=94.77  E-value=0.016  Score=61.55  Aligned_cols=51  Identities=27%  Similarity=0.615  Sum_probs=39.6

Q ss_pred             CCCCcccccccccccCCCceEEe-CCCCccchhHHHHHHhcCC------CCCCccccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWG------TFCPVCKHD  345 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~L-pC~H~FH~~CI~~Wl~~~~------~~CPlCR~~  345 (357)
                      .....+|.||.+.++..+.+--- .|-|+||-.||..|-.+..      =.||.|+..
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            34567999999999887765433 3999999999999988732      159999843

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

Probab=94.66  E-value=0.0093  Score=57.17  Aligned_cols=52  Identities=25%  Similarity=0.602  Sum_probs=41.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .....+|.+|-.-|-+..  .+..|-|.||+.||-..|...+ .||.|...|...
T Consensus        12 ~n~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~~~-~CP~C~i~ih~t   63 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEESK-YCPTCDIVIHKT   63 (331)
T ss_pred             cccceehhhccceeecch--hHHHHHHHHHHHHHHHHHHHhc-cCCccceeccCc
Confidence            445679999988776642  3456999999999999999966 599999877654

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.60  E-value=0.021  Score=40.60  Aligned_cols=48  Identities=21%  Similarity=0.455  Sum_probs=33.9

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      ....|..|...=..   -.++||+|+....|.+-+  +-+ -||+|-+++...+
T Consensus         6 ~~~~~~~~~~~~~~---~~~~pCgH~I~~~~f~~~--rYn-gCPfC~~~~~~~~   53 (55)
T PF14447_consen    6 PEQPCVFCGFVGTK---GTVLPCGHLICDNCFPGE--RYN-GCPFCGTPFEFDD   53 (55)
T ss_pred             cceeEEEccccccc---cccccccceeeccccChh--hcc-CCCCCCCcccCCC
Confidence            34567766655333   468999999999998864  223 4999988886543

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

Probab=94.46  E-value=0.016  Score=54.82  Aligned_cols=45  Identities=31%  Similarity=0.676  Sum_probs=38.8

Q ss_pred             cccccccccccCC-CceEEeCCCCccchhHHHHHHhcCCCCCCcccc
Q 018364          299 ETCAICLEDYQDG-EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH  344 (357)
Q Consensus       299 ~~CaICLe~f~~~-~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~  344 (357)
                      ..|+||.+.+-.. +.+..++|+|.-|..|++.-...+ ..||+|..
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence            3499999997766 457789999999999999988887 78999987

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

Probab=94.31  E-value=0.016  Score=51.73  Aligned_cols=44  Identities=32%  Similarity=0.594  Sum_probs=35.6

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCccccc
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD  345 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~  345 (357)
                      ...|-||-++|+..   .++.|||.||..|.-.=.+... .|-+|-..
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            45999999999985   4678999999999877666644 59999654

>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=93.81  E-value=0.03  Score=37.99  Aligned_cols=42  Identities=24%  Similarity=0.694  Sum_probs=24.9

Q ss_pred             cccccccccCCCceEEeCCCCccchhHHHHHHhcCCC-CCCcc
Q 018364          301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGT-FCPVC  342 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~-~CPlC  342 (357)
                      |.+|-+-...|+....-.|+=.+|..|++.+++.++. .||.|
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            6788888777754444458889999999999999663 49988

; PDB: 3NW0_A 2CT0_A.

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

Probab=93.63  E-value=0.02  Score=54.06  Aligned_cols=42  Identities=26%  Similarity=0.645  Sum_probs=29.5

Q ss_pred             CcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCc
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ...|+||++.-.   .+..|+|||. =+.+|-..     -..||+||+.|.
T Consensus       300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkr-----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKR-----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCc---ceEEeecCcEEeehhhccc-----cccCchHHHHHH
Confidence            568999999733   3678999996 34455322     125999998764

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

Probab=93.60  E-value=0.14  Score=44.65  Aligned_cols=39  Identities=21%  Similarity=0.158  Sum_probs=30.6

Q ss_pred             CCCcceEEEEEcCCCCh-------------------HHHHHHHHHcCCcEEEEecccC
Q 018364          144 DADHINFVLIVRGQCIF-------------------EDKIRNAQAAGYRAAIVYNDRE  182 (357)
Q Consensus       144 ~~~~~~I~LV~RG~CsF-------------------~~K~~~Aq~aGA~avIv~~~~~  182 (357)
                      .+.++|||||.+|+=.|                   ..|.+.|+++||+|||++++..
T Consensus        46 ~DVkGKiVvvl~~~P~~~~~~~~~f~~~~~~~~~~~~~K~~~A~~~GA~gvi~v~~~~  103 (157)
T cd04821          46 LDVKGKTVVILVNDPGFATPDSGLFNGKAMTYYGRWTYKYEEAARQGAAGALIVHETE  103 (157)
T ss_pred             CCcCCcEEEEEcCCCCcccccccccCcccccccccHHHHHHHHHHCCCeEEEEEeCCC
Confidence            45678888888775433                   3599999999999999998643

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

>PF04641 Rtf2: Rtf2 RING-finger

Probab=93.55  E-value=0.081  Score=49.96  Aligned_cols=52  Identities=19%  Similarity=0.468  Sum_probs=40.2

Q ss_pred             CCCCcccccccccccCCCceEEe-CCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~L-pC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ......|+|...+|....+...| ||||+|-..+|++- . ....||+|-.++..
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k-~~~~Cp~c~~~f~~  162 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-K-KSKKCPVCGKPFTE  162 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-c-ccccccccCCcccc
Confidence            45567999999999666555555 89999999999996 3 23359999887653

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

Probab=93.41  E-value=0.026  Score=60.18  Aligned_cols=42  Identities=21%  Similarity=0.594  Sum_probs=31.9

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCccccc
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD  345 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~  345 (357)
                      ...|+.|--..+..  ...--|+|.||..|++    .+...||-|+-+
T Consensus       840 ~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e----~~~~~CP~C~~e  881 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP--FVHFLCGHSYHQHCLE----DKEDKCPKCLPE  881 (933)
T ss_pred             eeeecccCCccccc--eeeeecccHHHHHhhc----cCcccCCccchh
Confidence            36999998776653  3445699999999998    334569999873

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

Probab=93.26  E-value=0.083  Score=51.13  Aligned_cols=49  Identities=20%  Similarity=0.434  Sum_probs=39.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ..+++.|+||...-   -.-...||+|.=|..||.+=+.+.+. |=.|+..+.
T Consensus       419 ~sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~-CFfCktTv~  467 (489)
T KOG4692|consen  419 DSEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKR-CFFCKTTVI  467 (489)
T ss_pred             CcccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCe-eeEecceee
Confidence            45678999998752   22357799999999999999999874 999998776

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.23  E-value=0.06  Score=51.81  Aligned_cols=54  Identities=17%  Similarity=0.484  Sum_probs=38.4

Q ss_pred             CCCcccccccccccCCCc-eEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          296 HGGETCAICLEDYQDGEK-LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~-vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ++++.|+.|+|++...|+ ..-.|||-..|.-|-..--+.-+..||-||+...++
T Consensus        12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            346679999999988775 334468888888886554333234699999977654

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=93.00  E-value=0.1  Score=37.00  Aligned_cols=34  Identities=26%  Similarity=0.813  Sum_probs=29.5

Q ss_pred             CCcccccccccccCCCceEEeC-CCCccchhHHHH
Q 018364          297 GGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDS  330 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~  330 (357)
                      ....|.+|-+.|+++|.+.+-| |+-.||++|-+.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            4578999999999888888887 999999999654

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

Probab=92.74  E-value=0.071  Score=46.88  Aligned_cols=55  Identities=25%  Similarity=0.622  Sum_probs=38.1

Q ss_pred             CcccccccccccCC----CceEEeCCCCccchhHHHHHHhc----CC------CCCCcccccCcCCCCC
Q 018364          298 GETCAICLEDYQDG----EKLKVLSCKHEFHASCVDSWLTK----WG------TFCPVCKHDMRNNSES  352 (357)
Q Consensus       298 ~~~CaICLe~f~~~----~~vr~LpC~H~FH~~CI~~Wl~~----~~------~~CPlCR~~i~~~~~~  352 (357)
                      --.|-||..---.|    +.+--..||.-||.-|+..||+.    ++      ..||.|-.+|.-+.++
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmSg  233 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMSG  233 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeeccC
Confidence            45788887533233    22334459999999999999976    21      1599999988776544

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

Probab=92.60  E-value=0.048  Score=58.10  Aligned_cols=47  Identities=21%  Similarity=0.682  Sum_probs=38.2

Q ss_pred             cccccccccccCCCceEEeCCCCccchhHHHHHHhcCCC-CCCcccccCcCC
Q 018364          299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGT-FCPVCKHDMRNN  349 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~-~CPlCR~~i~~~  349 (357)
                      ..|.||++    .+...+.+|+|.|+.+|+.+-++.... .||+||..+.+.
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~  502 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEK  502 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHH
Confidence            79999999    456778899999999999987777432 499999877543

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

Probab=92.53  E-value=0.046  Score=51.74  Aligned_cols=48  Identities=25%  Similarity=0.384  Sum_probs=38.7

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      -...|-||-+.|...   .++.|+|.|+..|--.=++... .|++|-+.+..
T Consensus       240 ~Pf~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~qk~~-~c~vC~~~t~g  287 (313)
T KOG1813|consen  240 LPFKCFICRKYFYRP---VVTKCGHYFCEVCALKPYQKGE-KCYVCSQQTHG  287 (313)
T ss_pred             CCccccccccccccc---hhhcCCceeehhhhccccccCC-cceeccccccc
Confidence            356899999999886   5678999999999777666655 49999876643

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.23  E-value=0.063  Score=49.83  Aligned_cols=52  Identities=25%  Similarity=0.583  Sum_probs=38.4

Q ss_pred             CCCCcccccccccccCCCce-EEeCC-----CCccchhHHHHHHhcCC-------CCCCcccccC
Q 018364          295 CHGGETCAICLEDYQDGEKL-KVLSC-----KHEFHASCVDSWLTKWG-------TFCPVCKHDM  346 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~v-r~LpC-----~H~FH~~CI~~Wl~~~~-------~~CPlCR~~i  346 (357)
                      .+.+..|=||++.=+++..- -+-||     .|-.|.+|+..|+..++       ..||-|+.+.
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            45677999999984444211 25576     48899999999998842       3699998865

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

Probab=92.19  E-value=0.066  Score=57.46  Aligned_cols=36  Identities=22%  Similarity=0.461  Sum_probs=29.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHH
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSW  331 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~W  331 (357)
                      ...+++|.+|.-.+... .-.+-||||.||++||..=
T Consensus       814 ~ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~  849 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRH  849 (911)
T ss_pred             ecCccchHHhcchhhcC-cceeeeccchHHHHHHHHH
Confidence            56689999998887664 5667899999999998753

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

Probab=91.44  E-value=0.22  Score=49.00  Aligned_cols=30  Identities=20%  Similarity=0.726  Sum_probs=23.5

Q ss_pred             CCCccchhHHHHHHhcCC------------CCCCcccccCcC
Q 018364          319 CKHEFHASCVDSWLTKWG------------TFCPVCKHDMRN  348 (357)
Q Consensus       319 C~H~FH~~CI~~Wl~~~~------------~~CPlCR~~i~~  348 (357)
                      |.=.+|.+|+-+||..+|            ..||+||+...-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            556789999999998853            269999998653

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

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=89.79  E-value=0.34  Score=41.98  Aligned_cols=36  Identities=25%  Similarity=0.622  Sum_probs=21.3

Q ss_pred             CcccccccccccCCC---------ceEEeCCCCc-cchhHHHHHHh
Q 018364          298 GETCAICLEDYQDGE---------KLKVLSCKHE-FHASCVDSWLT  333 (357)
Q Consensus       298 ~~~CaICLe~f~~~~---------~vr~LpC~H~-FH~~CI~~Wl~  333 (357)
                      +..|+||||-=.+.-         -+|---|+-. =|..|+|+.-+
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            568999999733320         0122225433 47889998744

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=89.61  E-value=0.18  Score=48.30  Aligned_cols=51  Identities=31%  Similarity=0.760  Sum_probs=38.1

Q ss_pred             CcccccccccccCCCc-eEEeCCC-----CccchhHHHHHHhcCC-CCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEK-LKVLSCK-----HEFHASCVDSWLTKWG-TFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~-vr~LpC~-----H~FH~~CI~~Wl~~~~-~~CPlCR~~i~~  348 (357)
                      +..|-||.++..+.+. .-+.||.     +..|+.|++.|+..++ ..|.+|......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~  135 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN  135 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence            5789999998765432 4567873     5689999999999653 469999876543

>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=88.62  E-value=0.32  Score=51.85  Aligned_cols=52  Identities=23%  Similarity=0.623  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccCCCceEEeCCCC-----ccchhHHHHHHhcCC-CCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKH-----EFHASCVDSWLTKWG-TFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H-----~FH~~CI~~Wl~~~~-~~CPlCR~~i~  347 (357)
                      .++...|-||..+=.+++.+ .-||+.     ..|++|+.+|+.... +.|-+|+.++.
T Consensus         9 N~d~~~CRICr~e~~~d~pL-fhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPL-FHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             CccchhceeecCCCCCCCcC-cccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            44568999999997777766 458743     489999999999854 45999988764

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

Probab=87.99  E-value=0.3  Score=47.01  Aligned_cols=45  Identities=20%  Similarity=0.524  Sum_probs=34.7

Q ss_pred             CCCCcccccccccccCCCceEEeCC--CCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSC--KHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC--~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ..+-.+|+||.+.+...    +..|  ||+-+..|-.+   . .+.||.||.++.
T Consensus        45 ~~~lleCPvC~~~l~~P----i~QC~nGHlaCssC~~~---~-~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPP----IFQCDNGHLACSSCRTK---V-SNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCccc----ceecCCCcEehhhhhhh---h-cccCCccccccc
Confidence            34456999999998885    5557  89999999653   2 335999999886

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

Probab=87.79  E-value=0.23  Score=47.37  Aligned_cols=44  Identities=25%  Similarity=0.619  Sum_probs=28.0

Q ss_pred             cccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      -.|--|=-.+.  -.=|.+||+|+||.+|-..  .. .+.||.|--.|.
T Consensus        91 HfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~-dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DS-DKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCcce--eeecccccchhhhhhhhhc--Cc-cccCcCcccHHH
Confidence            35555533322  2347899999999999653  12 236999965553

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

Probab=87.72  E-value=0.17  Score=52.51  Aligned_cols=44  Identities=30%  Similarity=0.531  Sum_probs=32.6

Q ss_pred             CcccccccccccCCCc-eEEeCCCCccchhHHHHHHhcCCCCCCccccc
Q 018364          298 GETCAICLEDYQDGEK-LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD  345 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~-vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~  345 (357)
                      .-.|.||+..|..... -+.|-|||..+..|+..-.+.   +|| |+++
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~---scp-~~~D   55 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA---SCP-TKRD   55 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc---cCC-CCcc
Confidence            3489999998876532 245569999999999886544   599 7654

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

Probab=86.25  E-value=0.24  Score=55.33  Aligned_cols=47  Identities=32%  Similarity=0.692  Sum_probs=38.0

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCccccc
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD  345 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~  345 (357)
                      .....|.||++....-  --+..|+|.++..|+..|+..+. .||+|+..
T Consensus      1151 ~~~~~c~ic~dil~~~--~~I~~cgh~~c~~c~~~~l~~~s-~~~~~ksi 1197 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQ--GGIAGCGHEPCCRCDELWLYASS-RCPICKSI 1197 (1394)
T ss_pred             hcccchHHHHHHHHhc--CCeeeechhHhhhHHHHHHHHhc-cCcchhhh
Confidence            3445999999998732  14667999999999999999977 59999853

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]

Probab=86.16  E-value=0.25  Score=51.45  Aligned_cols=44  Identities=23%  Similarity=0.692  Sum_probs=30.3

Q ss_pred             CCCccccccccc-----ccCCCceEEeCCCCccchhHHHHHHhcCCCCCCccc
Q 018364          296 HGGETCAICLED-----YQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK  343 (357)
Q Consensus       296 ~~~~~CaICLe~-----f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR  343 (357)
                      .....|.||-.+     |+.....|...|+|+||+.|+..    .+..||.|-
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r----~s~~CPrC~  557 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR----KSPCCPRCE  557 (580)
T ss_pred             cCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc----cCCCCCchH
Confidence            345688888332     44444456677999999999654    444599993

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

Probab=85.54  E-value=0.45  Score=49.69  Aligned_cols=52  Identities=27%  Similarity=0.743  Sum_probs=43.0

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESNE  354 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~~~~  354 (357)
                      .+..+.|.||+++.    ..|+.+|.   |..|+..|+..+. .||+|+..+..+.+.+.
T Consensus       476 ~~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~-~~pl~~~~~~~~~~~~~  527 (543)
T KOG0802|consen  476 REPNDVCAICYQEM----SARITPCS---HALCLRKWLYVQE-VCPLCHTYMKEDDFLSK  527 (543)
T ss_pred             hcccCcchHHHHHH----Hhcccccc---chhHHHhhhhhcc-ccCCCchhhhcccccCc
Confidence            45578999999998    45788899   9999999999966 59999988877666554

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=84.50  E-value=0.44  Score=47.63  Aligned_cols=40  Identities=28%  Similarity=0.607  Sum_probs=30.7

Q ss_pred             CCCcccccccccc-cCCCceEEeCCCCccchhHHHHHHhcC
Q 018364          296 HGGETCAICLEDY-QDGEKLKVLSCKHEFHASCVDSWLTKW  335 (357)
Q Consensus       296 ~~~~~CaICLe~f-~~~~~vr~LpC~H~FH~~CI~~Wl~~~  335 (357)
                      ....+|.||..++ ...+...++-|+|.|+.+|+.+-+..+
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            3467999999544 443555567799999999999888854

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

Probab=83.79  E-value=0.43  Score=43.59  Aligned_cols=40  Identities=28%  Similarity=0.714  Sum_probs=27.9

Q ss_pred             cccccccccCCCceEEeCCCC-ccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          301 CAICLEDYQDGEKLKVLSCKH-EFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       301 CaICLe~f~~~~~vr~LpC~H-~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      |-.|-+.   +-.|..|||.| .++..|=+.     -..||+|+.....
T Consensus       161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLPCRHLCLCGICDES-----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcC---CceEEeecccceEeccccccc-----CccCCCCcChhhc
Confidence            7777665   44588999977 577778554     1249999976544

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

Probab=82.36  E-value=1.1  Score=44.26  Aligned_cols=50  Identities=20%  Similarity=0.347  Sum_probs=42.0

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCC--CCCCcccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG--TFCPVCKH  344 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~--~~CPlCR~  344 (357)
                      ..+...|+|=.+.=.+.+.-..|.|||+..++=|+.--+...  ..||.|=.
T Consensus       331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            455679999988888888888999999999999999777765  56999943

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

Probab=81.35  E-value=1  Score=48.11  Aligned_cols=53  Identities=11%  Similarity=0.197  Sum_probs=40.0

Q ss_pred             CCCCcccccccccccCC-CceEEeC---CCCccchhHHHHHHhc-----CCCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDG-EKLKVLS---CKHEFHASCVDSWLTK-----WGTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~-~~vr~Lp---C~H~FH~~CI~~Wl~~-----~~~~CPlCR~~i~  347 (357)
                      ..+.+.|.||.-++... |..-.+|   |.|.|+..||..|...     ....|++|...|.
T Consensus        93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~  154 (1134)
T KOG0825|consen   93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG  154 (1134)
T ss_pred             cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence            44567888888888773 3455666   9999999999999887     2345899987653

>smart00249 PHD PHD zinc finger

Probab=80.95  E-value=0.51  Score=31.20  Aligned_cols=31  Identities=26%  Similarity=0.690  Sum_probs=22.1

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHH
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDS  330 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~  330 (357)
                      .|.+|-.....++.|.--.|.+.||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECCCCCchhhhhhCCC
Confidence            4788888764444444446999999999754

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]

Probab=80.08  E-value=1  Score=47.94  Aligned_cols=26  Identities=31%  Similarity=0.674  Sum_probs=21.9

Q ss_pred             EEeCCCCccchhHHHHHHhcCCCCCCc
Q 018364          315 KVLSCKHEFHASCVDSWLTKWGTFCPV  341 (357)
Q Consensus       315 r~LpC~H~FH~~CI~~Wl~~~~~~CPl  341 (357)
                      ....|+|+-|.+|..+|+.... .||.
T Consensus      1044 ~Cg~C~Hv~H~sc~~eWf~~gd-~Cps 1069 (1081)
T KOG0309|consen 1044 FCGTCGHVGHTSCMMEWFRTGD-VCPS 1069 (1081)
T ss_pred             hhccccccccHHHHHHHHhcCC-cCCC
Confidence            3445999999999999999977 5984

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	357
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		1e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		3e-06
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		9e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		4e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		7e-05
3eif_A	936	1.9 Angstrom Crystal Structure Of The Active Form O		3e-04

>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein 38 Length = 75

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           C +C+ D++  + L+VL C HEFHA CVD WL K    CP+C+ D
Sbjct: 26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWL-KANRTCPICRAD 69

>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 = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
           SS +      G  C +C EDY  GE ++ L C H FH SC+  WL +  + CPVC+  + 
Sbjct: 5   SSGTEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRKSLT 63
Query: 348 N-NSESNEVGV 357
             N+ +N  G+
Sbjct: 64  GQNTATNPPGL 74

>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5 Length = 55

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 298 GETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCK 343
           G  CA+CL + +DGE+ + L  C H FHA CVD WL    T CP+C+
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCR 50

>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain Length = 69

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/46 (43%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 301 CAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDM 346
           C ICL   ++GE ++ L C H FH  CVD WL      CP+C+ D+
Sbjct: 17  CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT-NKKCPICRVDI 61

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVC 342
           E CA+CLED++  ++L +  CKH FH  C+  WL +    CP+C
Sbjct: 16  ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWL-EVRKVCPLC 58

>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 = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 267 NQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCA-ICLEDYQDGEKLKVLSCKHEFHA 325
           N P S+    + ++ALP  L +    +   G E C  IC  +Y  G+    L C H FH 
Sbjct: 14  NPPASK----ESIDALPEILVTEDHGAV--GQEMCCPICCSEYVKGDVATELPCHHYFHK 67
Query: 326 SCVDSWLTKWGTFCPVCK 343
            CV  WL K GT CPVC+
Sbjct: 68  PCVSIWLQKSGT-CPVCR 84

>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 = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 150 FVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGV 209
             LI RG   F+DKI NA+ AG    ++Y++++KG  + +    +   + A F+S + G+
Sbjct: 292 IALIERGDIDFKDKIANAKKAGAVGVLIYDNQDKGFPIELPNVDQ---MPAAFISRKDGL 348
Query: 210 YLKEHAR 216
            LK++++
Sbjct: 349 LLKDNSK 355

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	357
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-24
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-22
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	8e-22
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	5e-21
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	7e-21
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-19
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-16
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	4e-15
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	8e-12
1xf1_A	926	C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {St	7e-11
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-11
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-09
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-08
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-08
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	4e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	6e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	7e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-06
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	3e-05
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	4e-05
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	2e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	2e-04
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-04
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	2e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	3e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-04
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	5e-04
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	6e-04
2ek8_A	421	Aminopeptidase; metalloproteinase, hydrolase; 1.80	7e-04
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	8e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	9e-04

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75

 Score = 93.5 bits (233), Expect = 3e-24
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 276 SKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW 335
           S     LP + F+  +         C +C+ D++  + L+VL C HEFHA CVD WL   
Sbjct: 3   SGSSGQLPSYRFNPNNHQS--EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 336 GTFCPVCKHDMRNNS 350
            T CP+C+ D   +S
Sbjct: 61  RT-CPICRADSGPSS 74

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91

 Score = 88.6 bits (220), Expect = 3e-22
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 274 LDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLT 333
              + ++ALP  L +    +       C IC  +Y  G+    L C H FH  CV  WL 
Sbjct: 17  ASKESIDALPEILVTEDHGAVGQEMC-CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQ 75

Query: 334 KWGTFCPVCKHDM 346
           K GT CPVC+   
Sbjct: 76  KSGT-CPVCRCMF 87

>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 = 90.6 bits (224), Expect = 8e-22
 Identities = 35/162 (21%), Positives = 57/162 (35%), Gaps = 14/162 (8%)

Query: 81  YLNLCFVVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHV---ADPADACSPLS 137
           YLN+ + V  +         ++        +  D       G L         +AC+P +
Sbjct: 36  YLNVSWRVPHTGV-----NRTVWELSEEGVYGQDSPLEPVAGVLVPPDGPGALNACNPHT 90

Query: 138 N---PVASNDADHINFV-LIVRGQ-CIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTAS 192
           N   P        ++++ LI RG  C F DKI  A   G   A+++N     + V   + 
Sbjct: 91  NFTVPTVWGSTVQVSWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSH 150

Query: 193 HEGVKVHAIFVSLETGVYLKEH-ARGETGECCIFPESNRGSW 233
              V + AI +    G  + +   RG      I      G W
Sbjct: 151 PGAVDIVAIMIGNLKGTKILQSIQRGIQVTMVIEVGKKHGPW 192

>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 = 84.7 bits (210), Expect = 5e-21
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 291 SSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
             ++    E C ICL   ++GE ++ L C H FH  CVD WL      CP+C+ D+    
Sbjct: 7   EGTEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDIEAQL 65

Query: 351 ES 352
            S
Sbjct: 66  PS 67

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74

 Score = 84.4 bits (209), Expect = 7e-21
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
           SS    + +  E CA+CLED++  ++L +  CKH FH  C+  WL      CP+C   + 
Sbjct: 5   SSGKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKV-CPLCNMPVL 63

Query: 348 NNSESN 353
             ++ +
Sbjct: 64  QLAQLS 69

>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 = 81.3 bits (201), Expect = 1e-19
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
           SS +      G  C +C EDY  GE ++ L C H FH SC+  WL +  + CPVC+  + 
Sbjct: 5   SSGTEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRKSLT 63

Query: 348 NNSESNE 354
             + +  
Sbjct: 64  GQNTATN 70

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55

 Score = 71.1 bits (175), Expect = 3e-16
 Identities = 23/49 (46%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 298 GETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           G  CA+CL + +DGE+ + L  C H FHA CVD WL    T CP+C+  
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLT 52

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 68.6 bits (168), Expect = 4e-15
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
           SS    Q    E C IC++   D     +L C H F   C+D W  +    CP+C+  M 
Sbjct: 5   SSGRVKQLTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRN-CPICRLQMT 59

Query: 348 NNSESN 353
             +ES+
Sbjct: 60  GANESS 65

>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 = 62.7 bits (153), Expect = 4e-13
 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 297 GGETCAICLEDYQDGEKL-KVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
           G   C ICLED      +  VL C H  H +C +  L +    CP+C 
Sbjct: 4   GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYR-CPLCS 50

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 59.3 bits (144), Expect = 8e-12
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
            E C ICLED  +      L C H F   C+  W+ +  T CP+CK  + 
Sbjct: 5   AERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPT-CPLCKVPVE 51

>1xf1_A C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {Streptococcus pyogenes} PDB: 3eif_A* Length = 926

 Score = 62.8 bits (152), Expect = 7e-11
 Identities = 26/129 (20%), Positives = 53/129 (41%), Gaps = 6/129 (4%)

Query: 87  VVSLSSATLVWKPLSLHFPDLPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDAD 146
           V S S    + + + +   D   K    ++++                   +    +   
Sbjct: 223 VASYSPDKQLTETVRVKTADQQDKEMPVLSTNRFEPNKAYDYAYANRGTKEDD-FKDVKG 281

Query: 147 HINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLE 206
            I   LI RG   F+DKI  A+ AG    ++Y++++KG  + +       ++ A F+S +
Sbjct: 282 KI--ALIERGDIDFKDKIAKAKKAGAVGVLIYDNQDKGFPIELPNVD---QMPAAFISRK 336

Query: 207 TGVYLKEHA 215
            G+ LK++ 
Sbjct: 337 DGLLLKDNP 345

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 56.5 bits (136), Expect = 7e-11
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 5/61 (8%)

Query: 288 SSASSSQCHGGETCAICLEDYQD----GEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
           SS +  +  G  +C IC++ Y +    G  +    C H F + C+   L    T CP C+
Sbjct: 5   SSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCR 63

Query: 344 H 344
            
Sbjct: 64  K 64

>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 = 52.1 bits (125), Expect = 3e-09
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 290 ASSSQCHGGETCAICLEDYQD----GEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
            +  +  G  +C IC++ Y +    G  +    C H F + C+   L    T CP C+  
Sbjct: 2   TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKK 60

Query: 346 MRNNS 350
           + +  
Sbjct: 61  INHKR 65

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 49.9 bits (119), Expect = 2e-08
 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 299 ETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           + C  C  + +  + + V   C H FH  C+  W+ +    CP+C+ D
Sbjct: 27  DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNR-CPLCQQD 73

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 49.0 bits (117), Expect = 3e-08
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)

Query: 300 TCAICLEDYQD----GEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
           +C IC++ Y +    G  +    C H F + C+   L    T CP C+  + +  
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHKR 58

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK-----HDMRNNSESNE 354
            C IC+E  +D        C      SC+  WLT+    CP C+      ++ N   + E
Sbjct: 24  RCFICMEKLRD--ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAEE 81

Query: 355 V 355
           V
Sbjct: 82  V 82

>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 = 51.3 bits (122), Expect = 2e-07
 Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 291 SSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCK 343
                   + C IC E+ +D    K+  C H    SC+ SW    G  CP C+
Sbjct: 325 YCEMGSTFQLCKICAENDKDV---KIEPCGHLMCTSCLTSWQESEGQGCPFCR 374

>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 = 47.3 bits (112), Expect = 4e-07
 Identities = 14/86 (16%), Positives = 25/86 (29%), Gaps = 3/86 (3%)

Query: 266 QNQPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHA 325
            N  L   + + + +            S+      C  C E            C+H    
Sbjct: 20  SNAKLWNEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELVFR---PITTVCQHNVCK 76

Query: 326 SCVDSWLTKWGTFCPVCKHDMRNNSE 351
            C+D         CP C++D+  +  
Sbjct: 77  DCLDRSFRAQVFSCPACRYDLGRSYA 102

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381

 Score = 49.9 bits (118), Expect = 6e-07
 Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 15/80 (18%)

Query: 282 LPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKV-----LSCKHEFHASCVDSWLTKWG 336
           +P +        + +    C IC     DG ++ +       C  + HA C++ W     
Sbjct: 292 MPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLM 351

Query: 337 TF----------CPVCKHDM 346
                       CP CK  +
Sbjct: 352 DGKTFLEVSFGQCPFCKAKL 371

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 45.6 bits (108), Expect = 7e-07
 Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 4/58 (6%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           SS  S +      C IC + +Q+     V  C+H F  SC           C +C   
Sbjct: 5   SSGGSEEEEIPFRCFICRQAFQNP---VVTKCRHYFCESCALEHFRATPR-CYICDQP 58

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWL-TKWGTFCPVCKHD 345
           + C IC      G+  +  +C    H  CV  +  +     CP C   
Sbjct: 16  KICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

>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 = 45.6 bits (107), Expect = 2e-06
 Identities = 16/65 (24%), Positives = 22/65 (33%), Gaps = 19/65 (29%)

Query: 299 ETCAICLED---------------YQDGEKLKVLSCKHEFHASCVDSWL---TKWGTF-C 339
           E C IC+E                       ++  C H FH  C+ +      K G+  C
Sbjct: 26  EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQC 85

Query: 340 PVCKH 344
           P CK 
Sbjct: 86  PSCKT 90

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 42.9 bits (101), Expect = 6e-06
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDM 346
           SS +++       CAICL+          L CKH F   CV       G  C +C+ ++
Sbjct: 5   SSGNTAPSLTVPECAICLQTCVHP---VSLPCKHVFCYLCVKGASWL-GKRCALCRQEI 59

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 15/50 (30%), Gaps = 3/50 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN 349
            C  C E            C H     C+          CP C+HD+  N
Sbjct: 80  MCVCCQELVYQP---VTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 126

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 1/58 (1%)

Query: 289 SASSSQCHGGETCAICLEDY-QDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           S S         C +C+E    D       +C ++    C     T     CP C+  
Sbjct: 2   SRSPDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 59

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 288 SSASSSQCHGGE---TCAICLEDYQDGEKL-KVLSCKHEFHASCVDSWLTKWGTF--CPV 341
           SS SS           C IC+E + + +   K+L C H     C++  L        CP 
Sbjct: 2   SSGSSGNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPF 61

Query: 342 CKH 344
           C  
Sbjct: 62  CSK 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 = 42.6 bits (100), Expect = 2e-05
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 10/55 (18%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH-----DMRNN 349
            C+ C    ++   + +  C+H F ++CV       GT CPVC       D++ N
Sbjct: 24  RCSRCTNILRE--PVCLGGCEHIFCSNCVSDC---IGTGCPVCYTPAWIQDLKIN 73

>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 = 42.1 bits (99), Expect = 3e-05
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
            C +C   + D     ++ C H F  +C+  +L     +CP+C   +    
Sbjct: 17  MCVLCGGYFID--ATTIIECLHSFCKTCIVRYLET-SKYCPICDVQVHKTR 64

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 3/54 (5%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESN 353
            C IC+E   +      L C H     C  S + K    CP C+  + + +  +
Sbjct: 17  QCGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYH 67

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN 349
            C+IC     D     +  C H F  SC+          CP C   +   
Sbjct: 17  LCSICKGYLID--ATTITECLHTFCKSCIVRHFYYSNR-CPKCNIVVHQT 63

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 40.0 bits (94), Expect = 4e-05
 Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 7/48 (14%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
            C  C  + +     K+L C H   + C    L   G  CP+C+    
Sbjct: 8   RCQQCQAEAKC---PKLLPCLHTLCSGC----LEASGMQCPICQAPWP 48

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 3/51 (5%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
            C  C          K   C H F  SC+ + L+     C  C+  +  + 
Sbjct: 17  KCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK 64

>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 = 38.4 bits (89), Expect = 2e-04
 Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 2/54 (3%)

Query: 299 ETCAICLEDYQDGEKLKVL--SCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS 350
           + C  C         LK++   C H    SCVD    +    CP C   +R ++
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN 57

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 4/53 (7%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSES 352
            C IC E + +      L+C H F + C++ W+ +    CP+C+ D+++ + S
Sbjct: 66  QCIICSEYFIEA---VTLNCAHSFCSYCINEWMKRKIE-CPICRKDIKSKTYS 114

>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 = 38.7 bits (90), Expect = 2e-04
 Identities = 7/34 (20%), Positives = 15/34 (44%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLT 333
            C +CL +Y   +   +  C+  F   C+  ++ 
Sbjct: 7   GCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVE 40

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Length = 92

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 3/46 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTF-CPVCKH 344
            C IC +   D   +    C + +   C+ + L +     CP C  
Sbjct: 15  LCLICKDIMTDAVVIP--CCGNSYCDECIRTALLESDEHTCPTCHQ 58

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 5/62 (8%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVL-SCK---HEFHASCVDSWL-TKWGTFCPVC 342
           SS +S      + C IC  +  D   L     C    H  H +C+  W+ +     C +C
Sbjct: 5   SSGTSITPSSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELC 64

Query: 343 KH 344
           K+
Sbjct: 65  KY 66

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 39.0 bits (90), Expect = 4e-04
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 5/49 (10%)

Query: 300 TCAICLEDYQDGEKLK----VLSCKHEFHASCVDSWLTKWGTFCPVCKH 344
           +C IC++ Y +  +         C H F + C+   L    T CP C+ 
Sbjct: 9   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRK 56

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH 344
           +C IC     D       SCKH F   C+   L   G++CP C++
Sbjct: 25  SCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRY 66

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 6/60 (10%)

Query: 288 SSASSSQCHGGE-TCAICLEDYQDGEKLKVLSCKHEFHASCV-DSWLTKWGTF-CPVCKH 344
           +S         E  C ICL+  Q       + C H F   C+     T  G F CP+CK 
Sbjct: 9   ASGQFVNKLQEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKT 65

>2ek8_A Aminopeptidase; metalloproteinase, hydrolase; 1.80A {Aneurinibacillus SP} PDB: 2ek9_A* Length = 421

 Score = 40.4 bits (94), Expect = 7e-04
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 149 NFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETG 208
              LI RG   F DK+RNA   G +A I+YN+ + G L       +   V A+ ++ + G
Sbjct: 116 KIALIQRGNISFADKVRNAAKQGAKAVIIYNNTD-GKLNGTLGGSDASFVAAVGITKQEG 174

Query: 209 VYLKEHAR 216
             L  + R
Sbjct: 175 DALAANLR 182

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 36.6 bits (85), Expect = 8e-04
 Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 3/46 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTF-CPVCKH 344
            C IC +   D   +    C + +   C+ + L +     CP C  
Sbjct: 17  LCLICKDIMTDAVVIP--CCGNSYCDECIRTALLESDEHTCPTCHQ 60

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165

 Score = 38.8 bits (90), Expect = 9e-04
 Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 2/45 (4%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH 344
            C ICL+  ++   +    C H F A C+ + L      CP C+ 
Sbjct: 56  MCPICLDMLKN--TMTTKECLHRFCADCIITALRSGNKECPTCRK 98

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	357
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	99.89
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.71
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.67
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.6
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.57
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.57
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.55
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.5
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.5
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.49
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.48
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.43
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.42
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.41
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.39
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.35
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.34
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.33
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.31
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.3
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.3
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.29
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.26
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.25
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.25
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.22
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.2
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.19
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.17
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.17
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.16
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.16
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.15
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.15
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.14
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.13
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.11
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.1
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.09
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.03
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.03
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.01
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.0
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.99
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.99
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.98
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.96
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.87
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.87
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.84
2ek8_A	421	Aminopeptidase; metalloproteinase, hydrolase; 1.80	98.83
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.83
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.79
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.77
3iib_A	444	Peptidase M28; YP_926796.1, structural genomics, J	98.76
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.75
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.73
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.71
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.71
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.68
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.65
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.65
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.61
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.59
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.57
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.5
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.49
3fed_A	707	Glutamate carboxypeptidase III; metallopeptidase,	98.4
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.35
3kas_A	640	Transferrin receptor protein 1; transferrin recept	98.32
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.2
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.18
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.12
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.09
3i6s_A	649	Subtilisin-like protease; PA-domain, FN3-domain, h	97.9
1y9z_A	441	Alkaline serine protease; subtilisin-like alpha/be	97.83
3nw0_A	238	Non-structural maintenance of chromosomes element	97.69
1xf1_A	926	C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {St	97.67
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.95
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	92.93
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	92.83
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	87.68
1we9_A	64	PHD finger family protein; structural genomics, PH	87.33
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	86.62
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	86.57
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.87
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	85.76
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	85.62
3vta_A	621	Cucumisin; subtilisin-like fold, serine protease,	84.13
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.58
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	82.7
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	81.81
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	81.7
2yt5_A	66	Metal-response element-binding transcription facto	81.25

>3icu_A E3 ubiquitin-protein ligase RNF128; E3 ligase, energy, PA domain, transmembrane,protein turnover conjugation pathway; HET: NAG; 2.10A {Homo sapiens}

Probab=99.89  E-value=3.8e-23  Score=183.96  Aligned_cols=130  Identities=22%  Similarity=0.337  Sum_probs=104.3

Q ss_pred             ecccccccccccCCCCeEEEEeeCC---CCCCCCCCCCCCCCC----CCCcceEEEEEcCC-CChHHHHHHHHHcCCcEE
Q 018364          104 FPDLPAKFAVDVNSSGTCGALHVAD---PADACSPLSNPVASN----DADHINFVLIVRGQ-CIFEDKIRNAQAAGYRAA  175 (357)
Q Consensus       104 ~~~~~a~Fg~~~~~~~~~g~l~~~~---p~~aC~~~~~~~~~~----~~~~~~I~LV~RG~-CsF~~K~~~Aq~aGA~av  175 (357)
                      +.+.+|+||...+..++.|.|+.+.   |.+||++.++...+.    +..+++||||+||+ |+|.+|++|||++||+||
T Consensus        54 ~~~e~a~FG~~~p~~~v~G~lv~~~~~~~~~GC~~~~~~~~~~~~~~~~~~gkIaLV~RG~~CsF~~Kv~nAq~aGA~av  133 (194)
T 3icu_A           54 ELSEEGVYGQDSPLEPVAGVLVPPDGPGALNACNPHTNFTVPTVWGSTVQVSWLALIQRGGGCTFADKIHLAYERGASGA  133 (194)
T ss_dssp             EEEEEEEECTTSCCSCEEEEEECBSSTTCTTCCSTTCCBCCCBCTTSSCBCCEEEEEESCTTCCHHHHHHHHHHTTCSEE
T ss_pred             ecccccccCCCCCCCCcEEEEEecCCCCCcCCCCCCccccCCcccccccCCCeEEEEECCCCcCHHHHHHHHHHCCCcEE
Confidence            6677999999999999999998763   789999987643221    12468999999999 999999999999999999


Q ss_pred             EEeccc-CcccccccccCCCcceeeEEEeehhhhhhhhhhcccC-CceeeecCCCCCcccc
Q 018364          176 IVYNDR-EKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHARGE-TGECCIFPESNRGSWS  234 (357)
Q Consensus       176 Iv~~~~-~~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~l~~~-~~~v~I~p~~s~~~~~  234 (357)
                      ||||+. +++.+++|..++ ..+||++||++++|+.|+++++.+ .+.+.+.....+.+|.
T Consensus       134 IIyNn~~~g~~~~~m~~~~-~~~IPsv~Is~~~G~~L~~~L~~G~~Vtvti~vg~~h~pw~  193 (194)
T 3icu_A          134 VIFNFPGTRNEVIPMSHPG-AVDIVAIMIGNLKGTKILQSIQRGIQVTMVIEVGKKHGPWV  193 (194)
T ss_dssp             EEECCTTCTTCCCCCCCTT-CCSSEEEEECHHHHHHHHHHHHTTCCEEEEEEEEEEECCCC
T ss_pred             EEEeCCCCCCceeeecCCC-CCceeEEEECHHHHHHHHHHHHCCCeEEEEEECCCccCCCC
Confidence            999985 334556676543 368999999999999999988765 4556666666666663

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=99.71  E-value=1.3e-17  Score=131.21  Aligned_cols=79  Identities=30%  Similarity=0.653  Sum_probs=68.1

Q ss_pred             CccccccchhHHhhccccccccCCCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          268 QPLSRRLDSKVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       268 ~~~~~~l~~~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      .....+++++.++.||...+...... ......|+||+++|..++.++.|||+|.||..||+.|++.+. +||+||+.+.
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~-~CP~Cr~~~~   88 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGA-VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSG-TCPVCRCMFP   88 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSS-SSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTC-BCTTTCCBSS
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccc-cCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCC-cCcCcCccCC
Confidence            34467899999999999888764433 456789999999999999999999999999999999999876 5999999886


Q ss_pred             C
Q 018364          348 N  348 (357)
Q Consensus       348 ~  348 (357)
                      .
T Consensus        89 ~   89 (91)
T 2l0b_A           89 P   89 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.3e-17  Score=124.81  Aligned_cols=70  Identities=34%  Similarity=0.812  Sum_probs=58.8

Q ss_pred             hHHhhccccccccCCCCCCCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          277 KVVEALPCFLFSSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       277 ~~i~~lp~~~~~~~~~~~~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..++++|..+++....  ..+..+|+||+++|..++.++.|||+|.||..||++|++.+. .||+||+++.+.
T Consensus         4 ~~i~~lp~~~~~~~~~--~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~-~CP~Cr~~~~~~   73 (75)
T 1x4j_A            4 GSSGQLPSYRFNPNNH--QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR-TCPICRADSGPS   73 (75)
T ss_dssp             CCCSSCCCEEBCSSSC--SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCS-SCTTTCCCCCCC
T ss_pred             hhHhhCCcEEecCccc--cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCC-cCcCcCCcCCCC
Confidence            3456788877765332  456789999999999999999999999999999999999976 599999998764

>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=99.60  E-value=1.3e-15  Score=113.16  Aligned_cols=58  Identities=38%  Similarity=0.843  Sum_probs=51.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESN  353 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~~~  353 (357)
                      ......|+||+++|..++.++.|||+|.||..||.+|+..+. +||+||+.+......+
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~~~   68 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNK-KCPICRVDIEAQLPSE   68 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCS-BCTTTCSBSCSCCCCC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCC-CCcCcCccccCcCCCC
Confidence            456779999999999988999999999999999999999977 4999999998765543

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=2.3e-15  Score=113.26  Aligned_cols=57  Identities=33%  Similarity=0.797  Sum_probs=50.6

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSES  352 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~~  352 (357)
                      .....+|+||+++|..++.+++|||+|.||..||++|++.+. +||+||+.+....+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~~~~~~   68 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRK-VCPLCNMPVLQLAQL   68 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCS-BCTTTCCBCSSCCSC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCC-cCCCcCccccccccc
Confidence            455789999999999999999999999999999999999977 599999999765543

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=99.57  E-value=1.1e-15  Score=108.26  Aligned_cols=51  Identities=43%  Similarity=1.051  Sum_probs=46.2

Q ss_pred             CCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          296 HGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ++..+|+||+++|+.++.++.+| |+|.||.+||++|++++. +||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~-~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCC-SCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCC-cCcCCCCEeE
Confidence            45689999999999999999998 999999999999999866 5999999874

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.55  E-value=3.9e-15  Score=113.16  Aligned_cols=55  Identities=38%  Similarity=0.954  Sum_probs=49.0

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      .....+|+||+++|..++.++.|||+|.||..||..|++.+. .||+||+.+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~   66 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHD-SCPVCRKSLTGQN   66 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTC-SCTTTCCCCCCSC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCC-cCcCcCCccCCcc
Confidence            455789999999999999999999999999999999998876 5999999986653

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=8.7e-15  Score=112.50  Aligned_cols=52  Identities=31%  Similarity=0.763  Sum_probs=41.7

Q ss_pred             CCccccccccccc-----------CCCceEEeC-CCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQ-----------DGEKLKVLS-CKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~-----------~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ++++|+||+++|+           .++.++.++ |+|.||.+||++||++++ +||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNN-RCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCC-BCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCC-CCCCcCCCcchh
Confidence            3566777777775           456677776 999999999999999977 599999988653

>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=99.50  E-value=1.7e-14  Score=117.55  Aligned_cols=59  Identities=24%  Similarity=0.496  Sum_probs=46.2

Q ss_pred             CCcccccccccccCCC---------------ceEEeCCCCccchhHHHHHHhc----CCCCCCcccccCcCCCCCCCC
Q 018364          297 GGETCAICLEDYQDGE---------------KLKVLSCKHEFHASCVDSWLTK----WGTFCPVCKHDMRNNSESNEV  355 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~---------------~vr~LpC~H~FH~~CI~~Wl~~----~~~~CPlCR~~i~~~~~~~~~  355 (357)
                      .+++|+|||++|..++               .++.++|+|.||.+||+.|+..    .+.+||+||+.+.......+-
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~  101 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPW  101 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTT
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCC
Confidence            3579999999997653               4557899999999999999953    234699999999776554443

>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=99.49  E-value=2.1e-14  Score=101.54  Aligned_cols=51  Identities=33%  Similarity=0.704  Sum_probs=44.2

Q ss_pred             CCCcccccccccccCC-CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          296 HGGETCAICLEDYQDG-EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~-~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      .+..+|+||+++|.++ +.++.+||+|.||.+||++|++.+. .||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGY-RCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTC-CCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCC-cCCCCCCcCC
Confidence            3568999999999665 4678899999999999999999975 5999999875

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=3.5e-14  Score=108.90  Aligned_cols=58  Identities=22%  Similarity=0.604  Sum_probs=48.4

Q ss_pred             CCCCcccccccccccCCCceEEeCCC-----CccchhHHHHHHhcCC-CCCCcccccCcCCCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCK-----HEFHASCVDSWLTKWG-TFCPVCKHDMRNNSESN  353 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~-----H~FH~~CI~~Wl~~~~-~~CPlCR~~i~~~~~~~  353 (357)
                      ..+.+.|.||+++|++++.+ ++||+     |.||.+||++||..++ .+||+||+.+..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~~   75 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLS   75 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCSC
T ss_pred             CCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcccC
Confidence            44568999999999988877 69996     9999999999999864 46999999997655443

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=7.9e-14  Score=102.95  Aligned_cols=53  Identities=25%  Similarity=0.678  Sum_probs=45.2

Q ss_pred             CCCCcccccccccccCC----CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDG----EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~----~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+..+|+||+++|.+.    +.+..++|+|.||.+||+.|++.+. .||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCS-SCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCC-CCCCCCCccCc
Confidence            45578999999999763    4567899999999999999999866 59999998864

>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=99.42  E-value=8.2e-14  Score=112.55  Aligned_cols=50  Identities=28%  Similarity=0.634  Sum_probs=42.8

Q ss_pred             CCcccccccccccCC---------------CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          297 GGETCAICLEDYQDG---------------EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       297 ~~~~CaICLe~f~~~---------------~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      +.+.|+||+++|+..               ..++.++|+|.||..||++||..+. +||+||+++.
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            468999999999854               1367889999999999999999976 5999999864

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.41  E-value=6.9e-14  Score=104.02  Aligned_cols=54  Identities=26%  Similarity=0.739  Sum_probs=46.1

Q ss_pred             CCCCcccccccccccC----CCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQD----GEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~----~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+..+|+||+++|.+    ++.+..++|||.||.+||++|++.+. .||+||+.+..+
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   64 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   64 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCS-BCTTTCCBCCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCC-CCCCCCCccChh
Confidence            3456799999999876    35668899999999999999999876 599999998754

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.39  E-value=1.1e-13  Score=100.58  Aligned_cols=52  Identities=23%  Similarity=0.663  Sum_probs=44.7

Q ss_pred             CCcccccccccccCC----CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQDG----EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~~~----~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      +..+|+||+++|.+.    +.+..++|||.||.+||++|++.+. .||+||+.+..+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCS-BCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCC-CCCCCCccCCcc
Confidence            357999999999753    5567899999999999999999966 599999998764

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=2.5e-13  Score=100.88  Aligned_cols=52  Identities=33%  Similarity=0.887  Sum_probs=44.7

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE  351 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~  351 (357)
                      ..+...|+||++.+.+    ..+||+|.||..||..|+..+. .||+||+.+.....
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHR-NCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCS-SCHHHHHCTTCCCC
T ss_pred             CCCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcC-cCCCcCCcccCCCc
Confidence            4557899999999877    7899999999999999999765 59999999986543

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=1.1e-12  Score=101.47  Aligned_cols=55  Identities=27%  Similarity=0.634  Sum_probs=46.8

Q ss_pred             CCCCcccccccccccCCCc-eEEeCCCCccchhHHHHHHhcC--CCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEK-LKVLSCKHEFHASCVDSWLTKW--GTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~-vr~LpC~H~FH~~CI~~Wl~~~--~~~CPlCR~~i~~~  349 (357)
                      ..+..+|+||++.|.+.+. .+.|+|||.||..||..|+..+  ...||+||+.+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             ccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            4557799999999998765 6788999999999999999986  34699999987654

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=99.33  E-value=7e-13  Score=97.81  Aligned_cols=50  Identities=34%  Similarity=0.780  Sum_probs=42.9

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ....+|+||++++.+  .+..+||+|.||..||..|++.+. .||+||+.+..
T Consensus         3 ~~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNP-TCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSC-STTTTCCCCCC
T ss_pred             CCCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcC-cCcCCChhhHh
Confidence            346799999999864  457899999999999999999876 59999998864

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=1.9e-12  Score=96.81  Aligned_cols=54  Identities=22%  Similarity=0.416  Sum_probs=44.4

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSE  351 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~  351 (357)
                      ..+...|+||++.|.+  .+..++|+|.||..||+.|++.+. .||+||+.+.....
T Consensus        12 ~~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~~~   65 (72)
T 2djb_A           12 LTPYILCSICKGYLID--ATTITECLHTFCKSCIVRHFYYSN-RCPKCNIVVHQTQP   65 (72)
T ss_dssp             CCGGGSCTTTSSCCSS--CEECSSSCCEECHHHHHHHHHHCS-SCTTTCCCCCSSCS
T ss_pred             cCCCCCCCCCChHHHC--cCEECCCCCHHHHHHHHHHHHcCC-cCCCcCcccCcccc
Confidence            4556799999999876  344459999999999999998865 59999999876543

>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=99.30  E-value=2.4e-13  Score=111.52  Aligned_cols=51  Identities=29%  Similarity=0.683  Sum_probs=1.1

Q ss_pred             CCcccccccccccC-------------CCc--eEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQD-------------GEK--LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~~-------------~~~--vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+.|+||+++|+.             ++.  +..++|+|.||..||++||..++ +||+||++...
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            46899999999976             222  33458999999999999999976 59999998643

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=9.2e-13  Score=98.28  Aligned_cols=51  Identities=27%  Similarity=0.521  Sum_probs=43.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+..+|+||++.+.+.   ..+||+|.||..||+.|+..+. .||+||..+..+
T Consensus        12 ~~~~~~C~IC~~~~~~~---~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~   62 (71)
T 2d8t_A           12 SLTVPECAICLQTCVHP---VSLPCKHVFCYLCVKGASWLGK-RCALCRQEIPED   62 (71)
T ss_dssp             SSSCCBCSSSSSBCSSE---EEETTTEEEEHHHHHHCTTCSS-BCSSSCCBCCHH
T ss_pred             CCCCCCCccCCcccCCC---EEccCCCHHHHHHHHHHHHCCC-cCcCcCchhCHh
Confidence            44567999999998663   6789999999999999999875 599999998643

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.29  E-value=2.2e-12  Score=94.71  Aligned_cols=52  Identities=21%  Similarity=0.473  Sum_probs=43.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.+.+.   ..++|||.||..||..|+...+..||+||+.+..+
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCCEECTTTCCEESSC---CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CCcCCCCCCCChHhcCe---eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            44567999999999765   24799999999999999975555699999998764

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=4e-12  Score=94.94  Aligned_cols=52  Identities=29%  Similarity=0.583  Sum_probs=43.0

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc--CCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK--WGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~--~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.|.+   ...++|||.||..||..|++.  .+..||+||+.+..+
T Consensus        17 ~~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           17 LQEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCCBCTTTCSBCSS---EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             CccCCEeccCCcccCC---eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            4557899999999885   356799999999999999973  344699999998764

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.25  E-value=6e-12  Score=94.68  Aligned_cols=52  Identities=21%  Similarity=0.520  Sum_probs=42.9

Q ss_pred             CCCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcCC-CCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWG-TFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~-~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.|.+.   ..|| |+|.||..||+.|+..++ ..||+||+.+...
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           12 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   65 (74)
T ss_dssp             SCGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCT
T ss_pred             CCCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCc
Confidence            44567999999999864   4689 999999999999999753 3699999986544

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.25  E-value=4e-12  Score=93.03  Aligned_cols=52  Identities=29%  Similarity=0.633  Sum_probs=42.9

Q ss_pred             Ccccccccc-cccCCCc-eEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLE-DYQDGEK-LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe-~f~~~~~-vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++ .|.+... +..++|||.||.+||+.|+.+.+..||+||+.+..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            568999999 7766543 346799999999999999887655799999998754

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=7.5e-12  Score=95.63  Aligned_cols=49  Identities=24%  Similarity=0.463  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ......|+||++.|.+.   .++||+|.||..||..|+.... .||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQNP---VVTKCRHYFCESCALEHFRATP-RCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCSE---EECTTSCEEEHHHHHHHHHHCS-BCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcCe---eEccCCCHhHHHHHHHHHHCCC-cCCCcCcccc
Confidence            44567999999998663   4689999999999999998865 5999999985

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.20  E-value=1.2e-11  Score=93.11  Aligned_cols=54  Identities=20%  Similarity=0.488  Sum_probs=44.4

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-CCCCCcccccCcCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-GTFCPVCKHDMRNNS  350 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPlCR~~i~~~~  350 (357)
                      .+..++|+||.+.+..++...  .|+|.||..||++||+++ +.+||+||++...+.
T Consensus        12 ~~~i~~C~IC~~~i~~g~~C~--~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSEECS--SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             cCCCCcCcchhhHcccCCccC--CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            345689999999999876444  899999999999999986 246999999886543

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.19  E-value=1.3e-11  Score=93.52  Aligned_cols=52  Identities=21%  Similarity=0.389  Sum_probs=43.6

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.|.+.   ..++|||.||..||..|+...+..||+||+.+...
T Consensus         5 ~~~~~~C~IC~~~~~~P---v~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDP---VIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSE---EEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CcccCCCCCccccccCC---EEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            44578999999998764   56799999999999999987455699999998654

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.17  E-value=9.5e-12  Score=103.15  Aligned_cols=53  Identities=25%  Similarity=0.703  Sum_probs=45.4

Q ss_pred             CCCcccccccccccCC----CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          296 HGGETCAICLEDYQDG----EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~----~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .+..+|+||++.|++.    +.++.++|||.||.+||++|++.++ +||+||+.+...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCS-BCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCC-CCCCCCCcCccc
Confidence            3467999999999763    5668899999999999999999876 599999988754

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.17  E-value=3.2e-11  Score=92.24  Aligned_cols=52  Identities=27%  Similarity=0.536  Sum_probs=43.7

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-----CCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-----GTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-----~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.|.+.   ..+||+|.||..||..|+...     ...||+||..+..+
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEP---VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CCTTTSCTTTCSCCSSC---EECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             CccCCCCcCCChhhCcc---eeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            45567999999998775   478999999999999999983     44699999998754

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=3e-11  Score=87.69  Aligned_cols=45  Identities=27%  Similarity=0.572  Sum_probs=37.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc--CCCCCCcc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK--WGTFCPVC  342 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~--~~~~CPlC  342 (357)
                      ..+...|+||++.|.+.   .+|+|||.||..||..|++.  .+..||+|
T Consensus        17 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQKP---VTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSSC---EECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCCe---EEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            45578999999999864   56799999999999999985  34469998

>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=99.16  E-value=1.1e-11  Score=98.81  Aligned_cols=51  Identities=27%  Similarity=0.597  Sum_probs=42.7

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      +...|+||++.|.+  .+..++|||.||..||..|+..++..||+||..+..+
T Consensus        21 ~~~~C~IC~~~~~~--p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           21 EVFRCFICMEKLRD--ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HHTBCTTTCSBCSS--EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCccCCccccC--ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            35699999999975  4444899999999999999999755699999998643

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.15  E-value=8.6e-12  Score=94.51  Aligned_cols=52  Identities=27%  Similarity=0.530  Sum_probs=43.3

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC------CCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW------GTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~------~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.|.+.   ..|||||.||..||..|+...      ...||+||..+..+
T Consensus         9 ~~~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A            9 VQEEVTCPICLELLTEP---LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCCCEETTTTEECSSC---CCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cccCCCCcCCCcccCCe---eECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            45578999999999764   458999999999999999873      44699999998653

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.15  E-value=1.4e-11  Score=103.97  Aligned_cols=48  Identities=29%  Similarity=0.879  Sum_probs=41.3

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++.|.+.   ..|||||.||..||..|+..+. .||+||.++...
T Consensus        53 ~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLNCAHSFCSYCINEWMKRKI-ECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEETTSCEEEHHHHHHHTTTCS-BCTTTCCBCCCE
T ss_pred             cCCCcccCcccCCc---eECCCCCCccHHHHHHHHHcCC-cCCCCCCcCCCC
Confidence            35799999999763   6789999999999999999866 599999998653

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.14  E-value=3e-11  Score=85.93  Aligned_cols=45  Identities=29%  Similarity=0.849  Sum_probs=37.3

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc--CCCCCCcc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK--WGTFCPVC  342 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~--~~~~CPlC  342 (357)
                      ..+...|+||++.+++.   ..|+|+|.||.+||..|+..  .+..||+|
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKEP---VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSSC---CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCcc---EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            45567999999999875   45899999999999999764  34569998

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=7.2e-11  Score=90.25  Aligned_cols=52  Identities=31%  Similarity=0.621  Sum_probs=43.1

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc-----CCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK-----WGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~-----~~~~CPlCR~~i~~~  349 (357)
                      ..+..+|+||++.|.+.   ..+||+|.||..||..|+..     ....||+||..+..+
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQP---LSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCCTTTCSCCSSC---BCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             ccCCCCCCCCCcccCCc---eeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            45568999999998764   45799999999999999988     234699999998754

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.11  E-value=2.5e-11  Score=100.57  Aligned_cols=53  Identities=26%  Similarity=0.772  Sum_probs=45.0

Q ss_pred             CCCcccccccccccC----CCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          296 HGGETCAICLEDYQD----GEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       296 ~~~~~CaICLe~f~~----~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .+...|+||+++|++    ++....++|||.||..||++|+..++ +||+||..+..+
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCS-BCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCC-CCCCCCCcCChh
Confidence            346789999999876    34557889999999999999999977 599999998764

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.10  E-value=8.7e-11  Score=91.74  Aligned_cols=50  Identities=22%  Similarity=0.541  Sum_probs=42.2

Q ss_pred             CCCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcCC-CCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWG-TFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~-~~CPlCR~~i~  347 (357)
                      ..+...|+||++.|.+.   ..|| |||.||..||..|+..++ ..||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            45678999999999864   5789 999999999999998643 46999999874

>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=99.09  E-value=4.6e-11  Score=98.70  Aligned_cols=48  Identities=23%  Similarity=0.458  Sum_probs=41.8

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ...|+||++.|.+.   ..+||||.||..||..|+..+...||+||..+..
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            46899999999863   5679999999999999999766579999999976

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.06  E-value=5.6e-11  Score=94.26  Aligned_cols=48  Identities=23%  Similarity=0.624  Sum_probs=40.6

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ...|+||++.|.+  .+..++|||.||..||..|+..+. .||+||..+..
T Consensus        22 ~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNI--AMIIPQCSHNYCSLCIRKFLSYKT-QCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSS--EEECTTTCCEEEHHHHHHHHTTCC-BCTTTCCBCCG
T ss_pred             CCCcccCChhhCC--cCEECCCCCHhhHHHHHHHHHCCC-CCCCCCCcCCh
Confidence            5689999999986  344448999999999999999865 59999998865

>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=99.05  E-value=7e-11  Score=102.41  Aligned_cols=50  Identities=26%  Similarity=0.652  Sum_probs=42.0

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      +...|+||++.|.+  .+..+||||.||..||+.|+...+..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKN--TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhC--cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            34599999999886  455559999999999999999855569999999854

>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=99.03  E-value=1.1e-10  Score=94.18  Aligned_cols=50  Identities=22%  Similarity=0.688  Sum_probs=42.2

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      +...|+||++.|.+  .+..++|||.||..||..|+..+. .||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID--ATTIIECLHSFCKTCIVRYLETSK-YCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHTSCS-BCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC--cCEeCCCCChhhHHHHHHHHHhCC-cCcCCCcccccc
Confidence            36799999999875  454459999999999999999865 599999998764

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=99.03  E-value=2e-10  Score=87.45  Aligned_cols=55  Identities=16%  Similarity=0.454  Sum_probs=43.5

Q ss_pred             CCCCcccccccccccCCCceEEeC--CCCccchhHHHHHHhcCCCCCCcccccCcCCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLS--CKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~Lp--C~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      ..+..+|+||++.+...+. +.+|  |||.||..|+..+.......||+||+.+...+
T Consensus         8 ~~~~~~CpICle~~~~~d~-~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDI-NFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTT-TCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cccCCcCCccCccCccccc-cccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            4556799999999875443 3455  99999999999998665557999999987654

>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=99.01  E-value=1.6e-10  Score=93.25  Aligned_cols=49  Identities=31%  Similarity=0.633  Sum_probs=41.2

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCC--CCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG--TFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~--~~CPlCR~~i~~~  349 (357)
                      ...|+||++.|.+.   ..+||||.||..||..|+..++  ..||+||..+...
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            46899999998764   3579999999999999999753  3599999988764

>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=99.00  E-value=1.7e-10  Score=94.55  Aligned_cols=52  Identities=25%  Similarity=0.515  Sum_probs=44.1

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.+.+.   ..++|||.||..||..|+...+..||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           15 LESKYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcCChhhcCe---EECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            45567999999998764   56899999999999999998764699999988653

>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=98.99  E-value=1.9e-10  Score=98.45  Aligned_cols=49  Identities=24%  Similarity=0.514  Sum_probs=42.5

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++.|.+.   .+|||||.||..||..|+......||+||..+...
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            46899999998764   45899999999999999998665699999998765

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.99  E-value=1.4e-10  Score=82.46  Aligned_cols=50  Identities=22%  Similarity=0.573  Sum_probs=40.8

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCCC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSES  352 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~~  352 (357)
                      .+...|+||++.|.+.   +.|||+|.||..||..|    ...||+||+.+....++
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~~~   53 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGADT   53 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCSSC
T ss_pred             ccCCCceEeCCccCCe---EEcCCCCcccHHHHccC----CCCCCcCCcEeecCCcC
Confidence            4567899999999864   67899999999999883    33599999998876443

>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=98.98  E-value=8.5e-11  Score=95.90  Aligned_cols=49  Identities=31%  Similarity=0.613  Sum_probs=41.7

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++.+.+.   ..++|||.||..||..|+...+..||+||..+...
T Consensus        23 ~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           23 SISCQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcHhcCc---EEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            56899999998763   45899999999999999998554699999998654

>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=98.96  E-value=9.8e-11  Score=95.37  Aligned_cols=49  Identities=27%  Similarity=0.645  Sum_probs=41.7

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      +...|+||++.|.+.   ..|+|||.||..||..|+...+..||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSSC---EECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCce---eEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            356899999998764   5679999999999999998755579999998853

>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=98.87  E-value=9.8e-10  Score=107.09  Aligned_cols=51  Identities=31%  Similarity=0.765  Sum_probs=42.3

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ....+|+||++.+..   ...+||||.||..||..|+......||+||+.+...
T Consensus       330 ~~~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          330 STFQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             TSSSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            345799999999855   578999999999999999995444699999988653

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.87  E-value=1.6e-09  Score=78.25  Aligned_cols=51  Identities=29%  Similarity=0.621  Sum_probs=39.7

Q ss_pred             CCCCcccccccccccCCCceEEeCCC--C---ccchhHHHHHHhcC-CCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCK--H---EFHASCVDSWLTKW-GTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~--H---~FH~~CI~~Wl~~~-~~~CPlCR~~i~~  348 (357)
                      .++...|.||+++.  ++.+ ++||.  |   .||.+||++|+... +.+||+||..+..
T Consensus         3 ~~~~~~CrIC~~~~--~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            3 DEDVPVCWICNEEL--GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEEC--SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCEeEEeecCC--CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            34578999999983  3445 68964  4   89999999999863 4569999988753

>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=98.84  E-value=1.1e-09  Score=79.92  Aligned_cols=47  Identities=23%  Similarity=0.537  Sum_probs=38.8

Q ss_pred             CCcccccccccccCCCceEEe--CCCCc-cchhHHHHHHhcCCCCCCcccccCc
Q 018364          297 GGETCAICLEDYQDGEKLKVL--SCKHE-FHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~L--pC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ++.+|.||++++.+.   ..+  ||||. |+.+|++.|.+.++ .||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~-~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKNG---CIVHGKTGHLMACFTCAKKLKKRNK-PCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSCE---EEEETTEEEEEECHHHHHHHHHTTC-CCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCCE---EEECCCCCChhhHHHHHHHHHHcCC-cCCCcCcchh
Confidence            457999999986553   344  99999 78999999998766 5999999885

>2ek8_A Aminopeptidase; metalloproteinase, hydrolase; 1.80A {Aneurinibacillus SP} PDB: 2ek9_A*

Probab=98.83  E-value=1.8e-08  Score=99.83  Aligned_cols=92  Identities=24%  Similarity=0.323  Sum_probs=67.4

Q ss_pred             CCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcc
Q 018364          117 SSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGV  196 (357)
Q Consensus       117 ~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i  196 (357)
                      ..++.|.|++..-. ..+++.     ..+.+++||||+||+|+|.+|+++|+++||+|||||++.+. ....+.++....
T Consensus        90 ~g~v~a~lv~~~~G-~~~D~~-----~~dv~GkIvlv~~g~~~~~~k~~~A~~~GA~gvIi~~~~~~-~~~g~~~~~~~~  162 (421)
T 2ek8_A           90 NSDVTAELVYVGLG-TTADVA-----GKDLNGKIALIQRGNISFADKVRNAAKQGAKAVIIYNNTDG-KLNGTLGGSDAS  162 (421)
T ss_dssp             CEEEEEEEEECTTC-CTTTTT-----TSCCTTSEEEEECCSSCHHHHHHHHHHTTCSEEEEECSSSS-CCCCBCSSCCTT
T ss_pred             CCCcceEEEECCCC-ChhhcC-----CCCcCceEEEEeCCCCCHHHHHHHHHHCCCeEEEEEeCCCc-ccccccCCCCCC
Confidence            34678888764332 111111     12357899999999999999999999999999999998643 222222333456


Q ss_pred             eeeEEEeehhhhhhhhhhc
Q 018364          197 KVHAIFVSLETGVYLKEHA  215 (357)
Q Consensus       197 ~Ip~v~is~~~G~~L~~~l  215 (357)
                      .||++.|+.++++.|++.+
T Consensus       163 ~IP~~~Is~~~a~~L~~~l  181 (421)
T 2ek8_A          163 FVAAVGITKQEGDALAANL  181 (421)
T ss_dssp             CCEEEEECHHHHHHHHHHH
T ss_pred             CccEEEeCHHHHHHHHHHh
Confidence            8999999999999999877

>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=8.1e-10  Score=93.53  Aligned_cols=51  Identities=20%  Similarity=0.390  Sum_probs=43.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+...|+||++.+.+.   .+++|||.||..||..|+......||+||.++..
T Consensus        28 l~~~~~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP---FQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             CCcCcCCCCCChhhcCc---EECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            45567999999998875   4589999999999999998766569999998743

>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=98.79  E-value=3e-09  Score=84.72  Aligned_cols=50  Identities=10%  Similarity=-0.049  Sum_probs=43.1

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+...|+||++-|++.   .++||||.|++.||..|+..+. +||+||..+..
T Consensus        26 ~p~~~~CpI~~~~m~dP---V~~~cGhtf~r~~I~~~l~~~~-~cP~~~~~l~~   75 (100)
T 2kre_A           26 APDEFRDPLMDTLMTDP---VRLPSGTIMDRSIILRHLLNSP-TDPFNRQTLTE   75 (100)
T ss_dssp             CSTTTBCTTTCSBCSSE---EEETTTEEEEHHHHHHHTTSCS-BCSSSCCBCCT
T ss_pred             CcHhhCCcCccCcccCC---eECCCCCEEchHHHHHHHHcCC-CCCCCCCCCCh
Confidence            44567999999998875   5789999999999999999755 59999998865

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=98.77  E-value=4.8e-09  Score=80.97  Aligned_cols=50  Identities=10%  Similarity=-0.064  Sum_probs=43.0

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+...|+||++-|++.   .+++|||.|++.||..|+..+. +||+||..+..
T Consensus        11 ~p~~~~CpI~~~~m~dP---V~~~cGhtf~r~~I~~~l~~~~-~cP~~~~~l~~   60 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTDP---VRLPSGTVMDRSIILRHLLNSP-TDPFNRQMLTE   60 (85)
T ss_dssp             CCTTTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHCS-BCTTTCCBCCG
T ss_pred             CchheECcccCchhcCC---eECCCCCEECHHHHHHHHhcCC-CCCCCcCCCCh
Confidence            34567999999998875   5789999999999999999865 59999998864

>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=98.76  E-value=2.7e-08  Score=99.34  Aligned_cols=107  Identities=8%  Similarity=-0.023  Sum_probs=75.6

Q ss_pred             cccccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCC---------hHHH----HHHHHHcCCc
Q 018364          107 LPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCI---------FEDK----IRNAQAAGYR  173 (357)
Q Consensus       107 ~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~Cs---------F~~K----~~~Aq~aGA~  173 (357)
                      .+..+++..+..+++|+|+.....+.|....     ..+.++|||||+||.|.         |..|    +.+|+++||+
T Consensus        93 ~~l~~s~~tp~~~vta~lV~v~~~~~~~~~~-----~~dvkGKIVlv~~~~~~~~~~~~y~~~~~kr~~~a~~A~~aGA~  167 (444)
T 3iib_A           93 TALGGSIATPAQGLSATIVRFDTLQDLQNAE-----AGSLNDKIAFIDAKTERHRDGKGYGQTASGRSRGAVAAAEKGAV  167 (444)
T ss_dssp             EECBTCCCCCTTCEEEEEEEESSHHHHHTSC-----TTTTTTCEEEECCCCCCCTTCHHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             EeccCCCCCCCCCeEEEEEecCCHHHHhhcc-----ccccCccEEEEeCCCCCCcccccccchhhhhhhHHHHHHHCCCe
Confidence            3344565556788999998876555554431     12357899999999995         6677    4579999999


Q ss_pred             EEEEecccCccc---cc-ccccCCCcceeeEEEeehhhhhhhhhhcccC
Q 018364          174 AAIVYNDREKGS---LV-SMTASHEGVKVHAIFVSLETGVYLKEHARGE  218 (357)
Q Consensus       174 avIv~~~~~~~~---~~-~m~~~~~~i~Ip~v~is~~~G~~L~~~l~~~  218 (357)
                      ||||+|+..+..   .. .|...+....||++.|+.++|+.|+++++.+
T Consensus       168 avIi~~~~~~~~~~~~tg~~~~~~~~~~IP~~~Is~~da~~L~~~l~~g  216 (444)
T 3iib_A          168 GIIIRSIGTDHDRMAHTGMMRYEEGVTAIPAAAISNPDADLINAMLKRD  216 (444)
T ss_dssp             EEEEECSCSCCSSCCCCCBCCCCTTSCCCCEEEECHHHHHHHHHHHTTT
T ss_pred             EEEEEccCCcccccccCCccccCCCCCCCCeEEecHHHHHHHHHHHhCC
Confidence            999999754321   11 1211223468999999999999999887654

>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=98.75  E-value=2.4e-09  Score=77.95  Aligned_cols=47  Identities=21%  Similarity=0.534  Sum_probs=38.6

Q ss_pred             CCcccccccccccCCCceEEe--CCCCc-cchhHHHHHHhcCCCCCCcccccCc
Q 018364          297 GGETCAICLEDYQDGEKLKVL--SCKHE-FHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~L--pC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ....|.||++...+.   ..+  ||||. |+.+|+..|.+.+. .||+||+++.
T Consensus         6 ~~~~C~IC~~~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~-~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG---NIIHGRTGHLVTCFHCARRLKKAGA-SCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCE---EEEETTEEEEEECHHHHHHHHHTTC-BCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCe---EEEecCCCCHhHHHHHHHHHHHhCC-cCCCcCchhh
Confidence            457999999986552   344  99998 99999999988765 5999999885

>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=98.73  E-value=8.7e-09  Score=81.75  Aligned_cols=51  Identities=14%  Similarity=-0.018  Sum_probs=43.3

Q ss_pred             CCCCcccccccccccCCCceEEeCCC-CccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCK-HEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~-H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++-|++.   .+++|| |.|++.||..|+..+. +||+||..+...
T Consensus        19 ~p~~~~CpI~~~~m~dP---V~~~cG~htf~r~cI~~~l~~~~-~cP~~~~~l~~~   70 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQ-TDPFNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSC-BCTTTCSBCCTT
T ss_pred             CcHhcCCcCccccccCC---eECCCCCeEECHHHHHHHHHhCC-CCCCCCCCCChh
Confidence            34567999999998875   568999 9999999999999865 599999988653

>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=98.71  E-value=2.8e-09  Score=87.04  Aligned_cols=45  Identities=29%  Similarity=0.584  Sum_probs=38.5

Q ss_pred             CcccccccccccCCCceEEe-CCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~L-pC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ...|+||++.|.+.   ..+ +|||.||..||..|+.   ..||+||..+..
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            57999999999764   455 9999999999999998   359999998854

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=98.71  E-value=3.3e-09  Score=100.93  Aligned_cols=55  Identities=25%  Similarity=0.634  Sum_probs=42.8

Q ss_pred             CCCCcccccccccccCCCce-----EEeCCCCccchhHHHHHHhcCC----------CCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKL-----KVLSCKHEFHASCVDSWLTKWG----------TFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~v-----r~LpC~H~FH~~CI~~Wl~~~~----------~~CPlCR~~i~~~  349 (357)
                      .....+|+||++.+.+++.+     .-.+|+|.||..||.+||++..          ..||.||++|..+
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            34677999999999884332     2346999999999999998731          2599999998754

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.68  E-value=5.5e-09  Score=78.42  Aligned_cols=43  Identities=21%  Similarity=0.592  Sum_probs=36.6

Q ss_pred             CcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ...|+||++.+.+   ...+||||. |+..|+..|    . .||+||+.+..
T Consensus        24 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----D-KCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC----S-BCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC----c-cCCCcCcCccC
Confidence            4689999998765   467899999 999999998    3 59999998864

>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=98.65  E-value=8.8e-09  Score=89.47  Aligned_cols=52  Identities=25%  Similarity=0.515  Sum_probs=43.9

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++.|.+.   .+++|||.|+..||..|+...+..||+||..+..+
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCChhhcCc---EECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            45567999999998864   45899999999999999988654699999988654

>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=98.65  E-value=1.2e-08  Score=94.73  Aligned_cols=51  Identities=14%  Similarity=0.202  Sum_probs=43.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ......|+||++-|.+.   .++||||.|++.||..|+..+..+||+||.++..
T Consensus       205 ~~~~~~c~i~~~~~~dP---v~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          205 IPDYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CCSTTBCTTTCSBCSSE---EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCcccCCcCcCCHhcCC---eECCCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            44567999999998875   5789999999999999999865569999998864

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.61  E-value=3.4e-08  Score=72.97  Aligned_cols=46  Identities=22%  Similarity=0.707  Sum_probs=37.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+...|.||++...+   +..+||+|. |+..|+..    .+ .||+||+.|..
T Consensus        12 ~~~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~-~CP~CR~~i~~   58 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQ-QCPMCRQFVQE   58 (68)
T ss_dssp             CCCSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CS-SCTTTCCCCCC
T ss_pred             CCCCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CC-CCCCCCcchhc
Confidence            4456799999998654   578899999 99999984    23 59999998865

>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=98.59  E-value=1.2e-08  Score=79.99  Aligned_cols=49  Identities=22%  Similarity=0.670  Sum_probs=40.8

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-------CCCCCc--cccc
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-------GTFCPV--CKHD  345 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-------~~~CPl--CR~~  345 (357)
                      +..+|+||++++...+.++.++|+|.|+.+|+..++...       ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            457899999999877666666899999999999998752       236999  9987

>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=98.57  E-value=2.8e-08  Score=78.06  Aligned_cols=47  Identities=23%  Similarity=0.579  Sum_probs=38.7

Q ss_pred             CCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcC-----CCCCCc--cccc
Q 018364          296 HGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKW-----GTFCPV--CKHD  345 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~-----~~~CPl--CR~~  345 (357)
                      .....|+||++.|++.   .++| |||.|++.||..|+..+     ..+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            4467999999998864   4575 99999999999999875     246999  9865

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.50  E-value=3.4e-08  Score=74.18  Aligned_cols=44  Identities=20%  Similarity=0.585  Sum_probs=35.6

Q ss_pred             CcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+|+||++.+.+   ...+||||. |+..|+..    .. .||+||..+...
T Consensus        25 ~~~C~IC~~~~~~---~~~~pCgH~~~C~~C~~~----~~-~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVPCGHLVTCKQCAEA----VD-KCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSSSCCCCBCHHHHHH----CS-BCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCC---EEEecCCCHHHHHHHhhC----CC-CCccCCceecCc
Confidence            4689999999765   356899999 99999964    23 599999988653

>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=5.9e-08  Score=85.10  Aligned_cols=51  Identities=14%  Similarity=0.193  Sum_probs=43.1

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..+...|+||++-|.+.   .++||||.|.+.||..|+..+..+||+||.++..
T Consensus       103 ip~~f~CPI~~elm~DP---V~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          103 IPDYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CcHhhcccCccccCCCC---eECCCCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            45567999999998874   4679999999999999999864469999998864

>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=98.40  E-value=3.8e-07  Score=95.72  Aligned_cols=99  Identities=16%  Similarity=0.077  Sum_probs=68.2

Q ss_pred             CCCCeEEEEeeCCCCCCCCCCCCC---CCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcc--------
Q 018364          116 NSSGTCGALHVADPADACSPLSNP---VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKG--------  184 (357)
Q Consensus       116 ~~~~~~g~l~~~~p~~aC~~~~~~---~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~--------  184 (357)
                      +.+.++|.|+++.  .||.. +..   .....+..++||||+||+|+|.+|+++||++||+|||||+|..+.        
T Consensus       123 ~~G~v~g~lV~v~--~G~~~-Df~~L~~~~~~~v~GkIvlv~~G~~~~~~Kv~~A~~~GA~gviiy~dp~d~~~~g~~~y  199 (707)
T 3fed_A          123 AQGMPEGDLVYVN--YARTE-DFFKLEREMGINCTGKIVIARYGKIFRGNKVKNAMLAGAIGIILYSDPADYFAPEVQPY  199 (707)
T ss_dssp             CCBCCEECEEECT--TCCHH-HHHHHHHTSCCCCTTCEEEEECCSSCHHHHHHHHHHTTCSEEEEECCHHHHCCTTCCBT
T ss_pred             CCCceEEEEEEec--CCchh-hHHHHHhccCCCCCCeEEEEECCCCCHhHHHHHHHHCCCEEEEEEcCchhccccccccC
Confidence            3456788988874  35521 110   000123578999999999999999999999999999999973210        


Q ss_pred             -------------cccc-c--ccCC--------------------CcceeeEEEeehhhhhhhhhhccc
Q 018364          185 -------------SLVS-M--TASH--------------------EGVKVHAIFVSLETGVYLKEHARG  217 (357)
Q Consensus       185 -------------~~~~-m--~~~~--------------------~~i~Ip~v~is~~~G~~L~~~l~~  217 (357)
                                   ..+. +  .+|+                    ....||++-|+.++|+.|++.+.+
T Consensus       200 P~~~~~p~~~vqrGsv~~~~~~GDp~TPG~ps~~~~~r~~~~~~~~~p~IP~~pIS~~da~~Ll~~l~g  268 (707)
T 3fed_A          200 PKGWNLPGTAAQRGNVLNLNGAGDPLTPGYPAKEYTFRLDVEEGVGIPRIPVHPIGYNDAEILLRYLGG  268 (707)
T ss_dssp             TTSSBCCTTCCCCCCCCCCTTCCSTTCTTSCCCTTCCCCCGGGCTTCCSSCEEEECHHHHHHHHHTBCB
T ss_pred             CCCccCCCccccccceecccCCCCCCCCCCcccCCCcccChhhccCCCCCCeEecCHHHHHHHHHHhcC
Confidence                         0000 0  0111                    125899999999999999998754

>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=98.35  E-value=1.2e-07  Score=72.13  Aligned_cols=43  Identities=26%  Similarity=0.658  Sum_probs=35.8

Q ss_pred             CcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCcC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ...|.||++.+.+   ...+||||. |+..|+..|    . .||+||..+..
T Consensus        18 ~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----Q-SCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----S-BCTTTCCBCCE
T ss_pred             CCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----C-cCCCCCchhhC
Confidence            4689999998655   577899999 999999876    2 59999998854

>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=98.32  E-value=6.8e-07  Score=92.87  Aligned_cols=96  Identities=17%  Similarity=0.169  Sum_probs=66.0

Q ss_pred             CCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccc--------
Q 018364          117 SSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVS--------  188 (357)
Q Consensus       117 ~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~--------  188 (357)
                      ...+.|.|+++.  .|+.. +..... .+.+++||||+||+|+|.+|+++|+++||+|||||++..+...+.        
T Consensus       105 ~g~v~g~lV~vg--~G~~~-D~~~l~-vdv~GkIvlv~~g~~~~~~K~~~A~~~GA~gvii~~~~~~~~~~~~~~~~~G~  180 (640)
T 3kas_A          105 AATVTGKLVHAN--FGTKK-DFEDLY-TPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGH  180 (640)
T ss_dssp             CEEEEECEEECT--TCCHH-HHHTCS-SCCTTSEEEEESCSSCHHHHHHHHHTTTCSEEEEECCTTTCCCSCTTCCCCEE
T ss_pred             CCceEEEEEEec--CCChh-hHHHhh-cccCCcEEEEecCCCCHHHHHHHHHHCCCeEEEEEeccccccccccccccccc
Confidence            345678887763  34422 111110 245789999999999999999999999999999999864321100        


Q ss_pred             --c-ccC-------------------CCcceeeEEEeehhhhhhhhhhcc
Q 018364          189 --M-TAS-------------------HEGVKVHAIFVSLETGVYLKEHAR  216 (357)
Q Consensus       189 --m-~~~-------------------~~~i~Ip~v~is~~~G~~L~~~l~  216 (357)
                        . .++                   .....||++-|+.++++.|++.+.
T Consensus       181 ~~~~~Gdp~tpg~ps~~~~~~~~~~~~~~p~IP~~~Is~~~a~~Ll~~l~  230 (640)
T 3kas_A          181 AHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNME  230 (640)
T ss_dssp             CCSSSSCSCCCSSCC---CCCCCCSSCCCCSSCEEECCHHHHHHHHTTEE
T ss_pred             cccCCCCCCCCCcccccccccccccccCCCCCCEEecCHHHHHHHHHHcc
Confidence              0 011                   012479999999999999998764

>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=98.20  E-value=4.8e-07  Score=65.31  Aligned_cols=48  Identities=15%  Similarity=0.226  Sum_probs=40.3

Q ss_pred             CcccccccccccCCCceEEe-CCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~L-pC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++-+++.   .++ +|||+|-++||++|++.+++ ||+++.++...
T Consensus         3 ~~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~-cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGN-DPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSB-CTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCC-CcCCcCCCChh
Confidence            35899999999854   456 89999999999999998775 99999988643

>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=98.18  E-value=3.9e-07  Score=87.88  Aligned_cols=44  Identities=23%  Similarity=0.682  Sum_probs=37.2

Q ss_pred             CCcccccccccccCCCceEEeCCCCc-cchhHHHHHHhcCCCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHE-FHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~-FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      +...|+||++.+..   ...|||||. ||..|+..|    . .||+||..+..
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            45799999999865   467899999 999999988    3 59999998864

>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=98.12  E-value=8.1e-07  Score=81.85  Aligned_cols=51  Identities=24%  Similarity=0.493  Sum_probs=41.8

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-CCCCCc--ccccCcC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-GTFCPV--CKHDMRN  348 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-~~~CPl--CR~~i~~  348 (357)
                      .....|+||++-|++  .|+.+.|||.|++.||..|+..+ ...||+  ||+.+..
T Consensus       179 ~~el~CPIcl~~f~D--PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          179 KIELTCPITCKPYEA--PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             BCCSBCTTTSSBCSS--EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             ceeeECcCccCcccC--CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            345699999999866  57767999999999999999874 336999  9987654

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.09  E-value=2.1e-06  Score=67.28  Aligned_cols=47  Identities=23%  Similarity=0.468  Sum_probs=38.7

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      -|.+|--.+..  ..|.+||+|+|+.+|+..|..+....||+|+.+|..
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            47777666554  679999999999999999987765579999998854

>3i6s_A Subtilisin-like protease; PA-domain, FN3-domain, hydrolase; HET: NAG FUC; 2.50A {Solanum lycopersicum} PDB: 3i74_A*

Probab=97.90  E-value=1e-05  Score=84.31  Aligned_cols=88  Identities=9%  Similarity=0.029  Sum_probs=66.6

Q ss_pred             EEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcceeeEEE
Q 018364          123 ALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIF  202 (357)
Q Consensus       123 ~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i~Ip~v~  202 (357)
                      .|+++...+.|.+...+... .+..++|+|++||.|.|.+|..+++++||.++|++|+..  .   +..  ....+|+++
T Consensus       260 plv~~~~~~~C~~~~l~~~~-vdl~GkIvlc~~g~~~~~~k~~~~~~~Ga~g~i~~n~~~--~---~~~--~~~~~P~~~  331 (649)
T 3i6s_A          260 PVIYNKTLSDCSSEELLSQV-ENPENTIVICDDNGDFSDQMRIITRARLKAAIFISEDPG--V---FRS--ATFPNPGVV  331 (649)
T ss_dssp             EEECCTTTTTCCCHHHHTTS-SSGGGCEEEECCCSCHHHHHHHHHHHTCSEEEEECCCGG--G---GGC--CCCCSCEEE
T ss_pred             eeEecccccccccccccccc-cccCCcEEEEeCCCccHHHHHHHHHhcCceEEEEecCcc--c---ccc--ccCcCCEEE
Confidence            45555566789875322211 112789999999999999999999999999999999752  1   111  224789999


Q ss_pred             eehhhhhhhhhhcccC
Q 018364          203 VSLETGVYLKEHARGE  218 (357)
Q Consensus       203 is~~~G~~L~~~l~~~  218 (357)
                      |+.++|+.|+++++..
T Consensus       332 v~~~~g~~i~~yi~s~  347 (649)
T 3i6s_A          332 VNKKEGKQVINYVKNS  347 (649)
T ss_dssp             ECHHHHHHHHHHHHTC
T ss_pred             EcHHHHHHHHHHHhcC
Confidence            9999999999988654

>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=97.83  E-value=3.5e-05  Score=76.55  Aligned_cols=73  Identities=19%  Similarity=0.233  Sum_probs=56.7

Q ss_pred             CCcceEEEEEcCCC-----ChHHHHHHHHHcCCcEEEEecccCcccccc--cccCCCcceeeEEEeehhhhhhhhhhccc
Q 018364          145 ADHINFVLIVRGQC-----IFEDKIRNAQAAGYRAAIVYNDREKGSLVS--MTASHEGVKVHAIFVSLETGVYLKEHARG  217 (357)
Q Consensus       145 ~~~~~I~LV~RG~C-----sF~~K~~~Aq~aGA~avIv~~~~~~~~~~~--m~~~~~~i~Ip~v~is~~~G~~L~~~l~~  217 (357)
                      ..+++|+|++||.|     .|.+|+.+++++||+++|||||.+......  .........||+++|+.++|+.|++++..
T Consensus       271 ~~~gkivl~~rg~~~~~~~~~~~~~~~~~~aGa~gvii~~~~~~~g~~~~~~~~~~~~~~~p~~~v~~~~g~~l~~~~~~  350 (441)
T 1y9z_A          271 NMANKICLVERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSVDRATGLALKAKLGQ  350 (441)
T ss_dssp             CCTTEEEEEECCSCSSSSCTHHHHHHHHHHTTCSEEEEECCTTSCSCCCCEEECTTCCCCSCEEEECHHHHHHHHTTTTS
T ss_pred             CccccEEEEeccccCcccccHHHHHHHHHhcCCeEEEEEeCCCccccccccccccccCccccEEEEeHHHHHHHHHHhcC
Confidence            35789999999987     899999999999999999999864322110  11122335899999999999999987744

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=97.69  E-value=1.9e-05  Score=72.22  Aligned_cols=51  Identities=22%  Similarity=0.554  Sum_probs=41.6

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCC-CCCCcccccCcCC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG-TFCPVCKHDMRNN  349 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~-~~CPlCR~~i~~~  349 (357)
                      ....|.||.+-...|..+.  .|+|.||..|++.|++.++ ..||.|+...+..
T Consensus       179 ~i~~C~iC~~iv~~g~~C~--~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCEECS--SSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCCcccC--ccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            4679999999999874433  3999999999999998753 4699999987554

>1xf1_A C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {Streptococcus pyogenes} PDB: 3eif_A*

Probab=97.67  E-value=6e-05  Score=81.62  Aligned_cols=66  Identities=30%  Similarity=0.498  Sum_probs=54.5

Q ss_pred             CCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcceeeEEEeehhhhhhhhh
Q 018364          145 ADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKE  213 (357)
Q Consensus       145 ~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~  213 (357)
                      ...++|+|++||.|+|.+|+.+++++||.++|+||+..+...+.+.   ....||+++|+.++|+.|+.
T Consensus       278 ~v~Gkivl~~rg~~~~~~k~~~~~~~Ga~gvi~~n~~~~~~~~~~~---~~~~iP~~~i~~~~g~~l~~  343 (926)
T 1xf1_A          278 DVKGKIALIERGDIDFKDKIAKAKKAGAVGVLIYDNQDKGFPIELP---NVDQMPAAFISRKDGLLLKD  343 (926)
T ss_dssp             TCTTSEEEEECCSSCHHHHHHHHHHTTCSEEEEECSSTTCCCEECC---CSTTCCEEEECHHHHHHHHH
T ss_pred             hcCCeEEEEECCCCCHHHHHHHHHhCCCcEEEEEecCCCCcccccC---ccccccEEEEeHHHHHHHHh
Confidence            3578999999999999999999999999999999986543333221   23579999999999998874

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=93.95  E-value=0.049  Score=39.38  Aligned_cols=50  Identities=26%  Similarity=0.524  Sum_probs=35.2

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~~i~  347 (357)
                      ......|.||-+   .++.|.--.|...||..|+++-|...   .=.||.|+.+..
T Consensus         9 ~~~~~~C~vC~~---~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C            9 LAPGARCGVCGD---GTDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             CCTTCCCTTTSC---CTTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCCCcCCCCC---CCeEEECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            344568999974   34444333589999999999887763   226999986543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=92.93  E-value=0.053  Score=42.06  Aligned_cols=34  Identities=15%  Similarity=0.444  Sum_probs=26.7

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHH
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSW  331 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~W  331 (357)
                      ...|.||+++|...-...-++|+|.|+..|+..+
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            4689999988644433445899999999999983

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=87.68  E-value=0.14  Score=37.71  Aligned_cols=54  Identities=19%  Similarity=0.401  Sum_probs=35.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc---CCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK---WGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~---~~~~CPlCR~~i~~  348 (357)
                      ..+...|.||-.....+..|.-=-|.--||..|+..-...   ..-.||.|+..+..
T Consensus        15 ~~~~~~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           15 GNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             SCEEECBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCCCcCCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            3445679999887543223332348999999999764433   23469999876643

>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=87.33  E-value=0.18  Score=35.79  Aligned_cols=50  Identities=26%  Similarity=0.475  Sum_probs=34.7

Q ss_pred             CCCcccccccccccCCC-ceEEeCCCCccchhHHHHHHh----cCCCCCCccccc
Q 018364          296 HGGETCAICLEDYQDGE-KLKVLSCKHEFHASCVDSWLT----KWGTFCPVCKHD  345 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~-~vr~LpC~H~FH~~CI~~Wl~----~~~~~CPlCR~~  345 (357)
                      .+...|+||...+.+++ .|.--.|..-||..|+..-..    .....||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            45678999999886543 344345899999999864322    134579999763

>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=86.62  E-value=0.51  Score=35.54  Aligned_cols=36  Identities=19%  Similarity=0.520  Sum_probs=24.5

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHH
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSW  331 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~W  331 (357)
                      ...++.|.||- -|..++...-=-|+-+||..|+++=
T Consensus        12 ~~~D~~C~VC~-~~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           12 VVNDEMCDVCE-VWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTTC-CCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCcccCccc-cccccceeccccccccccHhhcccc
Confidence            44678999994 4444442222237999999999984

>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=86.57  E-value=0.22  Score=39.44  Aligned_cols=49  Identities=29%  Similarity=0.601  Sum_probs=33.1

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc---CCCCCCccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK---WGTFCPVCK  343 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~---~~~~CPlCR  343 (357)
                      ...++.|.||.+.-+..+.|.--.|...||..|++..+..   ..-.||.|+
T Consensus         4 ~~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            4567899999886433333444568999999999887653   222466664

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.87  E-value=0.58  Score=37.13  Aligned_cols=48  Identities=23%  Similarity=0.439  Sum_probs=31.0

Q ss_pred             CCCcccccccccc------cCCCceEEeCCCCccchhHHHH------HHhcCCCCCCccc
Q 018364          296 HGGETCAICLEDY------QDGEKLKVLSCKHEFHASCVDS------WLTKWGTFCPVCK  343 (357)
Q Consensus       296 ~~~~~CaICLe~f------~~~~~vr~LpC~H~FH~~CI~~------Wl~~~~~~CPlCR  343 (357)
                      .....|.+|+..-      +.++-|.--.|+..||..|++.      -+...+-.||.|+
T Consensus         3 ~p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            3 EPIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CCCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             ccCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            3467899999863      2234444456999999999953      2333333477774

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=85.76  E-value=0.39  Score=33.86  Aligned_cols=47  Identities=26%  Similarity=0.638  Sum_probs=32.3

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc---CCCCCCcccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK---WGTFCPVCKH  344 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~---~~~~CPlCR~  344 (357)
                      ......|.||-+.   ++.+.--.|...||..|+++=+..   ..-.||.|+.
T Consensus         8 ~~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            8 TDHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             SCCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            4456799999863   443333358889999999975443   1236999975

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=85.62  E-value=0.2  Score=43.55  Aligned_cols=49  Identities=22%  Similarity=0.552  Sum_probs=34.3

Q ss_pred             CcccccccccccCCC----ceEEeCCCCccchhHHHH------HHh----cCCCCCCcccccC
Q 018364          298 GETCAICLEDYQDGE----KLKVLSCKHEFHASCVDS------WLT----KWGTFCPVCKHDM  346 (357)
Q Consensus       298 ~~~CaICLe~f~~~~----~vr~LpC~H~FH~~CI~~------Wl~----~~~~~CPlCR~~i  346 (357)
                      +..|+||...|.+++    -|.---|.+-||..|+..      =+.    .....||.|+..-
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            467999999999886    233335899999999642      111    1245799998653

>3vta_A Cucumisin; subtilisin-like fold, serine protease, hydrolase; HET: DFP NAG FUC BMA MAN; 2.75A {Cucumis melo}

Probab=84.13  E-value=1  Score=46.28  Aligned_cols=60  Identities=5%  Similarity=-0.082  Sum_probs=47.5

Q ss_pred             CcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccccccccCCCcceeeEEEeehhhhhhhhhhcc
Q 018364          146 DHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSLVSMTASHEGVKVHAIFVSLETGVYLKEHAR  216 (357)
Q Consensus       146 ~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~~~m~~~~~~i~Ip~v~is~~~G~~L~~~l~  216 (357)
                      ..++|+|.+|   .|..|..+++.+||.++|++++..+.        .....+|.+.++.++|..++.++.
T Consensus       280 v~gkivl~~~---~~~~~~~~~~~~Ga~gvi~~~~~~~~--------~~~~~lP~~~v~~~~g~~i~~~~~  339 (621)
T 3vta_A          280 LKGKIVVCEA---SFGPHEFFKSLDGAAGVLMTSNTRDY--------ADSYPLPSSVLDPNDLLATLRYIY  339 (621)
T ss_dssp             TTTSEEECSS---CCCHHHHHHHHTTCSEEEEECSCCSS--------CCCCSSSEEEECHHHHHHHHHHHH
T ss_pred             ccceEEEEec---CCChhHHhhhhcceeEEEEEecCCCc--------ccccccceEEECHHHHHHHHHHHh
Confidence            4689999865   46788999999999999999975421        123478999999999999987654

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=83.58  E-value=0.6  Score=35.60  Aligned_cols=50  Identities=20%  Similarity=0.419  Sum_probs=33.7

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccccCc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKHDMR  347 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~~i~  347 (357)
                      ....+.|.+|.+.   ++-+.--.|.-.||..|+++=+...   .-.||.|+..-.
T Consensus        22 d~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~   74 (88)
T 1fp0_A           22 DDSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   74 (88)
T ss_dssp             SSSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCc
Confidence            4557799999864   4433333478899999998755441   225999986543

>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=82.70  E-value=0.39  Score=33.89  Aligned_cols=49  Identities=29%  Similarity=0.622  Sum_probs=32.4

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccccC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKHDM  346 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~~i  346 (357)
                      ......|.||-+   .++.|.--.|...||..|+++=+...   .-.||.|+...
T Consensus         6 d~~~~~C~vC~~---~g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKD---GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCC---CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCC---CCCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            445678999975   24433333488899999998644431   22599997643

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.81  E-value=0.19  Score=34.84  Aligned_cols=47  Identities=26%  Similarity=0.646  Sum_probs=31.8

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccc
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKH  344 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~  344 (357)
                      ......|.||-+.   ++.|.--.|...||..|+++=+...   .-.||.|+.
T Consensus         6 ~~~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            4557789999874   4444433588999999998644331   225888864

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=81.70  E-value=0.54  Score=31.64  Aligned_cols=45  Identities=24%  Similarity=0.594  Sum_probs=29.5

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccc
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKH  344 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~  344 (357)
                      .|.||.+.-..++.|.--.|...||..|+++=+...   .-.||.|+.
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            588898764444434333589999999997633331   225999964

>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=81.25  E-value=0.24  Score=35.31  Aligned_cols=52  Identities=21%  Similarity=0.529  Sum_probs=34.1

Q ss_pred             CCCcccccccccccC--CCceEEeCCCCccchhHHHHHHhc------CCCCCCcccccCc
Q 018364          296 HGGETCAICLEDYQD--GEKLKVLSCKHEFHASCVDSWLTK------WGTFCPVCKHDMR  347 (357)
Q Consensus       296 ~~~~~CaICLe~f~~--~~~vr~LpC~H~FH~~CI~~Wl~~------~~~~CPlCR~~i~  347 (357)
                      .+...|.||......  ++.|.---|.-.||..|+.+=+..      ..=.||.|+....
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            457899999987543  322322348999999998864321      2335999976543

---

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	357
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-13
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-11
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	8e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	4e-08
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	7e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	1e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-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 = 62.2 bits (151), Expect = 2e-13
 Identities = 23/49 (46%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 298 GETCAICLEDYQDGEKLKVL-SCKHEFHASCVDSWLTKWGTFCPVCKHD 345
           G  CA+CL + +DGE+ + L  C H FHA CVD WL    T CP+C+  
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-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 = 57.3 bits (138), Expect = 2e-11
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)

Query: 299 ETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
           + C IC E+ +D   +K+  C H    SC+ SW    G  CP C+ +++
Sbjct: 24  QLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 69

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 56.1 bits (135), Expect = 3e-11
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR 347
            E C ICLED  +      L C H F   C+  W+ +  T CP+CK  + 
Sbjct: 5   AERCPICLEDPSNYSM--ALPCLHAFCYVCITRWIRQNPT-CPLCKVPVE 51

>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 = 55.2 bits (132), Expect = 8e-11
 Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 2/53 (3%)

Query: 299 ETCAICLEDYQDGEKLKVL--SCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN 349
           + C  C         LK++   C H    SCVD    +    CP C   +R +
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS 56

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 3e-10
 Identities = 9/50 (18%), Positives = 18/50 (36%), Gaps = 1/50 (2%)

Query: 301 CAICLEDYQDGEK-LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN 349
           C +C+E  +  +      +C ++    C     T     CP C+     +
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 47.2 bits (112), Expect = 4e-08
 Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 7/46 (15%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHD 345
            C  C  + +     K+L C H   + C+++   +    CP+C+  
Sbjct: 8   RCQQCQAEAKCP---KLLPCLHTLCSGCLEASGMQ----CPICQAP 46

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 15/71 (21%), Positives = 21/71 (29%), Gaps = 16/71 (22%)

Query: 290 ASSSQCHGGETCAICLEDYQDGEK---------------LKVLSCKHEFHASCVDSWLTK 334
           A  +     + CAIC     D                  +    C H FH  C+  WL  
Sbjct: 13  ALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT 72

Query: 335 WGTFCPVCKHD 345
               CP+   +
Sbjct: 73  RQV-CPLDNRE 82

>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 = 43.7 bits (102), Expect = 7e-07
 Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 3/49 (6%)

Query: 299 ETCAICLEDYQDGEKL--KVLSCKHEFHASCVDSWL-TKWGTFCPVCKH 344
             C IC E+  +               H SC+ +WL     T C +C  
Sbjct: 7   PVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGV 55

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLT--KWGTFCPVCKHDMRNNS 350
            C ICLE  ++        C H F   C+   L   K  + CP+CK+D+   S
Sbjct: 23  ECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS 72

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKH 344
           +C IC     D       SCKH F   C+   L   G++CP C++
Sbjct: 25  SCQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRY 66

>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 = 43.1 bits (101), Expect = 3e-06
 Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 7/54 (12%)

Query: 297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLT------KWGTF-CPVCK 343
           G   C +CL +Y   +   +  C+  F   C+  ++             CP   
Sbjct: 4   GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 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 = 40.0 bits (92), Expect = 5e-05
 Identities = 14/69 (20%), Positives = 20/69 (28%), Gaps = 19/69 (27%)

Query: 294 QCHGGETCAICLEDY---------------QDGEKLKVLSCKHEFHASCVDSWLTK---- 334
           +    E C IC+E                       ++  C H FH  C+ +        
Sbjct: 21  KVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD 80

Query: 335 WGTFCPVCK 343
               CP CK
Sbjct: 81  GSLQCPSCK 89

>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 = 2e-04
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 288 SSASSSQCHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFC--PVCKHD 345
           S A+  +      C+ C    ++   L    C+H F ++CV   +      C  P    D
Sbjct: 12  SRAALDRLEKLLRCSRCTNILREPVCL--GGCEHIFCSNCVSDCIGTGCPVCYTPAWIQD 69

Query: 346 MRNN 349
           ++ N
Sbjct: 70  LKIN 73

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	357
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.7
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.57
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.52
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.48
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.47
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.45
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.42
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.24
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.19
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.18
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.15
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.12
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.96
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.93
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.9
d1de4c2	193	Transferrin receptor ectodomain, apical domain {Hu	98.81
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.61
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.45
d3bi1a2	233	Glutamate carboxypeptidase II {Human (Homo sapiens	98.44
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	92.62
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	91.74
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	90.88
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	88.12
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	88.12
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	86.23
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	83.37
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	80.18

>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=99.70  E-value=3e-18  Score=120.53  Aligned_cols=51  Identities=43%  Similarity=1.051  Sum_probs=46.0

Q ss_pred             CCCcccccccccccCCCceEEeC-CCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          296 HGGETCAICLEDYQDGEKLKVLS-CKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~Lp-C~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      +++.+|+|||++|+.++.++++| |+|.||.+||++|+++++ +||+||++|.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~-~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCC-SCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCC-cCCCCCCEeE
Confidence            45678999999999999998886 999999999999999977 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=99.57  E-value=2.7e-16  Score=109.14  Aligned_cols=50  Identities=18%  Similarity=0.493  Sum_probs=43.3

Q ss_pred             ccccccccccCCCc-eEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          300 TCAICLEDYQDGEK-LKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       300 ~CaICLe~f~~~~~-vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      +|+||+++|+.++. ++.++|+|.||.+||++|++..+.+||+||+++.++
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            79999999988765 456689999999999999998766799999998753

>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=99.52  E-value=3e-15  Score=109.60  Aligned_cols=49  Identities=35%  Similarity=0.798  Sum_probs=43.0

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRN  348 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~  348 (357)
                      ..++|+||++.|.+  .++.+||+|.||.+||.+|+++++ +||+||+++..
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~~~-~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNP-TCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSC-STTTTCCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHhCC-cCCCCCcchHh
Confidence            46789999999865  467899999999999999999977 59999999853

>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=99.48  E-value=1.3e-14  Score=116.62  Aligned_cols=58  Identities=24%  Similarity=0.484  Sum_probs=45.5

Q ss_pred             CCcccccccccccC---------------CCceEEeCCCCccchhHHHHHHhcCC----CCCCcccccCcCCCCCCC
Q 018364          297 GGETCAICLEDYQD---------------GEKLKVLSCKHEFHASCVDSWLTKWG----TFCPVCKHDMRNNSESNE  354 (357)
Q Consensus       297 ~~~~CaICLe~f~~---------------~~~vr~LpC~H~FH~~CI~~Wl~~~~----~~CPlCR~~i~~~~~~~~  354 (357)
                      .++.|+||++++..               .+.++.++|+|.||.+||+.||+..+    .+||+||+.+..+...++
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~qP  100 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQP  100 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCT
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCCC
Confidence            45789999999854               23467789999999999999998643    359999998877654433

>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=99.47  E-value=1.3e-14  Score=105.16  Aligned_cols=54  Identities=28%  Similarity=0.543  Sum_probs=43.5

Q ss_pred             CCcccccccccccCC--CceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCC
Q 018364          297 GGETCAICLEDYQDG--EKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNS  350 (357)
Q Consensus       297 ~~~~CaICLe~f~~~--~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~  350 (357)
                      ++.+|+||++++..+  ..+.+++|+|.||.+||..|+++.+..||+||+.+..++
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            357999999986443  345677899999999999999876556999999986543

>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=99.45  E-value=2e-14  Score=110.39  Aligned_cols=50  Identities=28%  Similarity=0.634  Sum_probs=42.1

Q ss_pred             CCcccccccccccCCC---------------ceEEeCCCCccchhHHHHHHhcCCCCCCcccccCc
Q 018364          297 GGETCAICLEDYQDGE---------------KLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMR  347 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~---------------~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~  347 (357)
                      ..+.|+||++++....               .+..++|+|+||.+||++||+.++ +||+||++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ-VCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCS-BCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCC-cCCCCCCccc
Confidence            4567999999886532               367889999999999999999987 5999999864

>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=99.42  E-value=6.3e-14  Score=105.44  Aligned_cols=49  Identities=33%  Similarity=0.805  Sum_probs=42.1

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++++++   .+++||||.||.+||+.||..+...||+||.+|...
T Consensus        23 ~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            4579999998765   678999999999999999987655699999999754

>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=99.24  E-value=8.2e-13  Score=92.54  Aligned_cols=50  Identities=22%  Similarity=0.567  Sum_probs=41.0

Q ss_pred             CCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCCCCCC
Q 018364          297 GGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNNSESN  353 (357)
Q Consensus       297 ~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~~~~~  353 (357)
                      +.-+|+||++.|++.   ++|||||.||..||+.|    +..||+||+++....+..
T Consensus         5 ~~l~C~IC~~~~~~p---~~lpCgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~~~~   54 (56)
T d1bora_           5 QFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGADTP   54 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCSSCC
T ss_pred             CCCCCcccCcccCCC---EEecCCCHHhHHHHHcC----CCcCcCCCCcccCCCCCC
Confidence            345999999999764   57899999999999764    446999999998776554

>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=99.19  E-value=3.6e-12  Score=96.98  Aligned_cols=49  Identities=31%  Similarity=0.609  Sum_probs=42.1

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++.+++   ..+++|||.|+..||.+|++.++..||+||.++.+.
T Consensus        23 ~l~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          23 SISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CcCCccCCcchhc---ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            4589999999876   367899999999999999987665799999988654

>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=99.18  E-value=2.5e-12  Score=90.05  Aligned_cols=47  Identities=15%  Similarity=0.251  Sum_probs=39.6

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .|+||++.+++  .+....|||+||++||.+||+++++ ||+||+++..+
T Consensus         2 ~C~Ic~~~~~~--Pv~~~~cGh~fc~~cI~~~l~~~~~-CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRR--PVLSPKSRTIFEKSLLEQYVKDTGN-DPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSS--EEEETTTTEEEEHHHHHHHHHHHSB-CTTTCCBCCGG
T ss_pred             CCccCCchHHh--cCccCCCCCcccHHHHHHHHhhccC-CCccCCcCCHH
Confidence            59999999876  3433359999999999999999874 99999988764

>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=99.15  E-value=9.5e-12  Score=88.22  Aligned_cols=51  Identities=27%  Similarity=0.615  Sum_probs=39.6

Q ss_pred             CCCCcccccccccccCCCceEEeCC-----CCccchhHHHHHHhc-CCCCCCcccccCcC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSC-----KHEFHASCVDSWLTK-WGTFCPVCKHDMRN  348 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC-----~H~FH~~CI~~Wl~~-~~~~CPlCR~~i~~  348 (357)
                      .++...|.||++++...   .+.||     +|.||..||..|+.. ++.+||+||+++..
T Consensus         3 ded~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            34577999999998654   23444     599999999999976 34569999998753

>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=99.12  E-value=1.5e-11  Score=96.75  Aligned_cols=49  Identities=31%  Similarity=0.633  Sum_probs=41.0

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCC--CCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWG--TFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~--~~CPlCR~~i~~~  349 (357)
                      .-.|+||++.|++.   ..+||||.||..||..|++.++  ..||+||..+..+
T Consensus        21 ~l~CpIC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (103)
T d1jm7a_          21 ILECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (103)
T ss_dssp             HTSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CcCCCccCchhCCe---EEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChh
Confidence            35799999999764   4589999999999999998754  3699999998654

>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=98.96  E-value=1.8e-10  Score=86.15  Aligned_cols=51  Identities=14%  Similarity=0.215  Sum_probs=43.6

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      .+...|+||++-|++.   .+++|||.|++.||..|+..++.+||+||..+...
T Consensus         5 P~~l~CpIc~~l~~dP---v~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           5 PDYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             CSTTBCTTTCSBCSSE---EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             CccccCcCcCchhhhh---cccCCcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            3467999999999874   47899999999999999998776799999988643

>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=98.93  E-value=3.4e-10  Score=84.20  Aligned_cols=52  Identities=21%  Similarity=0.389  Sum_probs=44.3

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++-|++.   .+++|||.|++.||..|+..+...||.|+..+...
T Consensus         5 iP~~l~CpIc~~~m~dP---V~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDP---VIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSE---EEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CCccCCCcCcCchhhCc---eEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            34567999999999774   47899999999999999998766799999988654

>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=98.90  E-value=1.3e-10  Score=90.22  Aligned_cols=47  Identities=23%  Similarity=0.506  Sum_probs=38.9

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ...|+||++.|.+.  +...+|||.||..||..|+..   .||.||.++...
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~CgH~fC~~Ci~~~~~~---~CP~Cr~~~~~~   68 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGGCEHIFCSNCVSDCIGT---GCPVCYTPAWIQ   68 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCSSSCCBCTTTGGGGTTT---BCSSSCCBCSCS
T ss_pred             cCCCccCCchhhcC--ceeCCCCCchhHHHHHHHHhc---cccccCCcCchh
Confidence            45899999999764  555689999999999999854   499999887653

>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=98.81  E-value=4.3e-09  Score=90.90  Aligned_cols=107  Identities=17%  Similarity=0.174  Sum_probs=73.0

Q ss_pred             cccccccccCCCCeEEEEeeCCCCCCCCCCCCCCCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCcccc
Q 018364          107 LPAKFAVDVNSSGTCGALHVADPADACSPLSNPVASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREKGSL  186 (357)
Q Consensus       107 ~~a~Fg~~~~~~~~~g~l~~~~p~~aC~~~~~~~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~~~~  186 (357)
                      .+..|-.--+...++|.|++++-.   ..-+.. ....+..++|+|++||+++|.+|+++||++||+|||||+|..+.+.
T Consensus        26 ~p~~~~ays~~G~v~g~lVy~n~G---~~~Df~-~L~~~v~GkI~l~r~G~~~~~~Kv~~A~~~GA~gviiysDp~d~~~  101 (193)
T d1de4c2          26 NPGGYVAYSKAATVTGKLVHANFG---TKKDFE-DLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPI  101 (193)
T ss_dssp             CCSCCEETCCCEEEEECEEECSTT---CHHHHH-TCSSCCTTSEEEEESCSSCHHHHHHHHHHTTCCCEEEECCTTTSCC
T ss_pred             CCCceeccCCCCceeEEEEEccCC---CHHHHH-HhccccCceEEEEeCCCCCHHHHHHHHHHcCceEEEEecCccccCC
Confidence            455565555566788999886431   111110 0112357899999999999999999999999999999987433111


Q ss_pred             c----------c-cccCC-------------------CcceeeEEEeehhhhhhhhhhccc
Q 018364          187 V----------S-MTASH-------------------EGVKVHAIFVSLETGVYLKEHARG  217 (357)
Q Consensus       187 ~----------~-m~~~~-------------------~~i~Ip~v~is~~~G~~L~~~l~~  217 (357)
                      .          . ..+|.                   .-..||+.-|+.+|++.|++.|.+
T Consensus       102 ~~~~~~~~g~~~~~~GDPlTPg~ps~~~~~~~~~~~~~lP~IP~~PIS~~dA~~lL~~L~G  162 (193)
T d1de4c2         102 VNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEG  162 (193)
T ss_dssp             SCTTCCCCEECCSSSSCTTSTTSCCCGGGTCCSCCCTTSCSSCEEECCHHHHHHHHTTBCS
T ss_pred             cCcccccccccccCCCCCCCCCcccccccccCccccCCCCcCCeeeCCHHHHHHHHHHcCC
Confidence            0          0 01110                   114799999999999999998865

>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=98.61  E-value=5.4e-09  Score=80.14  Aligned_cols=48  Identities=21%  Similarity=0.597  Sum_probs=39.5

Q ss_pred             CCCcccccccccccCCCceEEeCCCCccchhHHHHHHhcC-------CCCCCccc
Q 018364          296 HGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW-------GTFCPVCK  343 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~-------~~~CPlCR  343 (357)
                      ....+|+||++++...+.++.++|+|.||.+||..|++..       ...||.|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            3467999999999887777777899999999999999752       22599864

>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=98.45  E-value=7.7e-08  Score=74.33  Aligned_cols=51  Identities=14%  Similarity=-0.018  Sum_probs=42.3

Q ss_pred             CCCCcccccccccccCCCceEEeCCC-CccchhHHHHHHhcCCCCCCcccccCcCC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCK-HEFHASCVDSWLTKWGTFCPVCKHDMRNN  349 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~-H~FH~~CI~~Wl~~~~~~CPlCR~~i~~~  349 (357)
                      ..+...|+||++-|.+.   .++||+ |.|.+.||..||+.+. .||+||.++...
T Consensus        19 ~P~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~-~~P~~~~~l~~~   70 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQ-TDPFNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSC-BCTTTCSBCCTT
T ss_pred             CcHHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcC-Ccccccccccch
Confidence            34468999999999885   578865 5899999999999876 599999998653

>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=98.44  E-value=2.1e-07  Score=82.47  Aligned_cols=101  Identities=17%  Similarity=0.132  Sum_probs=68.6

Q ss_pred             CCCCeEEEEeeCCCCCCCCCCCCC---CCCCCCCcceEEEEEcCCCChHHHHHHHHHcCCcEEEEecccCc---------
Q 018364          116 NSSGTCGALHVADPADACSPLSNP---VASNDADHINFVLIVRGQCIFEDKIRNAQAAGYRAAIVYNDREK---------  183 (357)
Q Consensus       116 ~~~~~~g~l~~~~p~~aC~~~~~~---~~~~~~~~~~I~LV~RG~CsF~~K~~~Aq~aGA~avIv~~~~~~---------  183 (357)
                      ....++|.||+++-   |..-+..   .....+..++|+|+++|+++|.+|+++||++||+|||||+|..+         
T Consensus        49 ~~G~v~g~~Vyvny---G~~~Df~~L~~~~gi~~~gkIvl~ryG~~~~~~Kv~~A~~~GA~GviiysDP~d~~~~g~~~y  125 (233)
T d3bi1a2          49 PQGMPEGDLVYVNY---ARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSY  125 (233)
T ss_dssp             CCBCCEECEEECTT---CCHHHHHHHHHTSCCCCTTCEEEEECCSSCHHHHHHHHHHTTCSEEEEECCHHHHCCTTCCBT
T ss_pred             CCCceeEEEEEecC---CcHHHHHHHHHhcCCcccceEEEEeCCCCchhHHHHHHHHcCceEEEEecChHHccCcccccc
Confidence            34567888887653   2221110   01123457899999999999999999999999999999997311         


Q ss_pred             --------cc----ccc-c--ccCC--------------------CcceeeEEEeehhhhhhhhhhcccCC
Q 018364          184 --------GS----LVS-M--TASH--------------------EGVKVHAIFVSLETGVYLKEHARGET  219 (357)
Q Consensus       184 --------~~----~~~-m--~~~~--------------------~~i~Ip~v~is~~~G~~L~~~l~~~~  219 (357)
                              ..    .+. +  .+|.                    .-..||+.=|+.+|++.|++.|.+..
T Consensus       126 P~~~~~p~~~vqrgsv~~~~~~GDplTPg~ps~~~~~r~~~~~~~~lP~IP~~PIS~~dA~~lL~~L~G~~  196 (233)
T d3bi1a2         126 PDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSA  196 (233)
T ss_dssp             TSSSBCCTTCCCCEECCCCTTCCSTTCTTSCCCTTCCCCCGGGCSSCCSSCEEEECHHHHHHHHTTBCBBC
T ss_pred             cCCccCCCCceeEeeeeecCCCCCCCCCCCCCCCCCcccChhHhcCCCCCceeccCHHHHHHHHHHcCCCC
Confidence                    00    000 0  1110                    11489999999999999999887643

>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=92.62  E-value=0.019  Score=37.52  Aligned_cols=45  Identities=24%  Similarity=0.594  Sum_probs=30.4

Q ss_pred             ccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccc
Q 018364          300 TCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKH  344 (357)
Q Consensus       300 ~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~  344 (357)
                      .|.||-..-..++.|.--.|...||..|+++-+...   .-.||.||.
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            588897664444333222489999999999865542   225999975

>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=91.74  E-value=0.025  Score=38.68  Aligned_cols=50  Identities=26%  Similarity=0.478  Sum_probs=34.9

Q ss_pred             CCCcccccccccccCCCceE-EeCCCCccchhHHHHH---Hhc-CCCCCCccccc
Q 018364          296 HGGETCAICLEDYQDGEKLK-VLSCKHEFHASCVDSW---LTK-WGTFCPVCKHD  345 (357)
Q Consensus       296 ~~~~~CaICLe~f~~~~~vr-~LpC~H~FH~~CI~~W---l~~-~~~~CPlCR~~  345 (357)
                      .....|.||.+.+.+++... --.|+.-||..|++.=   ... .+..||.|+..
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            45679999999887766533 3359999999998631   111 24569999853

>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=90.88  E-value=0.053  Score=37.79  Aligned_cols=51  Identities=22%  Similarity=0.437  Sum_probs=32.9

Q ss_pred             CcccccccccccCCCceEEeCCCCccchhHHHHHHhcC---CCCCCcccccCcCCCC
Q 018364          298 GETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTKW---GTFCPVCKHDMRNNSE  351 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~~---~~~CPlCR~~i~~~~~  351 (357)
                      ...|.||-+   .++.|.-=.|...||..|+.+.+...   .-.||.|+..-..++.
T Consensus         7 c~~C~~C~~---~~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~~~   60 (70)
T d1fp0a1           7 ATICRVCQK---PGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEE   60 (70)
T ss_dssp             SSCCSSSCS---SSCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCCS
T ss_pred             CCCCCCCCC---cCEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCccCcc
Confidence            456777753   45433333489999999999876552   2359999765544433

>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=88.12  E-value=0.2  Score=35.71  Aligned_cols=33  Identities=24%  Similarity=0.674  Sum_probs=26.0

Q ss_pred             CCCCcccccccccccCCCceEEeC---CCCccchhHHHHH
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLS---CKHEFHASCVDSW  331 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~Lp---C~H~FH~~CI~~W  331 (357)
                      ...++.|.|| +-|...+.   +|   |+-+||..|+.+=
T Consensus        12 v~~D~mC~vC-~v~t~~~l---~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESL---FPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCC---SSCSSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Ccccccce---ecceeecchhhHHHHHHh
Confidence            5567899999 77776653   46   6899999999885

>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=88.12  E-value=0.077  Score=37.66  Aligned_cols=48  Identities=17%  Similarity=0.412  Sum_probs=31.3

Q ss_pred             CcccccccccccCCCceEEe--CCCCccchhHHHH----HHhc----CCCCCCcccccC
Q 018364          298 GETCAICLEDYQDGEKLKVL--SCKHEFHASCVDS----WLTK----WGTFCPVCKHDM  346 (357)
Q Consensus       298 ~~~CaICLe~f~~~~~vr~L--pC~H~FH~~CI~~----Wl~~----~~~~CPlCR~~i  346 (357)
                      ...| ||-+....++.+..-  -|..-||..|+.-    .-..    ....||.|+..-
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            4578 999887765544333  3999999999842    1110    135799998644

>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=86.23  E-value=0.08  Score=35.72  Aligned_cols=49  Identities=29%  Similarity=0.607  Sum_probs=32.4

Q ss_pred             CCCCcccccccccccCCCceEEeCCCCccchhHHHHHHhc---CCCCCCcccccC
Q 018364          295 CHGGETCAICLEDYQDGEKLKVLSCKHEFHASCVDSWLTK---WGTFCPVCKHDM  346 (357)
Q Consensus       295 ~~~~~~CaICLe~f~~~~~vr~LpC~H~FH~~CI~~Wl~~---~~~~CPlCR~~i  346 (357)
                      ....+.|.+|.+   .++.|.-=.|.-.||..|++.-+..   ..-.||.|+..-
T Consensus         6 d~~~~~C~~C~~---~g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           6 DHHMEFCRVCKD---GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCC---CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCcCCCcCCCC---CCeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            344568999975   3443333348899999999865554   233699997543

>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=83.37  E-value=0.077  Score=38.44  Aligned_cols=50  Identities=22%  Similarity=0.582  Sum_probs=30.9

Q ss_pred             CcccccccccccCC-CceEEe-CCCCccchhHHHHHHh-----c--CCCCCCcccccCc
Q 018364          298 GETCAICLEDYQDG-EKLKVL-SCKHEFHASCVDSWLT-----K--WGTFCPVCKHDMR  347 (357)
Q Consensus       298 ~~~CaICLe~f~~~-~~vr~L-pC~H~FH~~CI~~Wl~-----~--~~~~CPlCR~~i~  347 (357)
                      ...|.||....... +.+..- -|...||..|+.+-+.     .  ..-.||.|+....
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            45799998654332 223222 4899999999875432     1  1235999975543

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {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 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.18  E-value=1.5  Score=30.59  Aligned_cols=49  Identities=22%  Similarity=0.380  Sum_probs=30.9

Q ss_pred             cccccccccccCCCceE-EeCCCCccchhHHH--HHHhc--CCCCCCcccccCc
Q 018364          299 ETCAICLEDYQDGEKLK-VLSCKHEFHASCVD--SWLTK--WGTFCPVCKHDMR  347 (357)
Q Consensus       299 ~~CaICLe~f~~~~~vr-~LpC~H~FH~~CI~--~Wl~~--~~~~CPlCR~~i~  347 (357)
                      ..|-||-..+..++... -=.|.--||..|+.  ..-..  .+..||.|+....
T Consensus        12 pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          12 PVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            34449998776654332 22489999999985  22111  2357999986543