Citrus Sinensis ID: 028085

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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----
Protein Sequence
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQVHVSG
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHccccEEEEEEcccccccccccccccccEEEEEEcHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHccccEEEEcccccccccccccEEEEccccccccEEEEEccccccccccHHHHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHccccEEEEEEcccccEEEEcccccccEEEEEEEccccHHHHHHHHccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHcccHHHHHHHcccEEEEEccccccccccccEEEEEEccccccEEEEEccccHHHHHcccHHHHcccccccccHHHHHHcccccccccccccc
Coil and Loop (DISEMBL)
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKkspliymtypeganvpaFYVTLETGAylkehargeageccifplsyawNKHVEKIIVWGMLLLFVISIPLLFWFArklypidsprrhrpeqtrqlprstvnalpsfvfssvtsvrchgretLCSICLEdyregenlrvlpcrhefhsscVDSWLirwgtfcpvcrheirrstsnegneqvhvsg
Flexible Loop (DISEMBL)
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPidsprrhrpeqtrqlprstvnalPSFVFSsvtsvrchgRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIrrstsnegneqvhvsg
Low Complexity Region (SEG)
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQVHVSG
Disordered region (IsUnstruct)
*****CNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI******************VNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI****************
Disordered Region (DISOPRED)
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDS*****************NALPSFVFSSV******GRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCR*******************
Disordered Region (DISEMBL)
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPR************STVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR**************
Disordered Region (DISPRO)
***GQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQVHVSG
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	214	2.2.26 [Sep-21-2011]
Q90972	381	E3 ubiquitin-protein liga	yes	no	0.869	0.488	0.281	2e-18
O54965	381	E3 ubiquitin-protein liga	yes	no	0.836	0.469	0.290	7e-18
Q66HG0	380	E3 ubiquitin-protein liga	yes	no	0.836	0.471	0.290	7e-18
Q5RCV8	381	E3 ubiquitin-protein liga	yes	no	0.822	0.461	0.285	2e-17
O43567	381	E3 ubiquitin-protein liga	yes	no	0.822	0.461	0.285	2e-17
Q0VD51	380	E3 ubiquitin-protein liga	yes	no	0.822	0.463	0.285	2e-17
Q9H6Y7	350	E3 ubiquitin-protein liga	no	no	0.850	0.52	0.281	1e-16
Q5XIL0	349	E3 ubiquitin-protein liga	no	no	0.836	0.512	0.271	4e-16
Q91XF4	347	E3 ubiquitin-protein liga	no	no	0.836	0.515	0.276	6e-16
Q8VEM1	419	E3 ubiquitin-protein liga	no	no	0.887	0.453	0.274	3e-14

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

 Score = 92.0 bits (227), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 103/217 (47%), Gaps = 31/217 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
           R +CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct: 99  RLECNFDIKVLNAQRAGYKAAIVHNVDSDD-LISMGSNDIEILKKIDIPSVFIGEASANS 157

Query: 58  LKEHARGEAGECCIF------PLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI 111
           LKE    E G   +       PL Y     +  +I+ G+ L+ ++ I ++  F +  +  
Sbjct: 158 LKEEFTYEKGGHVVLIPEFSLPLEYYL---IPFLIIVGICLILIV-IFMITKFVQDRHRA 213

Query: 112 DSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              R  + +Q ++LP              V   +      +C+ICL++Y +G+ LR+LPC
Sbjct: 214 RRNRLRK-DQLKKLP--------------VHKFKKGDEYDVCAICLDEYEDGDKLRILPC 258

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNE 208
            H +H  CVD WL +    CPVC+ ++  S  +  +E
Sbjct: 259 SHAYHCKCVDPWLTKTKKTCPVCKQKVVPSQGDSDSE 295

E3 ubiquitin-protein ligase. May play a role in controlling cell proliferation, including that of muscle cells.
Gallus gallus (taxid: 9031)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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

 Score = 90.5 bits (223), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 99/210 (47%), Gaps = 31/210 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
           R  CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct: 99  RLDCNFDIKVLNAQRAGYKAAIVHNVDSDD-LISMGSNDIDTLKKIDIPSVFIGESSANS 157

Query: 58  LKEHARGEAGECCIF------PLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI 111
           LK+    E G   I       PL Y     +  +I+ G+ L+ ++ I ++  F +  +  
Sbjct: 158 LKDEFTYEKGGHIILVPELSLPLEYYL---IPFLIIVGICLILIV-IFMITKFVQDRHRN 213

Query: 112 DSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              R  + +Q ++LP              V   +      +C+ICLE+Y +G+ LR+LPC
Sbjct: 214 RRNRLRK-DQLKKLP--------------VHKFKKGDEYDVCAICLEEYEDGDKLRILPC 258

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            H +H  CVD WL +    CPVC+ ++  S
Sbjct: 259 SHAYHCKCVDPWLTKTKKTCPVCKQKVVPS 288

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 = 90.5 bits (223), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 99/210 (47%), Gaps = 31/210 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
           R  CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct: 99  RLDCNFDIKVLNAQRAGYKAAIVHNVDSDD-LISMGSNDIDILKKIDIPSVFIGESSANS 157

Query: 58  LKEHARGEAGECCIF------PLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI 111
           LK+    E G   I       PL Y     +  +I+ G+ L+ ++ I ++  F +  +  
Sbjct: 158 LKDEFTYEKGGHVILVPELSLPLEYYL---IPFLIIVGICLILIV-IFMITKFVQDRHRN 213

Query: 112 DSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              R  + +Q ++LP              V   +      +C+ICLE+Y +G+ LR+LPC
Sbjct: 214 RRNRLRK-DQLKKLP--------------VHKFKKGDEYDVCAICLEEYEDGDKLRILPC 258

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            H +H  CVD WL +    CPVC+ ++  S
Sbjct: 259 SHAYHCKCVDPWLTKTKKTCPVCKQKVVPS 288

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 = 89.4 bits (220), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 31/207 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
           R  CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct: 99  RLDCNFDIKVLNAQRAGYKAAIVHNVDSDD-LISMGSNDIEVLKKIDIPSVFIGESSANS 157

Query: 58  LKEHARGEAGECCIF------PLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI 111
           LK+    E G   I       PL Y     +  +I+ G+ L+ ++ I ++  F +  +  
Sbjct: 158 LKDEFTYEKGGHLILVPEFSLPLEYYL---IPFLIIVGICLILIV-IFMITKFVQDRHRA 213

Query: 112 DSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              R  + +Q ++LP              V   +      +C+ICL++Y +G+ LR+LPC
Sbjct: 214 RRNRLRK-DQLKKLP--------------VHKFKKGDEYDVCAICLDEYEDGDKLRILPC 258

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEI 198
            H +H  CVD WL +    CPVC+ ++
Sbjct: 259 SHAYHCKCVDPWLTKTKKTCPVCKQKV 285

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 = 89.4 bits (220), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 31/207 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
           R  CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct: 99  RLDCNFDIKVLNAQRAGYKAAIVHNVDSDD-LISMGSNDIEVLKKIDIPSVFIGESSANS 157

Query: 58  LKEHARGEAGECCIF------PLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI 111
           LK+    E G   I       PL Y     +  +I+ G+ L+ ++ I ++  F +  +  
Sbjct: 158 LKDEFTYEKGGHLILVPEFSLPLEYYL---IPFLIIVGICLILIV-IFMITKFVQDRHRA 213

Query: 112 DSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              R  + +Q ++LP              V   +      +C+ICL++Y +G+ LR+LPC
Sbjct: 214 RRNRLRK-DQLKKLP--------------VHKFKKGDEYDVCAICLDEYEDGDKLRILPC 258

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEI 198
            H +H  CVD WL +    CPVC+ ++
Sbjct: 259 SHAYHCKCVDPWLTKTKKTCPVCKQKV 285

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

 Score = 89.0 bits (219), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 31/207 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
           R  CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct: 99  RLDCNFDEKVLNAQRAGYKAAIVHNVDSDD-LISMGSNDIEVLKKIDIPSVFIGESSANS 157

Query: 58  LKEHARGEAGECCIF------PLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPI 111
           LK+    E G   I       PL Y     +  +I+ G+ L+ ++ I ++  F +  +  
Sbjct: 158 LKDEFTYEKGGHIILVPEFSLPLEYYL---IPFLIIVGICLILIV-IFMITKFVQDRHRA 213

Query: 112 DSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              R  + +Q ++LP              V   +      +C+ICL++Y +G+ LR+LPC
Sbjct: 214 RRNRLRK-DQLKKLP--------------VHKFKKGDEYDVCAICLDEYEDGDKLRILPC 258

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEI 198
            H +H  CVD WL +    CPVC+ ++
Sbjct: 259 SHAYHCKCVDPWLTKTKKTCPVCKQKV 285

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

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 99/213 (46%), Gaps = 31/213 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGAN----VPAFYVTLETGAYL 58
           R  CNF  K+ NAQ AGY AA+V+ +     L  +   E       +P+ ++   +  YL
Sbjct: 89  RFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSSEYL 148

Query: 59  KEHARGEAGECCI------FPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPID 112
           +     E G   +      FPL Y        I   G++ L V+++  +   AR +    
Sbjct: 149 RALFVYEKGARVLLVPDNTFPLGYYL------IPFTGIVGLLVLAMGAVM-IARCI---- 197

Query: 113 SPRRHRPE-QTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPC 171
              +HR   Q  +L +  +  +P+  +          +  +C+ICL++Y +G+ LRVLPC
Sbjct: 198 ---QHRKRLQRNRLTKEQLKQIPTHDYQK------GDQYDVCAICLDEYEDGDKLRVLPC 248

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSN 204
            H +HS CVD WL +    CP+C+  + R   +
Sbjct: 249 AHAYHSRCVDPWLTQTRKTCPICKQPVHRGPGD 281

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 = 84.7 bits (208), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 93/210 (44%), Gaps = 31/210 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGAN----VPAFYVTLETGAYL 58
           R  CNF  K+ NAQ AGY AA+V+ +     L  +   E       +P+ ++   +  YL
Sbjct: 89  RFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYL 148

Query: 59  KEHARGEAGECCI------FPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPID 112
           +     E G   +      FPL Y              L+ F   + LL      +  + 
Sbjct: 149 RALFVYEKGARVLLVPDNSFPLGY-------------YLIPFTGIVGLLVLAMGTVLIVR 195

Query: 113 SPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRE-TLCSICLEDYREGENLRVLPC 171
             +  +  Q  +L +  +  +P+  +         G E  +C+ICL++Y +G+ LR+LPC
Sbjct: 196 CIQHRKRLQRNRLTKEQLKQIPTHDYQK-------GDEYDVCAICLDEYEDGDKLRILPC 248

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            H +HS CVD WL +    CP+C+  + R 
Sbjct: 249 AHAYHSRCVDPWLTQTRKTCPICKQPVHRG 278

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

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 84.3 bits (207), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 93/210 (44%), Gaps = 31/210 (14%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGAN----VPAFYVTLETGAYL 58
           R  CNF  K+ NAQ AGY AA+V+ +     L  +   E       +P+ ++   +  YL
Sbjct: 89  RFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYL 148

Query: 59  KEHARGEAGECCI------FPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPID 112
           +     E G   +      FPL Y              L+ F   + LL      +  + 
Sbjct: 149 RALFVYEKGARVLLVPDNSFPLGY-------------YLIPFTGIVGLLVLAMGTVLIVR 195

Query: 113 SPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRE-TLCSICLEDYREGENLRVLPC 171
             +  +  Q  +L +  +  +P+  +         G E  +C+ICL++Y +G+ LRVLPC
Sbjct: 196 CIQHRKRLQRNRLTKEQLKQIPTHDYQK-------GDEYDVCAICLDEYEDGDKLRVLPC 248

Query: 172 RHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            H +HS CVD WL +    CP+C+  + R 
Sbjct: 249 AHAYHSRCVDPWLTQTRKTCPICKQPVHRG 278

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|Q8VEM1|GOLI_MOUSE E3 ubiquitin-protein ligase RNF130 OS=Mus musculus GN=Rnf130 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 107/211 (50%), Gaps = 21/211 (9%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETG----AYL 58
           RG C F  KI  A      A ++Y  + K   + MT+P   ++ A  +T   G    +YL
Sbjct: 110 RGNCTFKEKISRAAFHNAVAVVIYNNKSKEEPVTMTHPGTGDIIAVMITELRGKDILSYL 169

Query: 59  KEHARGE---AGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPR 115
           +++   +   A    + P +++    V   I + ++L+ + S  L+F+F +K+   ++  
Sbjct: 170 EKNISVQMTIAVGTRMPPKNFSRGSLVFVSISF-IVLMIISSAWLIFYFIQKIRYTNARD 228

Query: 116 RHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETL-----CSICLEDYREGENLRVLP 170
           R++    R+L  +   A+      +  +V+   +ET      C++C+E Y++ + +RVLP
Sbjct: 229 RNQ----RRLGDAAKKAISKL---TTRTVKKGDKETDPDFDHCAVCIESYKQNDVVRVLP 281

Query: 171 CRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           C+H FH SCVD WL    T CP+C+  I ++
Sbjct: 282 CKHVFHKSCVDPWLSEHCT-CPMCKLNILKA 311

Acts as an E3 ubiquitin-protein ligase (By similarity). May have a role during the programmed cell death of hematopoietic cells.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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	214
224133660	311	predicted protein [Populus trichocarpa]	0.934	0.643	0.420	2e-40
225431110	294	PREDICTED: E3 ubiquitin-protein ligase R	0.920	0.670	0.430	7e-38
297734999	352	unnamed protein product [Vitis vinifera]	0.920	0.559	0.430	1e-37
297797773	308	hypothetical protein ARALYDRAFT_497000 [	0.906	0.629	0.413	2e-35
42573810	290	receptor homology-transmembrane-ring H2	0.906	0.668	0.403	3e-34
15239276	310	receptor homology-transmembrane-ring H2	0.906	0.625	0.408	4e-34
357168387	270	PREDICTED: E3 ubiquitin-protein ligase R	0.892	0.707	0.39	4e-33
226502198	276	uncharacterized protein LOC100276255 pre	0.892	0.692	0.38	7e-31
326513248	277	predicted protein [Hordeum vulgare subsp	0.892	0.689	0.395	7e-31
413917979	296	putative protease-associated RING zinc f	0.892	0.645	0.38	8e-31

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

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 93/221 (42%), Positives = 130/221 (58%), Gaps = 21/221 (9%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY-PEGANVPAFYVTLETGAYLK 59
           ++RG+C F  KI+NAQ+AG+ AAIV+  +    LIYM   PEG  V A +VT   G  LK
Sbjct: 81  IVRGECAFEDKIKNAQSAGFRAAIVFDDKDNRNLIYMMVNPEGIKVHAVFVTKYAGEILK 140

Query: 60  EHARGEAGECCIFP--LSYAWN----KHVEKIIVWGMLLL-FVISIPLLFWFARKLYPID 112
           + ARG+ GECCI+      AW       +  +++ G+L+L FV     L W         
Sbjct: 141 DRARGKEGECCIYSSRTDAAWTVLAISLISVVVILGLLILVFVTPRHWLHW--------- 191

Query: 113 SPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCR 172
              +    + + +    V ALP F F + +  +CH  ET C+ICLEDY++GE L+VLPC 
Sbjct: 192 ---QRTNNRCKSVDSKMVEALPCFTFRNASLSQCHVGET-CAICLEDYKDGEVLKVLPCH 247

Query: 173 HEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQVHVS 213
           HEFHS+CVDSWL +WGTFCPVC+ +++  ++  G   VH S
Sbjct: 248 HEFHSTCVDSWLTKWGTFCPVCKLDMKDKSAYFGCVVVHSS 288

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  162 bits (411), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 93/216 (43%), Positives = 131/216 (60%), Gaps = 19/216 (8%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
           +IRG+C F  K++NAQ AG+ A IVY  R K  L+ M    +G  VPA +V+   G  LK
Sbjct: 85  IIRGKCAFEDKVRNAQDAGFHAVIVYDDRDKGNLVSMIGNSQGIWVPAVFVSKAAGETLK 144

Query: 60  EHARGEAGECCIFPLSY---AWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPID--SP 114
            +A+G+ GECCI   S+   AW      ++V   + L VI+  +L +F  +   ++    
Sbjct: 145 IYAQGQEGECCIINPSFPESAWT-----VMVISFISLLVIATVVLTFFLTRNRRLNQRGT 199

Query: 115 RRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHE 174
             HRP    +L    V  LP F FS   +  C   +T CSICLEDY++GE LRVLPC+HE
Sbjct: 200 NPHRPSVDAKL----VEVLPCFTFSQ--ACECRVGDT-CSICLEDYKDGERLRVLPCQHE 252

Query: 175 FHSSCVDSWLIRWGTFCPVCRHEIR-RSTSNEGNEQ 209
           FH+SCVDSWL +WGTFCPVC++++   +T ++ NE+
Sbjct: 253 FHASCVDSWLTKWGTFCPVCKYDLSTDATCSKVNER 288

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  162 bits (409), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 93/216 (43%), Positives = 131/216 (60%), Gaps = 19/216 (8%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
           +IRG+C F  K++NAQ AG+ A IVY  R K  L+ M    +G  VPA +V+   G  LK
Sbjct: 143 IIRGKCAFEDKVRNAQDAGFHAVIVYDDRDKGNLVSMIGNSQGIWVPAVFVSKAAGETLK 202

Query: 60  EHARGEAGECCIFPLSY---AWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPID--SP 114
            +A+G+ GECCI   S+   AW      ++V   + L VI+  +L +F  +   ++    
Sbjct: 203 IYAQGQEGECCIINPSFPESAWT-----VMVISFISLLVIATVVLTFFLTRNRRLNQRGT 257

Query: 115 RRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHE 174
             HRP    +L    V  LP F FS   +  C   +T CSICLEDY++GE LRVLPC+HE
Sbjct: 258 NPHRPSVDAKL----VEVLPCFTFSQ--ACECRVGDT-CSICLEDYKDGERLRVLPCQHE 310

Query: 175 FHSSCVDSWLIRWGTFCPVCRHEIR-RSTSNEGNEQ 209
           FH+SCVDSWL +WGTFCPVC++++   +T ++ NE+
Sbjct: 311 FHASCVDSWLTKWGTFCPVCKYDLSTDATCSKVNER 346

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 =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 84/203 (41%), Positives = 120/203 (59%), Gaps = 9/203 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY-PEGANVPAFYVTLETGAYLK 59
           +IRG+C+F  K+ NAQ +G+ A IVY       LI M   P+   V A +V+   G  L+
Sbjct: 87  IIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVSNVAGEILR 146

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRP 119
           ++ARG  GECC++P +      V  I  + +LL  +++  L+ +FA + +   +  R R 
Sbjct: 147 KYARGRDGECCLYPPTKGSAWTVLAISFFSLLL--IVTFLLIAFFAPRHW---TQWRGRH 201

Query: 120 EQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSC 179
            +T +L    V+ LP F F   T    H     C+ICLEDYR GE+LR+LPC+H FH SC
Sbjct: 202 NRTIRLDAKLVHTLPCFTF---TDSAHHKAGETCAICLEDYRFGESLRLLPCQHAFHLSC 258

Query: 180 VDSWLIRWGTFCPVCRHEIRRST 202
           +DSWL +WGT CPVC+H+IR  T
Sbjct: 259 IDSWLTKWGTSCPVCKHDIRTET 281

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 82/203 (40%), Positives = 118/203 (58%), Gaps = 9/203 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY-PEGANVPAFYVTLETGAYLK 59
           +IRG+C+F  K+ NAQ +G+ A IVY       LI M   P+   V A +V+   G  L+
Sbjct: 87  IIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVSNVAGEILR 146

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRP 119
           ++ARG  GECC+ P        V  I  + +LL  +++  L+ +FA + +   +  R R 
Sbjct: 147 KYARGRDGECCLNPPDRGSAWTVLAISFFSLLL--IVTFLLIAFFAPRHW---TQWRGRH 201

Query: 120 EQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSC 179
            +T +L    V+ LP F F+       H     C+ICLEDYR GE+LR+LPC+H FH +C
Sbjct: 202 TRTIRLDAKLVHTLPCFTFTDSAH---HKAGETCAICLEDYRFGESLRLLPCQHAFHLNC 258

Query: 180 VDSWLIRWGTFCPVCRHEIRRST 202
           +DSWL +WGT CPVC+H+IR  T
Sbjct: 259 IDSWLTKWGTSCPVCKHDIRTET 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

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 =  150 bits (379), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 83/203 (40%), Positives = 118/203 (58%), Gaps = 9/203 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY-PEGANVPAFYVTLETGAYLK 59
           +IRG+C+F  K+ NAQ +G+ A IVY       LI M   P+   V A +V+   G  L+
Sbjct: 87  IIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVSNVAGEILR 146

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRP 119
           ++ARG  GECC+ P        V  I  + +LL  +++  L+ +FA + +   +  R R 
Sbjct: 147 KYARGRDGECCLNPPDRGSAWTVLAISFFSLLL--IVTFLLIAFFAPRHW---TQWRGRH 201

Query: 120 EQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSC 179
            +T +L    V+ LP F F   T    H     C+ICLEDYR GE+LR+LPC+H FH +C
Sbjct: 202 TRTIRLDAKLVHTLPCFTF---TDSAHHKAGETCAICLEDYRFGESLRLLPCQHAFHLNC 258

Query: 180 VDSWLIRWGTFCPVCRHEIRRST 202
           +DSWL +WGT CPVC+H+IR  T
Sbjct: 259 IDSWLTKWGTSCPVCKHDIRTET 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357168387|ref|XP_003581622.1| PREDICTED: E3 ubiquitin-protein ligase RNF13-like [Brachypodium distachyon]

 Score =  147 bits (370), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 78/200 (39%), Positives = 117/200 (58%), Gaps = 9/200 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
           ++RG C+F  K++ AQ AG++A +VY   +K+ L  M    EG ++PA +++   G  LK
Sbjct: 74  VVRGNCSFEDKVREAQRAGFNAVVVYDDEEKASLYSMVGDSEGIHIPAVFLSKMAGETLK 133

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGML-LLFVISIPLLFWFARKLYPIDSPRRHR 118
           + ARGE  ECCI     + ++    ++V   + L+ +IS+   F FAR    +     +R
Sbjct: 134 KFARGEDSECCI---ESSMDETAGTVLVMSFVSLVVIISVLASFLFARNCRLLRHGVDNR 190

Query: 119 PEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSS 178
           P   +   +  V+ LP  V+ +  S      E  C+ICLEDY  G+ LR+LPCRHEFH+ 
Sbjct: 191 PPYIK---KHVVDKLPCLVYKAPCSSG-STSEDACAICLEDYDNGDMLRLLPCRHEFHTV 246

Query: 179 CVDSWLIRWGTFCPVCRHEI 198
           CVD WL +WGTFCPVC+ E+
Sbjct: 247 CVDPWLTKWGTFCPVCKLEV 266

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226502198|ref|NP_001143559.1| uncharacterized protein LOC100276255 precursor [Zea mays] gi|195622502|gb|ACG33081.1| hypothetical protein [Zea mays]

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 76/200 (38%), Positives = 114/200 (57%), Gaps = 9/200 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
           + RG C+F  K++ AQ AG+DA+IVY   +K+ L  M    +G ++PA +V+   G  LK
Sbjct: 80  IARGNCSFEEKVRAAQQAGFDASIVYDDEEKASLYSMVGESDGIHIPAIFVSKMAGETLK 139

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVI-SIPLLFWFARKLYPIDSPRRHR 118
           + ARGE  ECCI   + + ++    ++V   + L VI S+   F FAR    +     + 
Sbjct: 140 KFARGEDEECCI---NSSMDETAGTVLVMSFVSLVVIMSVLASFLFARNCRLLRHGVDNH 196

Query: 119 PEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSS 178
           P   +   +  V   P   +S+  S   + +E  C+ICLEDY  G+ LR LPC+HEFH  
Sbjct: 197 PPYVK---KQVVEKFPCSAYSAPCSSEDNFQEA-CAICLEDYNNGDMLRHLPCKHEFHKI 252

Query: 179 CVDSWLIRWGTFCPVCRHEI 198
           C+DSWL +WG FCP+C+ E+
Sbjct: 253 CIDSWLTKWGIFCPICKLEV 272

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326513248|dbj|BAK06864.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 79/200 (39%), Positives = 116/200 (58%), Gaps = 9/200 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
           + RG C+F  K++ AQ AG+DAA+V+    K+ L  M   PEG ++PA +V+   G  LK
Sbjct: 81  IARGNCSFEGKVRAAQLAGFDAALVHDDEDKASLYSMVGDPEGIHIPAVFVSKMAGQTLK 140

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLL-FWFARKLYPIDSPRRHR 118
           + ARGE GECCI   + + ++    ++V   + L VI   +  F FAR    +     + 
Sbjct: 141 KFARGEDGECCI---NSSMDETAGTVLVMSFVSLVVIISVVASFLFARNCRLLRHGVDNH 197

Query: 119 PEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSS 178
           P   +   +  V  +PS V+ +  S   +  E  C+ICLEDY  G+ LR+LPC+HEFH  
Sbjct: 198 PPCIK---KHVVEKIPSLVYKAPCSSG-NNCEEACAICLEDYDNGDMLRLLPCKHEFHVE 253

Query: 179 CVDSWLIRWGTFCPVCRHEI 198
           C+D WL +WGTFCPVC+ E+
Sbjct: 254 CIDPWLTKWGTFCPVCKLEV 273

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413917979|gb|AFW57911.1| putative protease-associated RING zinc finger domain family protein [Zea mays]

 Score =  139 bits (350), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 76/200 (38%), Positives = 114/200 (57%), Gaps = 9/200 (4%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
           + RG C+F  K++ AQ AG+DA+IVY   +K+ L  M    +G ++PA +V+   G  LK
Sbjct: 100 IARGNCSFEEKVRAAQQAGFDASIVYDDEEKASLYSMVGESDGIHIPAIFVSKMAGETLK 159

Query: 60  EHARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVI-SIPLLFWFARKLYPIDSPRRHR 118
           + ARGE  ECCI   + + ++    ++V   + L VI S+   F FAR    +     + 
Sbjct: 160 KFARGEDEECCI---NSSMDETAGTVLVMSFVSLVVIMSVLASFLFARNCRLLRHGVDNH 216

Query: 119 PEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSS 178
           P   +   +  V   P   +S+  S   + +E  C+ICLEDY  G+ LR LPC+HEFH  
Sbjct: 217 PPYVK---KQVVEKFPCSAYSAPCSSEDNFQEA-CAICLEDYNNGDMLRHLPCKHEFHKI 272

Query: 179 CVDSWLIRWGTFCPVCRHEI 198
           C+DSWL +WG FCP+C+ E+
Sbjct: 273 CIDSWLTKWGIFCPICKLEV 292

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	214
TAIR|locus:2156872	310	RMR1 "receptor homology region	0.911	0.629	0.421	7.2e-36
TAIR|locus:2199665	422	AT1G22670 [Arabidopsis thalian	0.915	0.464	0.373	3e-30
TAIR|locus:2016044	448	AT1G71980 [Arabidopsis thalian	0.920	0.439	0.370	4.9e-30
TAIR|locus:2133697	448	AT4G09560 [Arabidopsis thalian	0.929	0.444	0.347	1.7e-25
TAIR|locus:2014726	318	AT1G35630 [Arabidopsis thalian	0.911	0.613	0.325	1.3e-22
ZFIN|ZDB-GENE-040426-772	377	rnf13 "ring finger protein 13"	0.920	0.522	0.310	6.1e-19
UNIPROTKB|F1NUJ3	272	RNF13 "E3 ubiquitin-protein li	0.887	0.698	0.295	8.3e-19
UNIPROTKB|F1NA38	380	RNF13 "E3 ubiquitin-protein li	0.887	0.5	0.295	1.8e-18
UNIPROTKB|Q90972	381	RNF13 "E3 ubiquitin-protein li	0.887	0.498	0.295	1.8e-18
RGD|1594062	380	Rnf13 "ring finger protein 13"	0.878	0.494	0.302	3.1e-18

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

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 88/209 (42%), Positives = 125/209 (59%)

Query:     1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY-PEGANVPAFYVTLETGAYLK 59
             +IRG+C+F  K+ NAQ +G+ A IVY       LI M   P+   V A +V+   G  L+
Sbjct:    87 IIRGECSFEDKLLNAQNSGFQAVIVYDNIDNEDLIVMKVNPQDITVDAVFVSNVAGEILR 146

Query:    60 EHARGEAGECCIFP--LSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRH 117
             ++ARG  GECC+ P     AW   V  I  + +LL  +++  L+ +FA + +   +  R 
Sbjct:   147 KYARGRDGECCLNPPDRGSAWT--VLAISFFSLLL--IVTFLLIAFFAPRHW---TQWRG 199

Query:   118 RPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHS 177
             R  +T +L    V+ LP F F+   S      ET C+ICLEDYR GE+LR+LPC+H FH 
Sbjct:   200 RHTRTIRLDAKLVHTLPCFTFTD--SAHHKAGET-CAICLEDYRFGESLRLLPCQHAFHL 256

Query:   178 SCVDSWLIRWGTFCPVCRHEIRRST-SNE 205
             +C+DSWL +WGT CPVC+H+IR  T S+E
Sbjct:   257 NCIDSWLTKWGTSCPVCKHDIRTETMSSE 285

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:2199665 AT1G22670 [Arabidopsis thaliana (taxid:3702)]

 Score = 334 (122.6 bits), Expect = 3.0e-30, P = 3.0e-30
 Identities = 78/209 (37%), Positives = 115/209 (55%)

Query:     1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYP-EGANVPAFYVTLETGAYLK 59
             +IRG C+F YK++NAQ +G+ AAIVY    ++ L  M    +G  + A +V    G  LK
Sbjct:    84 IIRGGCSFEYKVRNAQRSGFKAAIVYDNVDRNFLSAMGGDSDGIKIQAVFVMKRAGEMLK 143

Query:    60 EHARGEAGECCIFPLSY---AWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRR 116
             ++A  E  E  + P +     W+ +    ++   L +F + +  +F+     Y   S  R
Sbjct:   144 KYAGSEEMEVMLVPPNTEDSVWSLYASIALILS-LAIFCVMVTCVFF-----YRYCSTIR 197

Query:   117 HRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFH 176
             +   Q   + R TV A+PS  F+        G    C+ICLEDY  G+ LRVLPC H+FH
Sbjct:   198 NSTSQFNGMCRRTVKAMPSVTFTCAKIDNTTGFS--CAICLEDYIVGDKLRVLPCSHKFH 255

Query:   177 SSCVDSWLIRWGTFCPVCRHEIRRSTSNE 205
              +CVDSWLI W TFCPVC+ + R +T++E
Sbjct:   256 VACVDSWLISWRTFCPVCKRDAR-TTADE 283

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

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

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

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 76/205 (37%), Positives = 109/205 (53%)

Query:     1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGA-NVPAFYVTLETGAYLK 59
             ++RG C+F  K++ AQ AG+ AAI+Y    +  LI M    G   + A +VT ETG  LK
Sbjct:    82 IVRGGCSFEEKVRKAQRAGFKAAIIYDNEDRGTLIAMAGNSGGIRIHAVFVTKETGEVLK 141

Query:    60 EHARGEAGECCIFPL--SYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRH 117
             E+A     +  + P   + AW+      I   +L +  + +   F+  R      + R  
Sbjct:   142 EYAGFPDTKVWLIPSFENSAWSIMAVSFI--SLLAMSAV-LATCFFVRRHRIRRRTSRSS 198

Query:   118 RPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHS 177
             R  +   + R  V A+PS +FSS            C+ICLEDY  G+ LR+LPC H+FH+
Sbjct:   199 RVREFHGMSRRLVKAMPSLIFSSFHEDNTTA--FTCAICLEDYTVGDKLRLLPCCHKFHA 256

Query:   178 SCVDSWLIRWGTFCPVCRHEIRRST 202
             +CVDSWL  W TFCPVC+ + R ST
Sbjct:   257 ACVDSWLTSWRTFCPVCKRDARTST 281

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 = 291 (107.5 bits), Expect = 1.7e-25, P = 1.7e-25
 Identities = 75/216 (34%), Positives = 112/216 (51%)

Query:     1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
             +IRG C+F  KI+NAQ AGY AAIVY       L+ M   P G  +   +V+  TG  LK
Sbjct:    84 IIRGGCSFEDKIRNAQKAGYKAAIVYDYEDFGFLVSMAGNPSGVLIYGTFVSKATGEVLK 143

Query:    60 EHARGEAGECCIFPL--SYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPR-- 115
             E+A     E  + P   + AW+     I+    + L  +S  L   F  + + +   R  
Sbjct:   144 EYAGRTDFEVWLMPSFETSAWS-----IMAISFISLLAMSAVLATCFFVRRHRVRRRRIL 198

Query:   116 RHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRET--LCSICLEDYREGENLRVLPCRH 173
                     ++P+S +  +P+ +F+ +    C    T  LC ICLE+Y +G+ LR+LPC H
Sbjct:   199 ALNGNDFHRMPKSMIIRMPTTIFNGI----CDEATTSILCCICLENYEKGDKLRILPCHH 254

Query:   174 EFHSSCVDSWLIRWGTFCPVCRHEIRR-STSNEGNE 208
             +FH +CVD WL +  +FCPVC+ + R  ST    +E
Sbjct:   255 KFHVACVDLWLGQRKSFCPVCKRDARSISTDKPPSE 290

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 = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 69/212 (32%), Positives = 108/212 (50%)

Query:     1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLK 59
             ++ G C+F  K++ AQ AGY AAIVY       L+ M     G ++    VT  +G  LK
Sbjct:    82 IVLGGCSFEEKVRKAQKAGYKAAIVYNDGYDELLVPMAGNSSGVDIHGLLVTRASGEVLK 141

Query:    60 EHARGEAGECCIFP---LSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRR 116
              +A  +  +  + P   +S +W+     I+    + L  +S  L   F  + + I    R
Sbjct:   142 GYADQDEMKLWLIPGFGIS-SWS-----IMGITFISLLAMSAILATCFVVRRHQIRQSVR 195

Query:   117 HRPEQTRQL---PRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRH 173
               P   + L   PR  + ++P+ V+S V           C+IC++DY  GE LR+LPC+H
Sbjct:   196 DLPHGGQGLSCMPRDLLQSMPTEVYSGVLEES--STSVTCAICIDDYCVGEKLRILPCKH 253

Query:   174 EFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE 205
             ++H+ C+DSWL R  +FCPVC+   R  T N+
Sbjct:   254 KYHAVCIDSWLGRCRSFCPVCKQNPR--TGND 283

GO:0005576 "extracellular region" evidence=ISM

GO:0008233 "peptidase activity" evidence=ISS

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

ZFIN|ZDB-GENE-040426-772 rnf13 "ring finger protein 13" [Danio rerio (taxid:7955)]

 Score = 230 (86.0 bits), Expect = 6.1e-19, P = 6.1e-19
 Identities = 68/219 (31%), Positives = 107/219 (48%)

Query:     3 RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
             R  CNF  K+ +AQ AGY AAIV+ +     LI M   +       ++P+ ++  E    
Sbjct:    99 RFDCNFDIKVLHAQKAGYKAAIVHNV-DSDDLISMGSEDLDILKQIDIPSVFIGEEAANS 157

Query:    58 LKE-HARGEAGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRR 116
             LKE +   + G   + P    ++  +E  ++   L++  I + L+  F    +  D   R
Sbjct:   158 LKEDYIYEKGGHVILMP---DFSLPLEYYLI-PFLIIVGICLILIVVFMITKFVQD---R 210

Query:   117 HRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFH 176
             HR  ++R L +  +  LP   F    S        +C+ICL++Y EGE LRVLPC H +H
Sbjct:   211 HRARRSR-LRKDQLKKLPIHKFKKGDSY------DVCAICLDEYEEGERLRVLPCSHAYH 263

Query:   177 SSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQVHV-SG 214
               CVD WL +    CPVC+ ++  S  +  ++   V SG
Sbjct:   264 CKCVDPWLTKTKKTCPVCKQKVVPSDGDSESDSDSVDSG 302

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 63/213 (29%), Positives = 105/213 (49%)

Query:     3 RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
             R +CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct:    57 RLECNFDIKVLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEILKKIDIPSVFIGEASANS 115

Query:    58 LKEHARGE-AGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRR 116
             LKE    E  G   + P    ++  +E  ++  ++++ +  I ++ +   K    D   R
Sbjct:   116 LKEEFTYEKGGHVVLIP---EFSLPLEYYLIPFLIIVGICLILIVIFMITKFVQ-D---R 168

Query:   117 HRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRE-TLCSICLEDYREGENLRVLPCRHEF 175
             HR  + R L +  +  LP   F         G E  +C+ICL++Y +G+ LR+LPC H +
Sbjct:   169 HRARRNR-LRKDQLKKLPVHKFKK-------GDEYDVCAICLDEYEDGDKLRILPCSHAY 220

Query:   176 HSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNE 208
             H  CVD WL +    CPVC+ ++  S  +  +E
Sbjct:   221 HCKCVDPWLTKTKKTCPVCKQKVVPSQGDSDSE 253

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

 Score = 226 (84.6 bits), Expect = 1.8e-18, P = 1.8e-18
 Identities = 63/213 (29%), Positives = 105/213 (49%)

Query:     3 RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
             R +CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct:    98 RLECNFDIKVLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEILKKIDIPSVFIGEASANS 156

Query:    58 LKEHARGE-AGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRR 116
             LKE    E  G   + P    ++  +E  ++  ++++ +  I ++ +   K    D   R
Sbjct:   157 LKEEFTYEKGGHVVLIP---EFSLPLEYYLIPFLIIVGICLILIVIFMITKFVQ-D---R 209

Query:   117 HRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRE-TLCSICLEDYREGENLRVLPCRHEF 175
             HR  + R L +  +  LP   F         G E  +C+ICL++Y +G+ LR+LPC H +
Sbjct:   210 HRARRNR-LRKDQLKKLPVHKFKK-------GDEYDVCAICLDEYEDGDKLRILPCSHAY 261

Query:   176 HSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNE 208
             H  CVD WL +    CPVC+ ++  S  +  +E
Sbjct:   262 HCKCVDPWLTKTKKTCPVCKQKVVPSQGDSDSE 294

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005765 "lysosomal membrane" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=IEA

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

 Score = 226 (84.6 bits), Expect = 1.8e-18, P = 1.8e-18
 Identities = 63/213 (29%), Positives = 105/213 (49%)

Query:     3 RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
             R +CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct:    99 RLECNFDIKVLNAQRAGYKAAIVHNV-DSDDLISMGSNDIEILKKIDIPSVFIGEASANS 157

Query:    58 LKEHARGE-AGECCIFPLSYAWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRR 116
             LKE    E  G   + P    ++  +E  ++  ++++ +  I ++ +   K    D   R
Sbjct:   158 LKEEFTYEKGGHVVLIP---EFSLPLEYYLIPFLIIVGICLILIVIFMITKFVQ-D---R 210

Query:   117 HRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRE-TLCSICLEDYREGENLRVLPCRHEF 175
             HR  + R L +  +  LP   F         G E  +C+ICL++Y +G+ LR+LPC H +
Sbjct:   211 HRARRNR-LRKDQLKKLPVHKFKK-------GDEYDVCAICLDEYEDGDKLRILPCSHAY 262

Query:   176 HSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNE 208
             H  CVD WL +    CPVC+ ++  S  +  +E
Sbjct:   263 HCKCVDPWLTKTKKTCPVCKQKVVPSQGDSDSE 295

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0051865 "protein autoubiquitination" evidence=ISS

RGD|1594062 Rnf13 "ring finger protein 13" [Rattus norvegicus (taxid:10116)]

 Score = 224 (83.9 bits), Expect = 3.1e-18, P = 3.1e-18
 Identities = 65/215 (30%), Positives = 105/215 (48%)

Query:     3 RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPE-----GANVPAFYVTLETGAY 57
             R  CNF  K+ NAQ AGY AAIV+ +     LI M   +       ++P+ ++   +   
Sbjct:    99 RLDCNFDIKVLNAQRAGYKAAIVHNV-DSDDLISMGSNDIDILKKIDIPSVFIGESSANS 157

Query:    58 LKEHARGE-AGECCIFP-LSYAWNKH-VEKIIVWGMLLLFVISIPLLFWFARKLYPIDSP 114
             LK+    E  G   + P LS     + +  +I+ G+ L+ ++    +F   +  +  D  
Sbjct:   158 LKDEFTYEKGGHVILVPELSLPLEYYLIPFLIIVGICLILIV----IFMITK--FVQD-- 209

Query:   115 RRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRE-TLCSICLEDYREGENLRVLPCRH 173
              RHR  + R L +  +  LP   F         G E  +C+ICLE+Y +G+ LR+LPC H
Sbjct:   210 -RHRNRRNR-LRKDQLKKLPVHKFKK-------GDEYDVCAICLEEYEDGDKLRILPCSH 260

Query:   174 EFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNE 208
              +H  CVD WL +    CPVC+ ++  S  +  ++
Sbjct:   261 AYHCKCVDPWLTKTKKTCPVCKQKVVPSQGDSDSD 295

GO:0000139 "Golgi membrane" evidence=IEA

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

GO:0005637 "nuclear inner membrane" evidence=IEA

GO:0005765 "lysosomal membrane" evidence=ISO;ISS

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0031902 "late endosome membrane" evidence=ISO;ISS

GO:0051865 "protein autoubiquitination" evidence=ISO;ISS

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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.

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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	214
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-16
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-12
cd00538	126	cd00538, PA, PA: Protease-associated (PA) domain	1e-10
pfam02225	96	pfam02225, PA, PA domain	2e-10
cd02123	153	cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-a	4e-10
smart00184	40	smart00184, RING, Ring finger	7e-09
cd04818	118	cd04818, PA_subtilisin_1, PA_subtilisin_1: Proteas	2e-08
cd02133	143	cd02133, PA_C5a_like, PA_C5a_like: Protease-associ	3e-08
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	4e-07
cd02125	127	cd02125, PA_VSR, PA_VSR: Protease-associated (PA)	8e-05
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	8e-05
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-04
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	6e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	0.002
cd02127	118	cd02127, PA_hPAP21_like, PA_hPAP21_like: Protease-	0.003
cd02130	122	cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-as	0.003

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

 Score = 76.6 bits (188), Expect = 2e-16
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 121 QTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCV 180
            +  +P +T     S    S+       +   C+IC+ ++ + + LRVLPC H FH  CV
Sbjct: 296 SSEAIPTTTTKG--SLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCV 353

Query: 181 DSWLIRWGTFCPVCRHEI 198
           D WL+ +   CPVCR  I
Sbjct: 354 DKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 62.4 bits (152), Expect = 1e-13
 Identities = 22/45 (48%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHE 197
           C ICL+++  GE + VLPC H FH  C+D WL    T CP+CR  
Sbjct: 3   CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNT-CPLCRAP 46

Length = 46

>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 = 58.6 bits (142), Expect = 3e-12
 Identities = 22/46 (47%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C ICLE++RE   + +LPC H F  SC+D WL      CP+CR  I
Sbjct: 2   CPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 56.8 bits (137), Expect = 1e-10
 Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 5/62 (8%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGA----NVPAFYVTLETGAYL 58
           RG C+FS K++NAQ AG  A I+Y      P   M          ++P   ++   G  L
Sbjct: 54  RGGCSFSEKVKNAQKAGAKAVIIYN-NGDDPGPQMGSVGLESTDPSIPTVGISYADGEAL 112

Query: 59  KE 60
             
Sbjct: 113 LS 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|216938 pfam02225, PA, PA domain

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 17/56 (30%), Positives = 25/56 (44%)

Query: 3  RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYL 58
          RG C+F  K +NAQ AG    I+Y          +  P    +P  +++ E G  L
Sbjct: 41 RGGCSFVEKAENAQRAGAAGVIIYNNDTGGLGGTVGDPSDVTIPVVFISYEDGEAL 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|239038 cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 31/79 (39%), Positives = 44/79 (55%), Gaps = 5/79 (6%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYM----TYPEGANVPAFYVTLETGA 56
           + RG C+F  K++NAQ AGY AAIVY   + + LI M       +G ++P+ +V   TG 
Sbjct: 73  IRRGNCSFETKVRNAQRAGYKAAIVYN-DESNDLISMSGNDQEIKGIDIPSVFVGKSTGE 131

Query: 57  YLKEHARGEAGECCIFPLS 75
            LK++A  E G   I  L 
Sbjct: 132 ILKKYASYEKGVILIPDLP 150

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|214546 smart00184, RING, Ring finger

 Score = 49.8 bits (119), Expect = 7e-09
 Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVC 194
           C ICLE+Y   ++  +LPC H F  SC+  WL      CP+C
Sbjct: 1   CPICLEEY--LKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 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|240122 cd04818, PA_subtilisin_1, PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGA-NVPAFYVTLETGAYLKE 60
           RG CNF+ K+ NAQ AG  A IV         I M   +    +PA  ++   G  LK 
Sbjct: 48  RGTCNFTVKVLNAQNAGAIAVIVANNVAGGAPITMGGDDPDITIPAVMISQADGDALKA 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|239048 cd02133, PA_C5a_like, PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKE 60
           RG+  F  KI NA+AAG    I+Y       LI  T  E   +P  +++ E G  LK 
Sbjct: 55  RGEITFVEKIANAKAAGAVGVIIY--NNVDGLIPGTLGEAVFIPVVFISKEDGEALKA 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|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVC 194
           C ICLE+ ++   + +LPC H F S 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|239040 cd02125, PA_VSR, PA_VSR: Protease-associated (PA) domain-containing plant vacuolar sorting receptor (VSR)

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 10/66 (15%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGA---------NVPAFYVTLE 53
           RG C F+ K  NAQ AG  A +V A     PL+ M  PE +          +P+  +T  
Sbjct: 50  RGGCFFTLKAWNAQQAGAAAVLV-ADNVDEPLLTMDTPEESGSADYIEKITIPSALITKA 108

Query: 54  TGAYLK 59
            G  LK
Sbjct: 109 FGEKLK 114

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

 Score = 38.6 bits (90), Expect = 8e-05
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRH 196
           E  C ICL+  R+   + + PC H F   C+  +L +  + CP+CR 
Sbjct: 2   ELECPICLDLLRD--PVVLTPCGHVFCRECILRYLKK-KSKCPICRT 45

Length = 45

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

 Score = 40.3 bits (94), Expect = 4e-04
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 11/53 (20%)

Query: 153 CSICLEDYREGENLRV----------LPCRHEFHSSCVDSWLIRWGTFCPVCR 195
           C+IC+++    ++  +          LPC H  H  C+ +WL R  T CP+CR
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQT-CPICR 341

Length = 491

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

 Score = 36.2 bits (84), Expect = 6e-04
 Identities = 19/54 (35%), Positives = 23/54 (42%), Gaps = 6/54 (11%)

Query: 149 RETLCSICLEDYREGENLRVLPCRH-EFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            + LC ICLE  R   N+  LPC H      C     +R    CP+CR  I   
Sbjct: 1   EDDLCVICLERPR---NVVFLPCGHLCLCEECAKR--LRSKKKCPICRQPIESV 49

Length = 49

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

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 11/54 (20%)

Query: 153  CSICLEDY-------REGENLRVLPCRHEFHSSCVDSWLIRWG-TFCPVCRHEI 198
            C+IC   Y       R   + R   C+++FH+ C+  W      + CP+CR EI
Sbjct: 1472 CAIC---YSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522

Length = 1525

>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 = 36.2 bits (84), Expect = 0.003
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIY--MTYPEG---ANVPAFYVTLETG 55
           + RG C+F  K  NAQ AG  A I+  +   S   Y  M   +    A++PA ++  + G
Sbjct: 40  IERGGCSFLTKAINAQKAGALAVIITDVNNDSDEYYVEMIQDDSSRRADIPAAFLLGKNG 99

Query: 56  AYLKEH 61
             +++ 
Sbjct: 100 YMIRKT 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|239045 cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY)

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 13/24 (54%), Positives = 15/24 (62%)

Query: 3  RGQCNFSYKIQNAQAAGYDAAIVY 26
          RG+C F  K   A AAG  AAI+Y
Sbjct: 52 RGECPFGDKSALAGAAGAAAAIIY 75

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	214
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.77
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.74
cd02125	127	PA_VSR PA_VSR: Protease-associated (PA) domain-con	99.71
cd02127	118	PA_hPAP21_like PA_hPAP21_like: Protease-associated	99.7
cd02123	153	PA_C_RZF_like PA_C-RZF_ like: Protease-associated	99.69
cd02129	120	PA_hSPPL_like PA_hSPPL_like: Protease-associated d	99.69
cd02122	138	PA_GRAIL_like PA _GRAIL_like: Protease-associated	99.68
cd04813	117	PA_1 PA_1: Protease-associated (PA) domain subgrou	99.67
cd02126	126	PA_EDEM3_like PA_EDEM3_like: protease associated d	99.67
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.59
cd02132	139	PA_GO-like PA_GO-like: Protease-associated domain	99.58
cd04817	139	PA_VapT_like PA_VapT_like: Protease-associated dom	99.58
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.57
PHA02929	238	N1R/p28-like protein; Provisional	99.53
PF02225	101	PA: PA domain; InterPro: IPR003137 The PA (Proteas	99.47
cd02130	122	PA_ScAPY_like PA_ScAPY_like: Protease-associated d	99.47
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.46
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.41
cd04816	122	PA_SaNapH_like PA_SaNapH_like: Protease-associated	99.41
cd04818	118	PA_subtilisin_1 PA_subtilisin_1: Protease-associat	99.4
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.37
cd02124	129	PA_PoS1_like PA_PoS1_like: Protease-associated (PA	99.36
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.34
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.32
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.3
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.3
cd02133	143	PA_C5a_like PA_C5a_like: Protease-associated domai	99.26
KOG2442	541	consensus Uncharacterized conserved protein, conta	99.26
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.24
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.23
cd00538	126	PA PA: Protease-associated (PA) domain. The PA dom	99.22
PF14634	44	zf-RING_5: zinc-RING finger domain	99.21
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.19
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.15
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.13
PHA02926	242	zinc finger-like protein; Provisional	99.12
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	99.12
cd04819	127	PA_2 PA_2: Protease-associated (PA) domain subgrou	99.05
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	99.05
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.05
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.05
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.96
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.9
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.89
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.89
KOG3920	193	consensus Uncharacterized conserved protein, conta	98.88
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.86
cd02120	126	PA_subtilisin_like PA_subtilisin_like: Protease-as	98.79
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.73
cd02128	183	PA_TfR PA_TfR: Protease-associated domain containi	98.71
cd04815	134	PA_M28_2 PA_M28_2: Protease-associated (PA) domain	98.67
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.64
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.63
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.61
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.59
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.48
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.46
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.45
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.44
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.43
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.42
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.39
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.3
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.24
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.18
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.13
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.09
KOG1941	518	consensus Acetylcholine receptor-associated protei	98.06
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.01
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.92
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.9
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.89
cd02121	220	PA_GCPII_like PA_GCPII_like: Protease-associated d	97.88
cd02131	153	PA_hNAALADL2_like PA_hNAALADL2_like: Protease-asso	97.86
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.65
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.6
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.59
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.56
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.56
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.46
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.44
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.43
cd04822	151	PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) do	97.36
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
cd04814	142	PA_M28_1 PA_M28_1: Protease-associated (PA) domain	97.32
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.3
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.27
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.24
PHA02862	156	5L protein; Provisional	97.23
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.21
cd04820	137	PA_M28_1_1 PA_M28_1_1: Protease-associated (PA) do	97.15
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.13
COG5152	259	Uncharacterized conserved protein, contains RING a	97.1
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.07
KOG4739	233	consensus Uncharacterized protein involved in syna	97.06
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	97.04
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.94
KOG2660	331	consensus Locus-specific chromosome binding protei	96.9
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.88
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.87
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.86
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.76
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.76
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.58
PHA03096	284	p28-like protein; Provisional	96.58
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.1
PF04641	260	Rtf2: Rtf2 RING-finger	96.05
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.82
KOG1940	276	consensus Zn-finger protein [General function pred	95.78
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.78
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	95.69
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.67
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.57
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.4
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.38
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.1
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	95.0
KOG3002	299	consensus Zn finger protein [General function pred	94.9
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	94.7
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	94.31
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	93.68
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.35
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.34
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	92.58
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.46
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	91.97
COG5109	396	Uncharacterized conserved protein, contains RING Z	91.51
KOG3899	381	consensus Uncharacterized conserved protein [Funct	91.44
KOG4367	699	consensus Predicted Zn-finger protein [Function un	91.31
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	91.27
KOG1609	323	consensus Protein involved in mRNA turnover and st	91.24
KOG1829	580	consensus Uncharacterized conserved protein, conta	90.96
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	90.94
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	90.77
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	90.43
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	89.73
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	89.68
KOG3356	147	consensus Predicted membrane protein [Function unk	89.46
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	89.28
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	89.19
KOG0269	839	consensus WD40 repeat-containing protein [Function	89.12
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.49
KOG2807	378	consensus RNA polymerase II transcription initiati	88.43
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	88.42
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	87.57
KOG0825	1134	consensus PHD Zn-finger protein [General function	86.1
cd04821	157	PA_M28_1_2 PA_M28_1_2: Protease-associated (PA) do	85.78
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	85.54
KOG3113	293	consensus Uncharacterized conserved protein [Funct	85.21
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	82.48
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	82.26
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	82.22
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	82.06
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	81.69

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

Probab=100.00  E-value=4.7e-45  Score=288.92  Aligned_cols=200  Identities=32%  Similarity=0.634  Sum_probs=158.6

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeee-CCCCCeeeEEEEchhhHHHHHHHhhcCCCceEEec-cc--c
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-YPEGANVPAFYVTLETGAYLKEHARGEAGECCIFP-LS--Y   76 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~-~~~~~~Ip~v~v~~~~g~~L~~~~~~~~~~~~~~p-~~--~   76 (214)
                      |+||+|+|.+|+++||++|++|+||||+.+.+.++.|. +..++.|+++||+...|+.|.++.......+...| +.  .
T Consensus        85 I~Rg~CsFe~Kv~~AQ~aGfkaaIVynn~~~~~lv~~~~~~~~v~i~~~~vs~~~ge~l~~~~~~~~~~~~~~~~~~~~~  164 (348)
T KOG4628|consen   85 IRRGGCSFEDKVLNAQRAGFKAAIVYNNVGSEDLVAMASNPSKVDIHIVFVSVFSGELLSSYAGRTEFECLLIPLGFDTS  164 (348)
T ss_pred             EEccCCchHHHHhhcccccCceEEEecCCCCchheeeccCCccceeEEEEEeeehHHHHHHhhcccceeeeeccccccCC
Confidence            58999999999999999999999999988776677665 77889999999999999999998877766666666 33  7


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCHHHHhcCCceeeeccccccCCCCCcccccc
Q 028085           77 AWNKHVEKIIVWGMLLLFVISIPLLFWFARKLYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSIC  156 (214)
Q Consensus        77 ~~~~~~~~i~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC  156 (214)
                      .|++..+  .++.++.  +..++++++++++.+.....|..  .+.+++.++.++++|...|.+....+..   +.|+||
T Consensus       165 ~ws~~~~--~~i~~l~--v~~il~~~f~i~~~~~~~~~r~~--~~~~r~~k~~l~~~p~~~f~~~~~~~~~---~~CaIC  235 (348)
T KOG4628|consen  165 PWSILAI--SLISLLT--VVAILVTCFFIYRIRRLIRARNR--LRRNRLIKRLLKKLPVRTFTKGDDEDAT---DTCAIC  235 (348)
T ss_pred             cchhhhh--hhhhHHH--HHHHHHHHHHHHHHHHHHHHHhH--hhhhhhHHHHHhhCCcEEeccccccCCC---ceEEEe
Confidence            8887433  3444444  44445555555554332211221  4567899999999999999887665432   589999


Q ss_pred             cccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccCCCCCcc
Q 028085          157 LEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQ  209 (214)
Q Consensus       157 l~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~~~~~  209 (214)
                      ||+|++||++|.|||+|.||..||++||...++.||+||+++.+..+.+...+
T Consensus       236 lEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~~~~~~e  288 (348)
T KOG4628|consen  236 LEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSGSEPVSE  288 (348)
T ss_pred             ecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCCCCCccC
Confidence            99999999999999999999999999999987779999999988877666554

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

Probab=99.77  E-value=1.3e-20  Score=144.87  Aligned_cols=52  Identities=44%  Similarity=1.123  Sum_probs=46.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      ...+|+||+++|..+|+++.|||.|.||..|+++|+...+..||+||.+++.
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            4478999999999999999999999999999999998555569999998864

>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=99.74  E-value=7.2e-19  Score=100.78  Aligned_cols=44  Identities=52%  Similarity=1.260  Sum_probs=39.6

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCR  195 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr  195 (214)
                      ++|+||++++.+++.+..++|||.||.+|+.+|++.+.+ ||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~-CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNS-CPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB--TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCc-CCccC
Confidence            369999999999999999999999999999999998765 99998

...

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

Probab=99.71  E-value=3.3e-17  Score=114.97  Aligned_cols=64  Identities=34%  Similarity=0.468  Sum_probs=54.7

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeee---------CCCCCeeeEEEEchhhHHHHHHHhhcC
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT---------YPEGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~---------~~~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                      |+||+|+|.+|+++||++||+||||||+.+. +++.|.         ..++++||+++|++++|+.|++.+..+
T Consensus        48 v~RG~C~F~~K~~~Aq~aGA~avII~n~~~~-~~~~m~~~~~~~~~~~~~~i~IP~v~Is~~~G~~L~~~l~~g  120 (127)
T cd02125          48 LDRGGCFFTLKAWNAQQAGAAAVLVADNVDE-PLLTMDTPEESGSADYIEKITIPSALITKAFGEKLKKAISNG  120 (127)
T ss_pred             EECCCcCHHHHHHHHHHCCCcEEEEEECCCC-ccccccCcccccccccCCCceEeEEEECHHHHHHHHHHHhcC
Confidence            5899999999999999999999999998765 566663         134578999999999999999987643

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

>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=99.70  E-value=7.9e-17  Score=111.66  Aligned_cols=65  Identities=26%  Similarity=0.369  Sum_probs=55.4

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCC--CCeeeeeC---CCCCeeeEEEEchhhHHHHHHHhhcC
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKK--SPLIYMTY---PEGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~--~~~~~m~~---~~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                      |+||+|+|.+|+++||++||+||||||+.+.  ...+.|..   ...++||+++|++.+|+.|++.+..+
T Consensus        40 v~RG~C~F~~K~~~Aq~aGA~avII~n~~~~~~~~~~~m~~~~~~~~i~IP~v~Is~~dG~~L~~~l~~g  109 (118)
T cd02127          40 IERGGCSFLTKAINAQKAGALAVIITDVNNDSDEYYVEMIQDDSSRRADIPAAFLLGKNGYMIRKTLERL  109 (118)
T ss_pred             EECCCCCHHHHHHHHHHCCCcEEEEEECCCCccccceEecCCCCCCCceEEEEEecHHHHHHHHHHHHcC
Confidence            5899999999999999999999999997643  35667763   35689999999999999999988644

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.

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

Probab=99.69  E-value=1.4e-16  Score=115.59  Aligned_cols=73  Identities=41%  Similarity=0.640  Sum_probs=60.1

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeC-C---CCCeeeEEEEchhhHHHHHHHhhcCCCceEEeccc
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY-P---EGANVPAFYVTLETGAYLKEHARGEAGECCIFPLS   75 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~-~---~~~~Ip~v~v~~~~g~~L~~~~~~~~~~~~~~p~~   75 (214)
                      |+||+|+|.+|+++||++||+||||||+.++ ++..|.. .   .+++||+++|++++|+.|++.+..... +...|+.
T Consensus        73 V~RG~CtF~~Kv~nAq~aGA~avII~n~~~~-~~~~m~~~~~~~~~v~IP~v~Is~~dg~~L~~~l~~~~~-~~~~~~~  149 (153)
T cd02123          73 IRRGNCSFETKVRNAQRAGYKAAIVYNDESN-DLISMSGNDQEIKGIDIPSVFVGKSTGEILKKYASYEKG-VILIPDL  149 (153)
T ss_pred             EECCCCCHHHHHHHHHHCCCCEEEEEECCCC-cceeccCCCCCCcCCEEEEEEeeHHHHHHHHHHHhcCCc-EEECCCC
Confidence            5899999999999999999999999998765 5667762 2   368999999999999999998876555 4444443

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

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

Probab=99.69  E-value=8.7e-17  Score=110.81  Aligned_cols=63  Identities=17%  Similarity=0.289  Sum_probs=51.8

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCee-eeeCCCCCeeeEEEEchhhHHHHHHHhh
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLI-YMTYPEGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~-~m~~~~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                      |+||+|+|.+|+++||++||+||||||+.+..+.. ..+....++||++||++++|+.|.+.+.
T Consensus        50 V~RG~CsF~~K~~~Aq~aGA~aVII~nn~~~~~~~~~~~~~~~v~IP~v~Is~~dG~~i~~~l~  113 (120)
T cd02129          50 VMRGNCTFYEKARLAQSLGAEGLLIVSRERLVPPSGNRSEYEKIDIPVALLSYKDMLDIQQTFG  113 (120)
T ss_pred             EECCCcCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCcCCcccEEEEeHHHHHHHHHHhc
Confidence            58999999999999999999999999987642111 1112366899999999999999998876

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.

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

Probab=99.68  E-value=1.6e-16  Score=113.06  Aligned_cols=64  Identities=23%  Similarity=0.354  Sum_probs=56.6

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCC-CCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhhc
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRK-KSPLIYMTYPEGANVPAFYVTLETGAYLKEHARG   64 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~-~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~~   64 (214)
                      |+||+|+|.+|+++||++||+||||||+.+ ....+.|.......||+++|++.+|+.|++.+..
T Consensus        66 V~RG~C~F~~K~~nA~~aGA~aVIIyn~~~~~~~~~~m~~~~~~~ip~v~Is~~~G~~l~~~l~~  130 (138)
T cd02122          66 IQRGNCTFEEKIKLAAERNASAVVIYNNPGTGNETVKMSHPGTGDIVAIMITNPKGMEILELLER  130 (138)
T ss_pred             EECCCCCHHHHHHHHHHCCCcEEEEEECCCCCCceeeccCCCCCcceEEEEcHHHHHHHHHHHHc
Confidence            589999999999999999999999999876 4457788866666899999999999999998853

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

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

Probab=99.67  E-value=1.9e-16  Score=109.46  Aligned_cols=63  Identities=27%  Similarity=0.334  Sum_probs=54.6

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeee---CCCCCeeeEEEEchhhHHHHHHHhh
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT---YPEGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~---~~~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                      |+||+|+|.+|+++||++||+||||||+.+...++.|.   ....++||+++|++++|+.|+.++.
T Consensus        45 V~RG~CsF~~K~~nAq~aGA~avII~n~~~~~~~~~m~~~~~~~~v~IPav~Is~~~g~~L~~l~~  110 (117)
T cd04813          45 VLRGGCGFLDKVMWAQRRGAKAVIVGDDEPGRGLITMFSNGDTDNVTIPAMFTSRTSYHLLSSLLP  110 (117)
T ss_pred             EECCCCCHHHHHHHHHHCCCcEEEEEECCCcccceecccCCCCCCcEEEEEEEcHHHHHHHHHhcc
Confidence            58999999999999999999999999987654566665   3456899999999999999998775

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

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

Probab=99.67  E-value=2.9e-16  Score=110.43  Aligned_cols=64  Identities=27%  Similarity=0.413  Sum_probs=54.2

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCC-----CeeeeeCC----CCCeeeEEEEchhhHHHHHHHhhc
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKS-----PLIYMTYP----EGANVPAFYVTLETGAYLKEHARG   64 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~-----~~~~m~~~----~~~~Ip~v~v~~~~g~~L~~~~~~   64 (214)
                      |+||+|+|.+|+++||++||.||||||+.+++     .++.|...    +.++||+++|++.+|+.|++.+..
T Consensus        46 v~RG~C~f~~K~~~Aq~aGA~avII~n~~~~~~~~~~~~~~m~~~~~~~~~~~IP~v~I~~~dG~~L~~~l~~  118 (126)
T cd02126          46 MERGDCMFVEKARRVQKAGAIGGIVIDNNEGSSSDTAPMFAMSGDGDSTDDVTIPVVFLFSKEGSKLLAAIKE  118 (126)
T ss_pred             EECCCCcHHHHHHHHHHCCCcEEEEEECCCCccccccceeEeecCCCCCCCCeEEEEEEEHHHHHHHHHHHHh
Confidence            58999999999999999999999999876542     45667622    368999999999999999998853

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

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

Probab=99.59  E-value=5.7e-16  Score=122.50  Aligned_cols=53  Identities=32%  Similarity=0.908  Sum_probs=44.2

Q ss_pred             CCccccccccc-ccCC---------CceEEecCCCccChhhHHHHHHhCCCCcccccccc-cccc
Q 028085          149 RETLCSICLED-YREG---------ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI-RRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~-~~~~---------~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i-~~~~  202 (214)
                      +|..|.||+|+ +..+         .++..|||||+||-+|++.|++++++ ||+||.++ ..+.
T Consensus       286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQT-CPICr~p~ifd~~  349 (491)
T COG5243         286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQT-CPICRRPVIFDQS  349 (491)
T ss_pred             CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccC-CCcccCccccccC
Confidence            67899999999 4444         25689999999999999999999887 99999994 4433

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

Probab=99.58  E-value=5.7e-15  Score=105.60  Aligned_cols=62  Identities=23%  Similarity=0.381  Sum_probs=52.5

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeee---C--CCCCeeeEEEEchhhHHHHHHHhhc
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT---Y--PEGANVPAFYVTLETGAYLKEHARG   64 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~---~--~~~~~Ip~v~v~~~~g~~L~~~~~~   64 (214)
                      |+||+|+|.+|+++||++||+||||||+.+.  +..|.   +  ...++||+++|++.+|+.|++.+..
T Consensus        65 V~RG~C~F~~K~~nA~~aGA~avIv~n~~~~--~~~~~~~~~~~~~~~~IP~v~Is~~~G~~L~~~l~~  131 (139)
T cd02132          65 VERGECAFTEKAKIAEAGGASALLIINDQEE--LYKMVCEDNDTSLNISIPVVMIPQSAGDALNKSLDQ  131 (139)
T ss_pred             EECCCCCHHHHHHHHHHcCCcEEEEEECCCc--ccccccCCCCCCCCCcEeEEEecHHHHHHHHHHHHc
Confidence            5899999999999999999999999997653  45554   1  1257999999999999999998864

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.

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

Probab=99.58  E-value=6.4e-15  Score=104.35  Aligned_cols=63  Identities=25%  Similarity=0.244  Sum_probs=51.8

Q ss_pred             Ccccccc-----HHHHHHHHHHcCCcEEEEEeCCCCCCeee--eeCC-CCCeeeEEEEchhhHHHHHHHhh
Q 028085            1 MIRGQCN-----FSYKIQNAQAAGYDAAIVYALRKKSPLIY--MTYP-EGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus         1 v~rg~C~-----f~~K~~~a~~~ga~aviv~~~~~~~~~~~--m~~~-~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                      |+||+|+     |.+|+++|+++||+||||||+.+.+..+.  +.+. ..++||+++|++.+|+.|++.+.
T Consensus        62 I~RG~c~~~~~~f~~Kv~~A~~aGA~avIIyNn~~~~g~~~~~lg~~~~~~~IP~v~is~~dG~~L~~~l~  132 (139)
T cd04817          62 IERGGNSKSVYPEIDKVKACQNAGAIAAIVYSNAALAGLQNPFLVDTNNDTTIPSVSVDRADGQALLAALG  132 (139)
T ss_pred             EECCCCCCCcccHHHHHHHHHHCCCeEEEEEeCCCCCCcccccccCCCCCceEeEEEeeHHHHHHHHHHhc
Confidence            5899999     99999999999999999999874322222  2333 36899999999999999998875

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.

>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=99.57  E-value=1.4e-15  Score=96.40  Aligned_cols=46  Identities=37%  Similarity=0.869  Sum_probs=35.6

Q ss_pred             CCcccccccccccCC----------CceEEecCCCccChhhHHHHHHhCCCCccccc
Q 028085          149 RETLCSICLEDYREG----------ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCR  195 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----------~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr  195 (214)
                      .++.|+||++.+.+.          -.+...+|||.||..||.+|++.+++ ||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~-CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNT-CPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB--TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCc-CCCCC
Confidence            345699999999322          24556689999999999999988775 99998

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 ....

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.53  E-value=6.2e-15  Score=112.96  Aligned_cols=73  Identities=26%  Similarity=0.549  Sum_probs=50.5

Q ss_pred             CCHHHHhcCCceeeeccccccCCCCCcccccccccccCCCc----e-EEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          125 LPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGEN----L-RVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~----~-~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      ..+..++.+|....+-......+ .+.+|+||++.+.+++.    + ..++|+|.||.+||.+|+..+.+ ||+||.++.
T Consensus       150 ~~~~~i~~lp~vl~~~e~~~~~~-~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~t-CPlCR~~~~  227 (238)
T PHA02929        150 NYKKFLKTIPSVLSEYEKLYNRS-KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNT-CPVCRTPFI  227 (238)
T ss_pred             hhHHHHHhcchhhhhhhhhhcCC-CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCC-CCCCCCEee
Confidence            34556666666544332222222 45789999999876531    2 34569999999999999987655 999999875

>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=99.47  E-value=1.2e-13  Score=93.67  Aligned_cols=62  Identities=29%  Similarity=0.546  Sum_probs=48.3

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCC-CCCeeeeeCCCCCeeeEEEEchhhHHHHHHHh
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRK-KSPLIYMTYPEGANVPAFYVTLETGAYLKEHA   62 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~-~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~   62 (214)
                      ++||+|+|.+|+++|+++||+|+||||..+ ......+......+||+++|++++|+.|++++
T Consensus        39 v~rg~~~~~~k~~~a~~~GA~gvIi~~~~~~~~~~~~~~~~~~~~iP~v~I~~~~g~~L~~~i  101 (101)
T PF02225_consen   39 VERGSCSFDDKVRNAQKAGAKGVIIYNPPPNNGSMIDSEDPDPIDIPVVFISYEDGEALLAYI  101 (101)
T ss_dssp             EESTSSCHHHHHHHHHHTTESEEEEE-TSCSCTTTTCEBTTTSTBSEEEEE-HHHHHHHHHHH
T ss_pred             EecCCCCHHHHHHHHHHcCCEEEEEEeCCccccCcccccCCCCcEEEEEEeCHHHHhhhhccC
Confidence            479999999999999999999999999222 11233334566789999999999999999864

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 ....

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

Probab=99.47  E-value=2e-13  Score=95.69  Aligned_cols=65  Identities=32%  Similarity=0.378  Sum_probs=52.2

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeee-eCCCCCeeeEEEEchhhHHHHHHHhhcC
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYM-TYPEGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m-~~~~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                      |+||+|+|.+|+++|+++||+|+||||+.+....... ...+...||+++|++++|+.|++.+..+
T Consensus        50 v~rg~c~f~~K~~~A~~aGA~~vIv~n~~~~~~~~~~~~~~~~~~Ip~v~Is~~~G~~L~~~l~~g  115 (122)
T cd02130          50 IERGECPFGDKSALAGAAGAAAAIIYNNVPAGGLSGTLGEPSGPYVPTVGISQEDGKALVAALANG  115 (122)
T ss_pred             EECCCCCHHHHHHHHHHCCCcEEEEEECCCCcccccccCCCCCCEeeEEEecHHHHHHHHHHHhcC
Confidence            5899999999999999999999999997732222212 2334678999999999999999987643

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

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

Probab=99.46  E-value=6e-14  Score=108.04  Aligned_cols=50  Identities=34%  Similarity=0.788  Sum_probs=43.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ....|.+||+...+.   ..+||||+||+.||..|...... ||+||.....++
T Consensus       238 a~~kC~LCLe~~~~p---SaTpCGHiFCWsCI~~w~~ek~e-CPlCR~~~~psk  287 (293)
T KOG0317|consen  238 ATRKCSLCLENRSNP---SATPCGHIFCWSCILEWCSEKAE-CPLCREKFQPSK  287 (293)
T ss_pred             CCCceEEEecCCCCC---CcCcCcchHHHHHHHHHHccccC-CCcccccCCCcc
Confidence            557899999998844   79999999999999999988776 999999876543

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.41  E-value=1.3e-13  Score=101.42  Aligned_cols=51  Identities=31%  Similarity=0.745  Sum_probs=41.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---------------CCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---------------GTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---------------~~~CP~Cr~~i~~~~  202 (214)
                      ++.+|+||++.+++   ...++|||+||+.||..|+...               ...||+||..+....
T Consensus        17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            56789999999874   4778999999999999998531               226999999987644

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

Probab=99.41  E-value=9.9e-13  Score=92.18  Aligned_cols=65  Identities=28%  Similarity=0.282  Sum_probs=52.3

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCee-eeeCC-CCCeeeEEEEchhhHHHHHHHhhcC
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLI-YMTYP-EGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~-~m~~~-~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                      ++||+|+|.+|+++|+++||+|+|+||+.+..... .+... ...+||+++|++++|+.|.+.+..+
T Consensus        49 v~rg~c~f~~K~~~A~~aGA~avIi~n~~~~~~~~~~~~~~~~~~~iP~~~Is~~~G~~l~~~l~~g  115 (122)
T cd04816          49 VDRGGCPFADKQKVAAARGAVAVIVVNNSDGGGTAGTLGAPNIDLKVPVGVITKAAGAALRRRLGAG  115 (122)
T ss_pred             EECCCCCHHHHHHHHHHCCCcEEEEEeCCCCccccccccCCCCCCeeeEEEEcHHHHHHHHHHHcCC
Confidence            47999999999999999999999999987642211 12222 4578999999999999999988643

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.

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

Probab=99.40  E-value=1.4e-12  Score=90.99  Aligned_cols=69  Identities=32%  Similarity=0.368  Sum_probs=57.0

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCC-CCCeeeEEEEchhhHHHHHHHhh-cCCCce
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYP-EGANVPAFYVTLETGAYLKEHAR-GEAGEC   69 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~-~~~~Ip~v~v~~~~g~~L~~~~~-~~~~~~   69 (214)
                      ++||+|+|.+|+.+|+++||+|+|+||+.+....+.|... ....||+++|++++|..|++++. ++++.+
T Consensus        46 ~~rg~c~f~~k~~~a~~aGA~gvIi~~~~~~~~~~~~~~~~~~~~iP~v~V~~~~g~~l~~~l~~g~~v~v  116 (118)
T cd04818          46 IDRGTCNFTVKVLNAQNAGAIAVIVANNVAGGAPITMGGDDPDITIPAVMISQADGDALKAALAAGGTVTV  116 (118)
T ss_pred             EECCCCCHHHHHHHHHHCCCeEEEEEECCCCCcceeccCCCCCCEEeEEEecHHHHHHHHHHHhcCCcEEE
Confidence            4789999999999999999999999998775445666643 35689999999999999999987 444443

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.

>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=99.37  E-value=4.1e-13  Score=78.91  Aligned_cols=46  Identities=39%  Similarity=0.947  Sum_probs=38.5

Q ss_pred             CcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      +..|.||++...   .+..+||||. |+..|+..|+..... ||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~-CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKK-CPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSB-BTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCC-CCcCChhhc
Confidence            357999999976   5789999999 999999999986555 999999885

...

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

Probab=99.36  E-value=2.6e-12  Score=90.49  Aligned_cols=62  Identities=23%  Similarity=0.297  Sum_probs=48.4

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhhcC
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                      |+||+|+|.+|+++|+++||+||||||+.+. .. .+...+...+|++++ +++|+.|++.+..+
T Consensus        61 v~rg~c~f~~K~~nA~~aGA~aviiyn~~~~-~~-~~~~~~~~~~~~~~~-~~~G~~l~~~l~~G  122 (129)
T cd02124          61 VRRGTCTFATKAANAAAKGAKYVLIYNNGSG-PT-DQVGSDADSIIAAVT-PEDGEAWIDALAAG  122 (129)
T ss_pred             EECCCCCHHHHHHHHHHcCCcEEEEEECCCC-cc-cccCCCCcceeeEEe-HHHHHHHHHHHhcC
Confidence            5899999999999999999999999998764 22 333333445666666 99999999987533

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.

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

Probab=99.34  E-value=6.2e-13  Score=99.64  Aligned_cols=53  Identities=34%  Similarity=0.648  Sum_probs=44.7

Q ss_pred             CCCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCC--CccccccccccccC
Q 028085          148 GRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT--FCPVCRHEIRRSTS  203 (214)
Q Consensus       148 ~~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~--~CP~Cr~~i~~~~~  203 (214)
                      +...+|.||||.-+   ..+++.|||+|||.||-+||..+..  .||+||..+...+-
T Consensus        45 ~~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v   99 (230)
T KOG0823|consen   45 GGFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV   99 (230)
T ss_pred             CCceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence            36679999999977   4489999999999999999988643  59999998876653

>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=99.32  E-value=1.5e-12  Score=74.64  Aligned_cols=45  Identities=49%  Similarity=1.122  Sum_probs=36.3

Q ss_pred             ccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      +|+||++.+.  +.+..++|||.||..|++.|+...+..||.||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999983  34555669999999999999987444599998764

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

Probab=99.30  E-value=1.3e-12  Score=93.73  Aligned_cols=51  Identities=31%  Similarity=0.633  Sum_probs=43.0

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ....|+|||+.+... .+.-+.|||+||+.||+.-++.... ||+||+.|+.+
T Consensus       130 ~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~-CP~C~kkIt~k  180 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNK-CPTCRKKITHK  180 (187)
T ss_pred             cccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCC-CCCcccccchh
Confidence            457899999999865 3356889999999999999988776 99999977644

>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=99.30  E-value=1.4e-12  Score=72.47  Aligned_cols=39  Identities=41%  Similarity=1.094  Sum_probs=32.2

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVC  194 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~C  194 (214)
                      |+||++.+.+  .+..++|||.||++|+.+|++.+ ..||+|
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            8999999884  45789999999999999999984 459998

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

Probab=99.26  E-value=2.8e-11  Score=87.18  Aligned_cols=67  Identities=31%  Similarity=0.409  Sum_probs=54.0

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhhcCCCceE
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGEAGECC   70 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~~~~~~~~   70 (214)
                      ++||+|+|.+|+++|+++||+|+|+||+.+.  ...|.......||+++|++++|+.|.+++.. ...+.
T Consensus        53 ~~rg~c~~~~K~~~a~~aGA~gvIi~n~~~~--~~~~~~~~~~~iP~v~Is~~dG~~L~~~l~~-~~~i~  119 (143)
T cd02133          53 IQRGEITFVEKIANAKAAGAVGVIIYNNVDG--LIPGTLGEAVFIPVVFISKEDGEALKAALES-SKKLT  119 (143)
T ss_pred             EECCCCCHHHHHHHHHHCCCeEEEEeecCCC--cccccCCCCCeEeEEEecHHHHHHHHHHHhC-CCeEE
Confidence            4799999999999999999999999998764  2334322346899999999999999999865 44444

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

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

Probab=99.26  E-value=1.5e-11  Score=101.03  Aligned_cols=73  Identities=25%  Similarity=0.463  Sum_probs=58.8

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeee-----CCCCCeeeEEEEchhhHHHHHHHh-hcCCCceEEecc
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT-----YPEGANVPAFYVTLETGAYLKEHA-RGEAGECCIFPL   74 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~-----~~~~~~Ip~v~v~~~~g~~L~~~~-~~~~~~~~~~p~   74 (214)
                      +.||+|+|.+|++.||++||+|+++-|+.++  +..|.     ...+++||++|+++++|..|.+.. .+..+++.+..|
T Consensus       101 v~RGnC~Ft~Ka~~Aq~aGAsaLliin~~~d--~~~~~~~~~~~~~dv~IPv~mi~~~~~~~l~~~~~~~~~V~~~lYaP  178 (541)
T KOG2442|consen  101 VFRGNCSFTEKAKLAQAAGASALLIINNKKD--LLFMPCGNKETSLDVTIPVAMISYSDGRDLNKSTRSNDNVELALYAP  178 (541)
T ss_pred             EecccceeehhhhhhhhcCceEEEEEcCchh--hccCCCCCCCccccccceEEEEEhhhHHHHHhhhccCCeEEEEEECC
Confidence            4699999999999999999999999997553  44443     445789999999999999998754 456677777655


Q ss_pred             c
Q 028085           75 S   75 (214)
Q Consensus        75 ~   75 (214)
                      .
T Consensus       179 k  179 (541)
T KOG2442|consen  179 K  179 (541)
T ss_pred             C
Confidence            4

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

Probab=99.24  E-value=4.8e-12  Score=71.09  Aligned_cols=39  Identities=36%  Similarity=0.886  Sum_probs=31.2

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHhCCC---Ccccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT---FCPVC  194 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~---~CP~C  194 (214)
                      |+||++.|.   +++.|+|||.|+..||..|++....   .||.|
T Consensus         1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            899999999   6689999999999999999987643   59987

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

Probab=99.23  E-value=7.7e-12  Score=79.73  Aligned_cols=50  Identities=32%  Similarity=0.820  Sum_probs=37.9

Q ss_pred             Cccccccccccc--------CCC--ceEEecCCCccChhhHHHHHHhCC--CCccccccccc
Q 028085          150 ETLCSICLEDYR--------EGE--NLRVLPCRHEFHSSCVDSWLIRWG--TFCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~--------~~~--~~~~l~C~H~FH~~Ci~~Wl~~~~--~~CP~Cr~~i~  199 (214)
                      ++.|.||...|.        +||  .+..-.|+|.||..||.+|+..++  ..||+||++..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            567999888876        223  333335999999999999998753  37999999764

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

Probab=99.22  E-value=4.7e-11  Score=84.03  Aligned_cols=63  Identities=30%  Similarity=0.447  Sum_probs=51.6

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeC----CCCCeeeEEEEchhhHHHHHHHhhc
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTY----PEGANVPAFYVTLETGAYLKEHARG   64 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~----~~~~~Ip~v~v~~~~g~~L~~~~~~   64 (214)
                      ++||+|+|.+|+++|+++||+|+||||+.+. ....|..    .....||+++|+.++|+.|.+++..
T Consensus        52 ~~~g~~~~~~k~~~a~~~GA~gvii~~~~~~-~~~~~~~~~~~~~~~~iP~~~is~~~g~~l~~~~~~  118 (126)
T cd00538          52 VRRGGCSFSEKVKNAQKAGAKAVIIYNNGDD-PGPQMGSVGLESTDPSIPTVGISYADGEALLSLLEA  118 (126)
T ss_pred             EECCCcCHHHHHHHHHHCCCEEEEEEECCCC-cccccccccCCCCCCcEeEEEeCHHHHHHHHHHHhc
Confidence            4689999999999999999999999998764 2223321    2456899999999999999998863

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

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.21  E-value=7.5e-12  Score=71.34  Aligned_cols=44  Identities=34%  Similarity=0.846  Sum_probs=37.3

Q ss_pred             ccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccc
Q 028085          152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRH  196 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~  196 (214)
                      .|.+|++.|.+.+..+.|+|||+|+..|+..+... ...||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~-~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGK-SVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCC-CCCCcCCCC
Confidence            49999999966668899999999999999998833 335999985

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

Probab=99.19  E-value=1.3e-11  Score=106.88  Aligned_cols=52  Identities=46%  Similarity=1.006  Sum_probs=45.2

Q ss_pred             CCcccccccccccCCCc--eEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGEN--LRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~--~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||+|.+..++.  +..|||+|+||..|+..|++++++ ||+||..+...
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qt-CP~CR~~~~~~  343 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQT-CPTCRTVLYDY  343 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCc-CCcchhhhhcc
Confidence            46789999999998765  789999999999999999999776 99999955443

>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=99.15  E-value=2.4e-11  Score=68.28  Aligned_cols=40  Identities=40%  Similarity=1.089  Sum_probs=33.6

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHh-CCCCcccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR-WGTFCPVC  194 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~-~~~~CP~C  194 (214)
                      |+||++.+.+.  ...++|||.||.+|+.+|++. ....||+|
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            89999998844  258899999999999999994 34479998

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

>smart00184 RING Ring finger

Probab=99.13  E-value=4.7e-11  Score=65.98  Aligned_cols=39  Identities=46%  Similarity=1.162  Sum_probs=33.0

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVC  194 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~C  194 (214)
                      |+||++...   .+..++|+|.||..|++.|+...+..||+|
T Consensus         1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999943   678999999999999999998444469987

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)

>PHA02926 zinc finger-like protein; Provisional

Probab=99.12  E-value=3.7e-11  Score=89.58  Aligned_cols=51  Identities=31%  Similarity=0.785  Sum_probs=38.1

Q ss_pred             CCcccccccccccCC----C-ceEEe-cCCCccChhhHHHHHHhCC-----CCccccccccc
Q 028085          149 RETLCSICLEDYREG----E-NLRVL-PCRHEFHSSCVDSWLIRWG-----TFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----~-~~~~l-~C~H~FH~~Ci~~Wl~~~~-----~~CP~Cr~~i~  199 (214)
                      .+.+|+||+|..-++    + ..-.| +|+|.||..||..|...+.     ..||+||..+.
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            457899999986432    1 22345 5999999999999998632     25999999765

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

Probab=99.12  E-value=6.3e-11  Score=97.32  Aligned_cols=51  Identities=33%  Similarity=0.832  Sum_probs=39.1

Q ss_pred             CCcccccccccccCC--------------CceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREG--------------ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~--------------~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      ....|+||+.+..-.              .....+||.|+||..|+.+|+...+-.||.||+++.
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            345799999875311              123467999999999999999965545999999875

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

Probab=99.05  E-value=9e-10  Score=77.63  Aligned_cols=66  Identities=23%  Similarity=0.080  Sum_probs=51.7

Q ss_pred             Cccccc--cHHHHHHHHHHcCCcEEEEEeCCCCCCeeeee--C--CCCCeeeEEEEchhhHHHHHHHhhcCC
Q 028085            1 MIRGQC--NFSYKIQNAQAAGYDAAIVYALRKKSPLIYMT--Y--PEGANVPAFYVTLETGAYLKEHARGEA   66 (214)
Q Consensus         1 v~rg~C--~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~--~--~~~~~Ip~v~v~~~~g~~L~~~~~~~~   66 (214)
                      |+||.|  +|.+|+++|+++||+|+|+||+.++.-.....  .  .....||++.|+.++|+.|...++.+.
T Consensus        50 v~~g~~~~~~~~k~~~A~~~GA~avi~~~~~~g~~~~~~~~~~~~~~~~~IP~v~Is~edg~~L~~~l~~g~  121 (127)
T cd04819          50 VKRDDPDVDRKEKYAKAVAAGAAAFVVVNTVPGVLPATGDEGTEDGPPSPIPAASVSGEDGLRLARVAERND  121 (127)
T ss_pred             EEcCCCchhHHHHHHHHHHCCCEEEEEEeCCCCcCcccccccccCCCCCCCCEEEEeHHHHHHHHHHHhcCC
Confidence            478999  99999999999999999999876542111111  1  234689999999999999999887543

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

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

Probab=99.05  E-value=4.6e-11  Score=91.12  Aligned_cols=54  Identities=26%  Similarity=0.698  Sum_probs=44.9

Q ss_pred             CCcccccccccccCCC-------ceEEecCCCccChhhHHHHHHhCCC-Ccccccccccccc
Q 028085          149 RETLCSICLEDYREGE-------NLRVLPCRHEFHSSCVDSWLIRWGT-FCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~-------~~~~l~C~H~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~~~~  202 (214)
                      ++..|+||-..+....       ....|.|+|+||+.||..|....+. +||.|+..+..+.
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            6789999998876553       6789999999999999999876644 7999998876554

>smart00504 Ubox Modified RING finger domain

Probab=99.05  E-value=1.8e-10  Score=71.02  Aligned_cols=48  Identities=25%  Similarity=0.593  Sum_probs=40.7

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ..|+||.+.+.+.   ..++|||+|++.||.+|++.+. .||+|+.++....
T Consensus         2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~-~cP~~~~~~~~~~   49 (63)
T smart00504        2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHG-TDPVTGQPLTHED   49 (63)
T ss_pred             cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCC-CCCCCcCCCChhh
Confidence            4699999999853   7889999999999999998855 4999999885443

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

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

Probab=99.05  E-value=1.3e-10  Score=65.24  Aligned_cols=39  Identities=36%  Similarity=0.769  Sum_probs=23.5

Q ss_pred             cccccccccCCC-ceEEecCCCccChhhHHHHHHhCC---CCcc
Q 028085          153 CSICLEDYREGE-NLRVLPCRHEFHSSCVDSWLIRWG---TFCP  192 (214)
Q Consensus       153 C~ICl~~~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~---~~CP  192 (214)
                      |+||.+ |.+.+ .++.|+|||+|+++|+++++..+.   ..||
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 75543 678899999999999999998652   2587

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

Probab=98.96  E-value=2.6e-10  Score=87.10  Aligned_cols=51  Identities=31%  Similarity=0.708  Sum_probs=42.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHH-HHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDS-WLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~-Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++...   ....++|||+||+.||.. |-..+-..||+||+....++
T Consensus       214 ~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         214 ADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             cccceeeeecccC---CcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            5678999999988   558999999999999999 87664446999999876543

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

Probab=98.90  E-value=1.2e-09  Score=67.75  Aligned_cols=47  Identities=30%  Similarity=0.640  Sum_probs=33.1

Q ss_pred             ccccccccCCCceE-Ee-cCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          154 SICLEDYREGENLR-VL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       154 ~ICl~~~~~~~~~~-~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +-|-....++++.. .. -|.|.||..||.+||.++.. ||++|++..-.
T Consensus        35 ~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~-CPld~q~w~~~   83 (88)
T COG5194          35 PECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGV-CPLDRQTWVLA   83 (88)
T ss_pred             cccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCC-CCCCCceeEEe
Confidence            33333333455332 23 49999999999999999777 99999976443

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

Probab=98.89  E-value=1.4e-09  Score=63.08  Aligned_cols=43  Identities=30%  Similarity=0.893  Sum_probs=34.2

Q ss_pred             ccccccccccCCCceEEecCC-----CccChhhHHHHHHhCCC-Cccccc
Q 028085          152 LCSICLEDYREGENLRVLPCR-----HEFHSSCVDSWLIRWGT-FCPVCR  195 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~-----H~FH~~Ci~~Wl~~~~~-~CP~Cr  195 (214)
                      .|.||++ ..+++....+||.     |.+|.+|+++|+...+. +||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 4444566789984     89999999999987643 699995

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.89  E-value=8.2e-10  Score=90.86  Aligned_cols=49  Identities=31%  Similarity=0.636  Sum_probs=41.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ....|+||++.|..   ...++|||.||..|+..|+..... ||+||..+...
T Consensus        25 ~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~-CP~Cr~~~~~~   73 (397)
T TIGR00599        25 TSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPK-CPLCRAEDQES   73 (397)
T ss_pred             cccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCC-CCCCCCccccc
Confidence            45789999999973   367899999999999999987554 99999987643

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

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

Probab=98.88  E-value=4.8e-10  Score=78.95  Aligned_cols=62  Identities=31%  Similarity=0.475  Sum_probs=50.5

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCC----Ceeeee---CCCCCeeeEEEEchhhHHHHHHHh
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKS----PLIYMT---YPEGANVPAFYVTLETGAYLKEHA   62 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~----~~~~m~---~~~~~~Ip~v~v~~~~g~~L~~~~   62 (214)
                      ++||+|||..|.++++++||.|+||.|+..++    ..+.|-   +-...+||++|+...+|-.++..+
T Consensus        93 ~eRGeCSFl~Ktl~~e~aGa~aiiitd~~~~~~sf~~YveMI~D~sq~~AniPa~fllg~~Gy~ir~sL  161 (193)
T KOG3920|consen   93 MERGECSFLVKTLNGEKAGATAIIITDSQNYEYSFHQYVEMIPDESQDRANIPAVFLLGVTGYYIRVSL  161 (193)
T ss_pred             EecCCceeeehhhhhhhcCceEEEEecCCCCchhHHHHHHhcCcccccccCCceEEEeccceEEEehhH
Confidence            58999999999999999999999999865433    256775   234579999999999998776655

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

Probab=98.86  E-value=1.1e-09  Score=90.79  Aligned_cols=50  Identities=28%  Similarity=0.563  Sum_probs=41.2

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCC----Ccccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT----FCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~----~CP~Cr~~i~~~~  202 (214)
                      +..|+|||+...   ....+.|||+||..||-+++.....    .||+||..|..+.
T Consensus       186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            678999999987   4467779999999999999987521    6999999887643

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

Probab=98.79  E-value=2e-08  Score=70.65  Aligned_cols=61  Identities=20%  Similarity=0.159  Sum_probs=50.4

Q ss_pred             ccccc-cHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhhcC
Q 028085            2 IRGQC-NFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus         2 ~rg~C-~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                      +||.| +|.+|+++|+++||.|+|++|+.++.  ..+. .....||+++|++++|+.|++++..+
T Consensus        58 ~~~~~~~~~~k~~~~~~~GA~gvI~~~~~~~~--~~~~-~~~~~iP~v~I~~~~g~~l~~y~~~~  119 (126)
T cd02120          58 DRGGNTSRVAKGDAVKAAGGAGMILANDPTDG--LDVV-ADAHVLPAVHVDYEDGTAILSYINST  119 (126)
T ss_pred             eCCCCccHHHHHHHHHHcCCcEEEEEecCCCC--ceec-ccccccceEEECHHHHHHHHHHHHcC
Confidence            68899 99999999999999999999977652  1222 12467999999999999999998754

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

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

Probab=98.73  E-value=1.7e-09  Score=66.55  Aligned_cols=50  Identities=30%  Similarity=0.740  Sum_probs=36.6

Q ss_pred             Cccccccccccc---------CCCceEEec-CCCccChhhHHHHHHhCCC--Cccccccccc
Q 028085          150 ETLCSICLEDYR---------EGENLRVLP-CRHEFHSSCVDSWLIRWGT--FCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~---------~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~--~CP~Cr~~i~  199 (214)
                      +..|-||.-.|.         .+|-+..+- |.|.||..||.+|+....+  .||+||+...
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            346888877764         233333443 9999999999999987644  6999998754

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

Probab=98.71  E-value=3.2e-08  Score=73.25  Aligned_cols=66  Identities=20%  Similarity=0.204  Sum_probs=49.2

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCC-C-----------------eeeee------------CC-CCCeeeEEE
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKS-P-----------------LIYMT------------YP-EGANVPAFY   49 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~-~-----------------~~~m~------------~~-~~~~Ip~v~   49 (214)
                      ++||+|+|.+|+++|+++||+|||+|++..+. .                 ..+++            +. .--+||++-
T Consensus        61 vr~G~~~~~~Kv~~A~~~GA~gvIiy~Dp~d~~~~~~~~~~~g~~~~~~GDplTPG~ps~~~~~~~~~~~~~lP~IPs~P  140 (183)
T cd02128          61 VRAGKISFAEKVANAEKLGAVGVLIYPDPADFPIDPSETALFGHVHLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPAQT  140 (183)
T ss_pred             EECCCCCHHHHHHHHHHCCCEEEEEecCHHHcCcccCcceeecceeccCCCcCCCCCccccccccCcccccCCCCCCEec
Confidence            47899999999999999999999999874210 0                 00111            00 113699999


Q ss_pred             EchhhHHHHHHHhhcCC
Q 028085           50 VTLETGAYLKEHARGEA   66 (214)
Q Consensus        50 v~~~~g~~L~~~~~~~~   66 (214)
                      |++++++.|++.+.+..
T Consensus       141 IS~~da~~lL~~l~G~~  157 (183)
T cd02128         141 ISAAAAAKLLSKMGGPV  157 (183)
T ss_pred             cCHHHHHHHHHHcCCCC
Confidence            99999999999887543

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

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

Probab=98.67  E-value=4.9e-08  Score=69.38  Aligned_cols=65  Identities=18%  Similarity=0.249  Sum_probs=50.8

Q ss_pred             Cccccc------cHHHH-------HHHHHHcCCcEEEEEeCCCCC---C-eeeeeC-CCCCeeeEEEEchhhHHHHHHHh
Q 028085            1 MIRGQC------NFSYK-------IQNAQAAGYDAAIVYALRKKS---P-LIYMTY-PEGANVPAFYVTLETGAYLKEHA   62 (214)
Q Consensus         1 v~rg~C------~f~~K-------~~~a~~~ga~aviv~~~~~~~---~-~~~m~~-~~~~~Ip~v~v~~~~g~~L~~~~   62 (214)
                      |+||.|      +|..|       .+.|+++||.|+|+||+.+.+   . ...+.. .....||++.|+.++|..|...+
T Consensus        45 v~~~~~~~~~~~~~~~k~~~r~~~~~~A~~~GA~avIv~s~~~~~~~~~~~G~~~~~~~~~~IP~v~is~ed~~~L~r~l  124 (134)
T cd04815          45 FNQPMVRTQTGSGYGPTVAYRRRGAVEAAKKGAVAVLIRSIGTDSHRSPHTGMMSYDDGVPKIPAAAISVEDADMLERLA  124 (134)
T ss_pred             ecCCccccCchhhcCchhhhhhHHHHHHHhCCCEEEEEEecCcccCCCCcCCccccCCCCCCCCEEEechhcHHHHHHHH
Confidence            478999      99999       799999999999999965331   1 222333 33468999999999999999888


Q ss_pred             hcC
Q 028085           63 RGE   65 (214)
Q Consensus        63 ~~~   65 (214)
                      +.+
T Consensus       125 ~~g  127 (134)
T cd04815         125 ARG  127 (134)
T ss_pred             hCC
Confidence            643

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

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

Probab=98.64  E-value=1.7e-08  Score=63.95  Aligned_cols=50  Identities=32%  Similarity=0.554  Sum_probs=38.7

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ...|+|+.+-+.   .++.+|+||.|.+.||..|+..+..+||+|+.++....
T Consensus         4 ~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    4 EFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             ccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            468999999999   55899999999999999999985556999999887654

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 ....

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

Probab=98.63  E-value=2.1e-08  Score=80.03  Aligned_cols=51  Identities=37%  Similarity=0.777  Sum_probs=41.3

Q ss_pred             CCcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccccC
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRSTS  203 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~  203 (214)
                      ...+|.||+++-+   ...+|||+|. .|..|.+...-+.+. ||+||+++....+
T Consensus       289 ~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~-CPICRqpi~~ll~  340 (349)
T KOG4265|consen  289 SGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNN-CPICRQPIEELLE  340 (349)
T ss_pred             CCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcC-CCccccchHhhhe
Confidence            4568999999987   4489999997 999999886644454 9999999876543

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

Probab=98.61  E-value=1.1e-08  Score=64.12  Aligned_cols=52  Identities=29%  Similarity=0.691  Sum_probs=25.0

Q ss_pred             CcccccccccccCCCce--EEe---cCCCccChhhHHHHHHhC---C----C---Cccccccccccc
Q 028085          150 ETLCSICLEDYREGENL--RVL---PCRHEFHSSCVDSWLIRW---G----T---FCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~--~~l---~C~H~FH~~Ci~~Wl~~~---~----~---~CP~Cr~~i~~~  201 (214)
                      +.+|.||++.+.+++++  ..-   .|++.||..||.+|+...   +    .   .||.|+.+|.-+
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            35799999987633322  222   389999999999999752   1    1   599999988643

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.59  E-value=3.5e-08  Score=78.20  Aligned_cols=53  Identities=32%  Similarity=0.683  Sum_probs=39.1

Q ss_pred             Cccccccccc-ccCCC-ceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          150 ETLCSICLED-YREGE-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~-~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      +..||+|.++ |...+ .+..-+|||.||..|++..+......||.|+.++....
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            4679999996 33333 22333799999999999977555446999999886554

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).

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

Probab=98.48  E-value=4.1e-08  Score=77.57  Aligned_cols=49  Identities=31%  Similarity=0.680  Sum_probs=41.9

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      -..|.||.+.|.   ...++||+|.||.-||...|..+-. ||.|+.++....
T Consensus        23 lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~-CP~C~~~~~Es~   71 (442)
T KOG0287|consen   23 LLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQ-CPTCCVTVTESD   71 (442)
T ss_pred             HHHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCC-CCceecccchhh
Confidence            357999999999   4489999999999999999977555 999999876543

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

Probab=98.46  E-value=9.1e-08  Score=62.51  Aligned_cols=47  Identities=30%  Similarity=0.685  Sum_probs=34.5

Q ss_pred             Ccccccccccc-------------cCCCceEEe-cCCCccChhhHHHHHHhCCCCccccccc
Q 028085          150 ETLCSICLEDY-------------REGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHE  197 (214)
Q Consensus       150 ~~~C~ICl~~~-------------~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~  197 (214)
                      -+.|+||..-+             ..++-.... -|.|.||..||.+||++++. ||+|.++
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~v-CPLdn~e  106 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNV-CPLDNKE  106 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCc-CCCcCcc
Confidence            35799987442             222323333 49999999999999999887 9999765

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

Probab=98.45  E-value=3.8e-08  Score=86.98  Aligned_cols=49  Identities=35%  Similarity=0.878  Sum_probs=38.0

Q ss_pred             CCcccccccccccCCCceEEec------CCCccChhhHHHHHHhCCC-Cccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP------CRHEFHSSCVDSWLIRWGT-FCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~------C~H~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~  199 (214)
                      +..+||||+.-+..-|  |.||      |+|-||..|+-+|+..... +||+||..++
T Consensus      1468 G~eECaICYsvL~~vd--r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1468 GHEECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CcchhhHHHHHHHHHh--ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            5568999998765222  2333      8999999999999988644 7999998875

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

Probab=98.44  E-value=6.8e-08  Score=75.30  Aligned_cols=54  Identities=26%  Similarity=0.416  Sum_probs=44.7

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccCCCC
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEG  206 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~~  206 (214)
                      ..+|+||+..-.   ....|+|+|.||.-||+.-.+..+..||+||.+|...-...+
T Consensus         7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~~~p   60 (324)
T KOG0824|consen    7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTIDFEP   60 (324)
T ss_pred             CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcchhcch
Confidence            468999999877   458999999999999999887776679999999987654433

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

Probab=98.43  E-value=8.5e-08  Score=78.49  Aligned_cols=48  Identities=33%  Similarity=0.812  Sum_probs=37.8

Q ss_pred             CCcccccccccccCCC-ceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGE-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .-.+|+||||.+-+.- -++.+.|.|.||..|+..|.  ..+ ||+||....
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~s-cpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSS-CPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCc-ChhhhhhcC
Confidence            3368999999986552 34566799999999999997  344 999998654

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

Probab=98.42  E-value=1e-07  Score=73.84  Aligned_cols=47  Identities=30%  Similarity=0.482  Sum_probs=40.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .-..|-||-+.+.   ....++|||.||.-||...|..+-. ||+||.+..
T Consensus        24 s~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~-CP~Cr~~~~   70 (391)
T COG5432          24 SMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPF-CPVCREDPC   70 (391)
T ss_pred             hHHHhhhhhheee---cceecccccchhHHHHHHHhcCCCC-CccccccHH
Confidence            3468999999999   4488999999999999999987655 999998754

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

Probab=98.39  E-value=1.2e-07  Score=76.26  Aligned_cols=45  Identities=29%  Similarity=0.834  Sum_probs=35.3

Q ss_pred             cccccccccccCCCceEEec-CCCccChhhHHHHHHhCCC--Cccccc
Q 028085          151 TLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGT--FCPVCR  195 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~--~CP~Cr  195 (214)
                      -.|.||.+-+...+.+.-+. |||+||..|+.+|+...-+  .||.||
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~   52 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ   52 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence            47999955555445666665 9999999999999987533  599999

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

Probab=98.30  E-value=2.1e-07  Score=75.32  Aligned_cols=44  Identities=43%  Similarity=0.871  Sum_probs=38.3

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRH  196 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~  196 (214)
                      +...|+||++.|...   ..+||+|.||..|+..++. ....||.||.
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence            557899999999966   8999999999999999997 3446999993

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

Probab=98.26  E-value=1.8e-07  Score=53.83  Aligned_cols=48  Identities=25%  Similarity=0.546  Sum_probs=35.9

Q ss_pred             CCcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .+++|.||+|.-.+.   ....|||. .|.+|-.+.++-..-.||+||+++.
T Consensus         6 ~~dECTICye~pvds---VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    6 WSDECTICYEHPVDS---VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cccceeeeccCcchH---HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            447899999986643   34569996 8899987766533335999999874

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

Probab=98.24  E-value=2.2e-07  Score=81.01  Aligned_cols=50  Identities=22%  Similarity=0.546  Sum_probs=42.6

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      -..|+.|-+...   ...++.|+|+||..|+.+-+..++..||.|..++..++
T Consensus       643 ~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  643 LLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             ceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            358999998877   44678899999999999999988778999999886553

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

Probab=98.18  E-value=1.1e-06  Score=71.21  Aligned_cols=50  Identities=34%  Similarity=0.831  Sum_probs=38.2

Q ss_pred             CCcccccccccccCC--CceEEecCCCccChhhHHHHHHhCCC-Ccccccccc
Q 028085          149 RETLCSICLEDYREG--ENLRVLPCRHEFHSSCVDSWLIRWGT-FCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~--~~~~~l~C~H~FH~~Ci~~Wl~~~~~-~CP~Cr~~i  198 (214)
                      ....|+|||+.++..  ..+..+.|||.|..+||+.||-+... .||.|.-..
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            346899999998644  35666779999999999999963211 699996543

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

Probab=98.13  E-value=3.4e-07  Score=72.95  Aligned_cols=51  Identities=25%  Similarity=0.562  Sum_probs=42.9

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+|||+-++..   +.++ |.|-||.+||..-++..+..||.||..+....
T Consensus        42 ~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr   93 (381)
T KOG0311|consen   42 IQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR   93 (381)
T ss_pred             hhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence            567899999999843   5666 99999999999999887778999999886554

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

Probab=98.09  E-value=5.6e-07  Score=78.36  Aligned_cols=51  Identities=31%  Similarity=0.503  Sum_probs=42.9

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ...|++||..+.++.....-+|+|.||..|++.|-+..++ ||+||..+..-
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqT-CPiDR~EF~~v  173 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQT-CPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhccc-Cchhhhhhhee
Confidence            3579999999887766666679999999999999988777 99999876543

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

Probab=98.06  E-value=1.1e-06  Score=70.86  Aligned_cols=48  Identities=40%  Similarity=0.792  Sum_probs=40.1

Q ss_pred             CcccccccccccCCC-ceEEecCCCccChhhHHHHHHhCCC-Cccccccc
Q 028085          150 ETLCSICLEDYREGE-NLRVLPCRHEFHSSCVDSWLIRWGT-FCPVCRHE  197 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~~-~CP~Cr~~  197 (214)
                      +.-|..|-+.+-..+ .+-.|||.|+||..|+...|+++.. +||.||+-
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl  414 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL  414 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            457999999986554 6778999999999999999988755 79999943

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

Probab=98.01  E-value=1.2e-06  Score=52.63  Aligned_cols=47  Identities=32%  Similarity=0.642  Sum_probs=23.1

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ..|++|.+-+..  .+....|.|+|++.|+..-+.  . .||+|+.+...++
T Consensus         8 LrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~--~-~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIG--S-ECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--SS---B---SSS--B-TTTGGGGTT--T-B-SSS--B-S-SS
T ss_pred             cCCcHHHHHhcC--CceeccCccHHHHHHhHHhcC--C-CCCCcCChHHHHH
Confidence            479999999872  334556999999999977442  3 4999999886654

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

Probab=97.92  E-value=5.7e-06  Score=49.44  Aligned_cols=43  Identities=26%  Similarity=0.623  Sum_probs=28.7

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCC-Cccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT-FCPV  193 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~-~CP~  193 (214)
                      ....|+|.+..|+  +.++-..|||+|-++.|.+|+..++. .||.
T Consensus        10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            4468999999988  45566689999999999999954433 6998

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

Probab=97.92  E-value=4e-06  Score=68.03  Aligned_cols=51  Identities=33%  Similarity=0.802  Sum_probs=38.6

Q ss_pred             CCcccccccccccCCC----ceEEec-CCCccChhhHHHHHHhCC------CCccccccccc
Q 028085          149 RETLCSICLEDYREGE----NLRVLP-CRHEFHSSCVDSWLIRWG------TFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~----~~~~l~-C~H~FH~~Ci~~Wl~~~~------~~CP~Cr~~i~  199 (214)
                      .+..|.||++...+.-    ...+|| |.|.||.+|+..|-...+      ..||.||....
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            5678999999976442    123456 999999999999995444      26999998654

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

Probab=97.90  E-value=3.5e-06  Score=68.26  Aligned_cols=47  Identities=38%  Similarity=0.946  Sum_probs=38.7

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhC-CCCcccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW-GTFCPVCRHEIRR  200 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~-~~~CP~Cr~~i~~  200 (214)
                      ..|-||-|+-+   .+++=||||..|..|+..|-... ...||.||..|--
T Consensus       370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            46999998844   67888999999999999998554 3369999998753

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

Probab=97.89  E-value=3.5e-06  Score=65.84  Aligned_cols=51  Identities=31%  Similarity=0.755  Sum_probs=42.6

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHh----------------------CCCCccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR----------------------WGTFCPVCRHEIRRS  201 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~----------------------~~~~CP~Cr~~i~~~  201 (214)
                      ..|+|||--|.+++....++|-|.||..|+.++|..                      ....||+||..|-..
T Consensus       116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            579999999999999999999999999999888741                      012599999987544

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

Probab=97.88  E-value=2.7e-05  Score=59.67  Aligned_cols=64  Identities=19%  Similarity=0.171  Sum_probs=47.5

Q ss_pred             ccccccHHHHHHHHHHcCCcEEEEEeCCCCC-------------------Ceeeee----------C-------------
Q 028085            2 IRGQCNFSYKIQNAQAAGYDAAIVYALRKKS-------------------PLIYMT----------Y-------------   39 (214)
Q Consensus         2 ~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~-------------------~~~~m~----------~-------------   39 (214)
                      ++|.|.+.+|+++|+++||+|||+|++..+.                   +.+.++          +             
T Consensus        78 r~G~~~~~~Kv~~A~~~GA~gVIiy~Dp~d~~~~~~~~~~~yP~g~~~~~~~vqRgsv~~~~~~~GDplTPG~ps~~~~~  157 (220)
T cd02121          78 RYGGIFRGLKVKNAQLAGAVGVIIYSDPADDGYITGENGKTYPDGPARPPSGVQRGSVLFMSIGPGDPLTPGYPSKPGAE  157 (220)
T ss_pred             ECCCccHHHHHHHHHHcCCEEEEEEeCchhcccccccccccCCCCCCCCCCcceecceeccccCCCCCCCCCCCCCCCCc
Confidence            5789999999999999999999999864211                   011110          0             


Q ss_pred             -----C--CCCeeeEEEEchhhHHHHHHHhhcC
Q 028085           40 -----P--EGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus        40 -----~--~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                           .  .--+||++-|+..+++.|++.+.+.
T Consensus       158 r~~~~~~~~lP~IPs~PIS~~da~~lL~~L~g~  190 (220)
T cd02121         158 RRDKEESKGLPKIPSLPISYRDAQPLLKALGGP  190 (220)
T ss_pred             ccCcccccCCCCCCcccCCHHHHHHHHHHcCCC
Confidence                 0  0136999999999999999998754

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

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

Probab=97.86  E-value=2.6e-05  Score=55.68  Aligned_cols=62  Identities=15%  Similarity=0.101  Sum_probs=43.9

Q ss_pred             ccccccHHHHHHHHHHcCCcEEEEEeCCCCC--------------------Ceeeee---------C-CCCCeeeEEEEc
Q 028085            2 IRGQCNFSYKIQNAQAAGYDAAIVYALRKKS--------------------PLIYMT---------Y-PEGANVPAFYVT   51 (214)
Q Consensus         2 ~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~--------------------~~~~m~---------~-~~~~~Ip~v~v~   51 (214)
                      +.|.-.+..|+++||++||.|||||.|..+.                    ++.+..         . ..--+||+.-|+
T Consensus        47 RyG~~~RG~Kv~~A~~~GA~GviIYsDP~d~~~~~~~~~~v~~v~~~~~GDP~TPG~PS~~~~~R~~~~~lP~IPs~PIS  126 (153)
T cd02131          47 KLGQAPLLYKLSLLEEAGFGGVLLYVDPCDLPKTRHTWHQAFMVSLNPGGDPSTPGYPSADQSCRQCRGNLTSLLVQPIS  126 (153)
T ss_pred             eccCcchHHHHHHHHHCCCeEEEEecChhhccCcCCCccceEEEecCCCCCCCCCCCccccCcccCCcCCCCCCcccccC
Confidence            4477889999999999999999999874211                    111110         0 011369999999


Q ss_pred             hhhHHHHHHHhh
Q 028085           52 LETGAYLKEHAR   63 (214)
Q Consensus        52 ~~~g~~L~~~~~   63 (214)
                      ..+.+.|++.-.
T Consensus       127 ~~dA~~lL~~~~  138 (153)
T cd02131         127 AYLAKKLLSAPP  138 (153)
T ss_pred             HHHHHHHHhCCc
Confidence            999999887553

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.

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

Probab=97.83  E-value=7.8e-06  Score=67.72  Aligned_cols=49  Identities=33%  Similarity=0.632  Sum_probs=41.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+.+|.||+..+.   .+..+||||.||..||++-+.... .||.||..+...
T Consensus        83 sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~-~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   83 SEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQET-ECPLCRDELVEL  131 (398)
T ss_pred             chhhhhhhHhhcC---CCccccccccccHHHHHHHhccCC-CCcccccccccc
Confidence            6689999999998   558889999999999999776544 499999998753

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

Probab=97.65  E-value=1.3e-05  Score=67.26  Aligned_cols=62  Identities=21%  Similarity=0.548  Sum_probs=49.7

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC----CCCccccccccccccCCCCCcccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW----GTFCPVCRHEIRRSTSNEGNEQVHVS  213 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~----~~~CP~Cr~~i~~~~~~~~~~~~~~~  213 (214)
                      ++.+|-+|-+.-+   ......|+|.||+-|+..++...    +.+||.|...+.-....|..+...+.
T Consensus       535 ~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~alek~~l~  600 (791)
T KOG1002|consen  535 GEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPALEKTDLK  600 (791)
T ss_pred             CceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhhhhcchh
Confidence            5678999999876   55788999999999998887543    44899999998888777777665554

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

Probab=97.61  E-value=5.1e-05  Score=57.05  Aligned_cols=54  Identities=28%  Similarity=0.609  Sum_probs=43.7

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC-------CCCccccccccccccC
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW-------GTFCPVCRHEIRRSTS  203 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~-------~~~CP~Cr~~i~~~~~  203 (214)
                      ....|..|-..+..+|.+ .|-|-|+||++|++.|-..-       ...||-|..+|..+.+
T Consensus        49 Y~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~N  109 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPIN  109 (299)
T ss_pred             CCCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcc
Confidence            445799999999999764 68899999999999998642       1169999999876643

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

Probab=97.60  E-value=0.00017  Score=55.96  Aligned_cols=49  Identities=20%  Similarity=0.451  Sum_probs=37.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC-CCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG-TFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~-~~CP~Cr~~i~  199 (214)
                      ++.+|++|-+.-..+  ....+|||+||..|+..=..... .+||.|..+..
T Consensus       238 ~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  238 SDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             CCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            567999999885533  35677999999999988665432 26999987764

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

Probab=97.59  E-value=4.5e-05  Score=70.85  Aligned_cols=53  Identities=26%  Similarity=0.602  Sum_probs=43.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC--------C-Cccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG--------T-FCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~--------~-~CP~Cr~~i~~~  201 (214)
                      .++.|.||+.+--.......|.|+|+||-+|....|+++=        . .||+|+.+|...
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence            6788999998877777889999999999999998887641        1 699999887543

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

Probab=97.56  E-value=2.1e-05  Score=56.06  Aligned_cols=30  Identities=37%  Similarity=0.822  Sum_probs=27.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChh
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSS  178 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~  178 (214)
                      +..+|.||||+++.+|++..|||--+||+.
T Consensus       176 dkGECvICLEdL~~GdtIARLPCLCIYHK~  205 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLPCLCIYHKQ  205 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccceEEEeecC
Confidence            446899999999999999999999999973

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.56  E-value=8.6e-05  Score=53.08  Aligned_cols=50  Identities=20%  Similarity=0.586  Sum_probs=37.1

Q ss_pred             CCcccccccccccCCCceEEecC--CC---ccChhhHHHHHHhCCC-Ccccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPC--RH---EFHSSCVDSWLIRWGT-FCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C--~H---~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~~~~  202 (214)
                      .+..|-||.++..  +.  .-||  ..   .-|.+|++.|+...+. .|++|+.+..-..
T Consensus         7 ~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~   62 (162)
T PHA02825          7 MDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKK   62 (162)
T ss_pred             CCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEE
Confidence            5578999998843  22  2464  44   4599999999987654 7999999876553

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

Probab=97.46  E-value=7e-05  Score=42.91  Aligned_cols=41  Identities=39%  Similarity=0.950  Sum_probs=28.0

Q ss_pred             cccccccccCCCceEEecC---C--CccChhhHHHHHHhCCC-Ccccc
Q 028085          153 CSICLEDYREGENLRVLPC---R--HEFHSSCVDSWLIRWGT-FCPVC  194 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C---~--H~FH~~Ci~~Wl~~~~~-~CP~C  194 (214)
                      |-||++.-.+++ ....||   |  -.-|.+|+.+|+..+.. .|++|
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            679999877665 556786   2  35899999999987543 69987

>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=97.44  E-value=5e-05  Score=52.92  Aligned_cols=35  Identities=17%  Similarity=0.527  Sum_probs=29.9

Q ss_pred             CcccccccccccCCCceEEecCC------CccChhhHHHHH
Q 028085          150 ETLCSICLEDYREGENLRVLPCR------HEFHSSCVDSWL  184 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~------H~FH~~Ci~~Wl  184 (214)
                      ..+|.||++.+.+++-+..++||      |.||.+|+++|-
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            56899999999985567777774      899999999994

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

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

Probab=97.43  E-value=7e-05  Score=62.64  Aligned_cols=53  Identities=30%  Similarity=0.664  Sum_probs=43.7

Q ss_pred             CCcccccccccccCCCceEE-ecCCCccChhhHHHHHHhCCCCccccccccccccCCC
Q 028085          149 RETLCSICLEDYREGENLRV-LPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE  205 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~-l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~  205 (214)
                      .+..|++|...+.+.   .. +.|||.||..|+..|+..+. .||.|+..+......+
T Consensus        20 ~~l~C~~C~~vl~~p---~~~~~cgh~fC~~C~~~~~~~~~-~cp~~~~~~~~~~~~~   73 (391)
T KOG0297|consen   20 ENLLCPICMSVLRDP---VQTTTCGHRFCAGCLLESLSNHQ-KCPVCRQELTQAEELP   73 (391)
T ss_pred             ccccCccccccccCC---CCCCCCCCcccccccchhhccCc-CCcccccccchhhccC
Confidence            557899999999855   34 58999999999999998844 5999999887666554

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

Probab=97.36  E-value=0.00066  Score=49.01  Aligned_cols=54  Identities=19%  Similarity=0.127  Sum_probs=37.0

Q ss_pred             ccHHHHHHHHHHcCCcEEEEEeCCCCCC--eeeeeCCCCCeeeEEEEchhhHHHHHHH
Q 028085            6 CNFSYKIQNAQAAGYDAAIVYALRKKSP--LIYMTYPEGANVPAFYVTLETGAYLKEH   61 (214)
Q Consensus         6 C~f~~K~~~a~~~ga~aviv~~~~~~~~--~~~m~~~~~~~Ip~v~v~~~~g~~L~~~   61 (214)
                      |+|..|+++|+++||.|||+||+.....  .-.+.. .+. -.+++++...-..+...
T Consensus        76 ~~~~~K~~~A~~~GA~aVIv~~d~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~~  131 (151)
T cd04822          76 AGLRYKATNARRHGAAAVIVVNGPNSHSGDADRLPR-FGG-TAPQRVDIAAADPWFTA  131 (151)
T ss_pred             cCHHHHHHHHHHCCCeEEEEEeCCcccCcccccccc-cCc-cceEEechHHHHHHhhh
Confidence            9999999999999999999999765421  111110 011 11777888877777664

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

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

Probab=97.33  E-value=0.00011  Score=60.17  Aligned_cols=49  Identities=27%  Similarity=0.536  Sum_probs=40.0

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC-------CCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG-------TFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~-------~~CP~Cr~~  197 (214)
                      .-..|-||+++....+....|||+|+||+.|+..+....-       -.||-+...
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            3468999999998878999999999999999999987531       158776553

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

Probab=97.32  E-value=0.00025  Score=50.57  Aligned_cols=56  Identities=13%  Similarity=0.134  Sum_probs=35.4

Q ss_pred             cHHHHHHHHHHcCCcEEEEEeCCCCCCe--eeeeCCCCCeee-EEEEchhhHHHHHHHh
Q 028085            7 NFSYKIQNAQAAGYDAAIVYALRKKSPL--IYMTYPEGANVP-AFYVTLETGAYLKEHA   62 (214)
Q Consensus         7 ~f~~K~~~a~~~ga~aviv~~~~~~~~~--~~m~~~~~~~Ip-~v~v~~~~g~~L~~~~   62 (214)
                      +|..|+++|+++||.|||++|+.+....  -.+.+...-.++ ...|+...+.+|.+..
T Consensus        77 ~~~~K~~~A~~~GA~gvIii~~~~~~~~p~~~~~~~~~~~~~~~~~i~~~~a~~l~~~a  135 (142)
T cd04814          77 RWTYKYEEAARHGAAGVLIVHELAPASYGWATWKNPAKVHPNLEAAIQRAVAVDLFEAS  135 (142)
T ss_pred             CHHHHHHHHHHCCCcEEEEEeCCCcccCChhhhhcccccCCceeeEecHHHHHHHHhhC
Confidence            6999999999999999999997653222  111111111222 3347777777766544

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

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

Probab=97.30  E-value=0.00016  Score=57.97  Aligned_cols=47  Identities=26%  Similarity=0.636  Sum_probs=41.0

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      +++.|+||...-.   .....||+|-=|+.||.+-+++.+. |=.|+..+.
T Consensus       421 Ed~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~-CFfCktTv~  467 (489)
T KOG4692|consen  421 EDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKR-CFFCKTTVI  467 (489)
T ss_pred             ccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCe-eeEecceee
Confidence            6678999998755   4478999999999999999999777 999999876

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

Probab=97.27  E-value=0.00019  Score=57.83  Aligned_cols=45  Identities=33%  Similarity=0.736  Sum_probs=33.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      ..+.|.||+++..+   ...+||||+-+  |..--.  +...||+||+.|..
T Consensus       304 ~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIRL  348 (355)
T ss_pred             CCCceEEecCCccc---eeeecCCcEEE--chHHHh--hCCCCchhHHHHHH
Confidence            55689999999884   58999999855  554432  23349999998753

>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=97.24  E-value=0.00013  Score=49.72  Aligned_cols=32  Identities=34%  Similarity=0.756  Sum_probs=27.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHH
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVD  181 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~  181 (214)
                      .+..|++|-..+..+ .....||||+||..|++
T Consensus        77 ~~~~C~vC~k~l~~~-~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGNS-VFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCCc-eEEEeCCCeEEeccccc
Confidence            345799999999874 78888999999999975

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 [].

>PHA02862 5L protein; Provisional

Probab=97.23  E-value=0.00019  Score=50.29  Aligned_cols=47  Identities=21%  Similarity=0.511  Sum_probs=35.3

Q ss_pred             cccccccccccCCCceEEecCC-----CccChhhHHHHHHhCCC-Cccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCR-----HEFHSSCVDSWLIRWGT-FCPVCRHEIRRS  201 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~-----H~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~~~  201 (214)
                      +.|-||.++-.  +.  .-||+     ..-|.+|+.+|+...+. .||+|+.+...+
T Consensus         3 diCWIC~~~~~--e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          3 DICWICNDVCD--ER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CEEEEecCcCC--CC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            57999999853  33  35652     35899999999977644 799999987544

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

Probab=97.21  E-value=0.00014  Score=57.07  Aligned_cols=52  Identities=27%  Similarity=0.568  Sum_probs=39.8

Q ss_pred             cccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCcccc-ccccccccCCC
Q 028085          151 TLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVC-RHEIRRSTSNE  205 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~C-r~~i~~~~~~~  205 (214)
                      ..|+.|..-+.   ....+| |+|.||++||..-|......||.| |+++......|
T Consensus       275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~p  328 (427)
T COG5222         275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTP  328 (427)
T ss_pred             ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCcccccchhhccCc
Confidence            58999998888   446777 899999999998887766679999 44554443333

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

Probab=97.15  E-value=0.00053  Score=48.66  Aligned_cols=25  Identities=20%  Similarity=0.117  Sum_probs=22.3

Q ss_pred             cHHHHHHHHHHcCCcEEEEEeCCCC
Q 028085            7 NFSYKIQNAQAAGYDAAIVYALRKK   31 (214)
Q Consensus         7 ~f~~K~~~a~~~ga~aviv~~~~~~   31 (214)
                      ++.+|+++|+++||.|||+|++...
T Consensus        73 ~~~~K~~~A~~~GA~aVIi~~d~~~   97 (137)
T cd04820          73 SSNEKARYAAKAGAIGMITLTTPRS   97 (137)
T ss_pred             cHHHHHHHHHHCCCeEEEEEeCCcc
Confidence            3889999999999999999997654

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

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

Probab=97.13  E-value=0.00026  Score=40.36  Aligned_cols=45  Identities=29%  Similarity=0.651  Sum_probs=21.9

Q ss_pred             cccccccccCCCceEEec--CCCccChhhHHHHHHhCCCCcccccccc
Q 028085          153 CSICLEDYREGENLRVLP--CRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~--C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      |++|.+++...+ ...+|  ||+-.+..|...-+......||-||.+.
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            789999984443 23555  7999999998887764344699999874

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

Probab=97.10  E-value=0.00014  Score=53.61  Aligned_cols=44  Identities=34%  Similarity=0.656  Sum_probs=36.8

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      ..|.||-.+|+   .++.+.|||.||..|...=++.... |-+|....
T Consensus       197 F~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~-C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDE-CGVCGKAT  240 (259)
T ss_pred             eeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCc-ceecchhh
Confidence            58999999999   5589999999999999887766444 99996643

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

Probab=97.07  E-value=0.00012  Score=57.26  Aligned_cols=42  Identities=33%  Similarity=0.769  Sum_probs=33.3

Q ss_pred             CcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      +..|+||++.-.   ....|+|||. -|.+|-...    + .||+||+-+.
T Consensus       300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkrm----~-eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKRM----N-ECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCc---ceEEeecCcEEeehhhcccc----c-cCchHHHHHH
Confidence            568999999977   5689999995 788886541    2 4999998764

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

Probab=97.06  E-value=0.0003  Score=53.85  Aligned_cols=47  Identities=26%  Similarity=0.638  Sum_probs=34.4

Q ss_pred             ccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .|--|.-.-. +++.+.+.|+|+||..|...-.   ...||+||.++....
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIRIIQ   51 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhcccCC---ccccccccceeeeee
Confidence            4666655433 7788999999999999986532   214999999875443

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

Probab=97.04  E-value=0.00033  Score=56.55  Aligned_cols=48  Identities=35%  Similarity=0.740  Sum_probs=40.6

Q ss_pred             cccccccccccCCC---ceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          151 TLCSICLEDYREGE---NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       151 ~~C~ICl~~~~~~~---~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      .+|-||-++|..++   .++.|.|||.|+..|+...+......||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998774   5688889999999999887766555799999984

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

Probab=96.94  E-value=2.4e-05  Score=63.34  Aligned_cols=51  Identities=25%  Similarity=0.644  Sum_probs=44.9

Q ss_pred             cccccccccccCC-CceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          151 TLCSICLEDYREG-ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       151 ~~C~ICl~~~~~~-~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ..|+||.+.+... +.+..+-|||.+|..|+.+||..... ||.|++.+....
T Consensus       197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~k-l~~~~rel~~~~  248 (465)
T KOG0827|consen  197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRK-LPSCRRELPKNG  248 (465)
T ss_pred             hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHH-hHHHHhhhhhhh
Confidence            4799999999877 77888899999999999999999665 999999987654

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

Probab=96.90  E-value=0.00019  Score=57.20  Aligned_cols=50  Identities=24%  Similarity=0.577  Sum_probs=40.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ....|.+|-..|.+..  .+..|=|.||+.||-..+...+. ||.|...+-..
T Consensus        14 ~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~~~~-CP~C~i~ih~t   63 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEESKY-CPTCDIVIHKT   63 (331)
T ss_pred             cceehhhccceeecch--hHHHHHHHHHHHHHHHHHHHhcc-CCccceeccCc
Confidence            3468999999998663  34569999999999999999665 99998877543

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

Probab=96.88  E-value=0.0017  Score=51.85  Aligned_cols=45  Identities=27%  Similarity=0.661  Sum_probs=35.7

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~  197 (214)
                      ....|++|+....++   ..+. -|-+||+.|+-.++.+.+. ||+=..+
T Consensus       299 ~~~~CpvClk~r~Np---tvl~vSGyVfCY~Ci~~Yv~~~~~-CPVT~~p  344 (357)
T KOG0826|consen  299 DREVCPVCLKKRQNP---TVLEVSGYVFCYPCIFSYVVNYGH-CPVTGYP  344 (357)
T ss_pred             ccccChhHHhccCCC---ceEEecceEEeHHHHHHHHHhcCC-CCccCCc
Confidence            556899999997755   3444 5999999999999998776 9975444

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

Probab=96.87  E-value=0.00055  Score=60.84  Aligned_cols=49  Identities=29%  Similarity=0.666  Sum_probs=37.9

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCC------CCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWG------TFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~------~~CP~Cr~~  197 (214)
                      ...+|.||.+.+...+.+--- .|-|+||..||..|-....      ..||.|+..
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            457999999999877654333 3899999999999987532      179999853

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.86  E-value=0.0013  Score=50.31  Aligned_cols=53  Identities=17%  Similarity=0.362  Sum_probs=44.5

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ....|++|.+.+.+.-....| ||||+|+.+|++..+..... ||+|-.++...+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v-~pv~d~plkdrd  273 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMV-DPVTDKPLKDRD  273 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccccc-ccCCCCcCcccc
Confidence            446899999999988777777 59999999999999887776 999988876543

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

Probab=96.76  E-value=0.0004  Score=54.51  Aligned_cols=45  Identities=24%  Similarity=0.449  Sum_probs=37.9

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      ..|-||-..|..   .+.+.|+|.||..|...=++.... |++|.+...
T Consensus       242 f~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~-c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEK-CYVCSQQTH  286 (313)
T ss_pred             cccccccccccc---chhhcCCceeehhhhccccccCCc-ceecccccc
Confidence            569999999994   489999999999999888866555 999977653

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.76  E-value=0.00063  Score=39.70  Aligned_cols=45  Identities=24%  Similarity=0.498  Sum_probs=33.2

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ..|..|...-.   +-..+||||+.+..|.+.+-  -+. ||.|..++...
T Consensus         8 ~~~~~~~~~~~---~~~~~pCgH~I~~~~f~~~r--Yng-CPfC~~~~~~~   52 (55)
T PF14447_consen    8 QPCVFCGFVGT---KGTVLPCGHLICDNCFPGER--YNG-CPFCGTPFEFD   52 (55)
T ss_pred             eeEEEcccccc---ccccccccceeeccccChhh--ccC-CCCCCCcccCC
Confidence            45666665544   44789999999999998753  355 99998887544

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

Probab=96.58  E-value=0.0024  Score=51.33  Aligned_cols=45  Identities=27%  Similarity=0.565  Sum_probs=34.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHH--HhCCCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWL--IRWGTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl--~~~~~~CP~Cr~~  197 (214)
                      +...|.||-+...   -...+||+|-.|.-|--..-  -..+ .||+||..
T Consensus        60 en~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K-~C~~CrTE  106 (493)
T COG5236          60 ENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQK-GCPLCRTE  106 (493)
T ss_pred             ccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhcc-CCCccccc
Confidence            4567999999987   66899999999888865432  2224 49999974

>PHA03096 p28-like protein; Provisional

Probab=96.58  E-value=0.001  Score=53.05  Aligned_cols=46  Identities=28%  Similarity=0.628  Sum_probs=33.4

Q ss_pred             cccccccccccCC----CceEEec-CCCccChhhHHHHHHhCCC--Ccccccc
Q 028085          151 TLCSICLEDYREG----ENLRVLP-CRHEFHSSCVDSWLIRWGT--FCPVCRH  196 (214)
Q Consensus       151 ~~C~ICl~~~~~~----~~~~~l~-C~H~FH~~Ci~~Wl~~~~~--~CP~Cr~  196 (214)
                      ..|.||++.....    ..--.|+ |.|.|+..|+..|......  +||.||.
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            5799999986643    1334566 9999999999999976532  4555544

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

Probab=96.10  E-value=0.0018  Score=57.64  Aligned_cols=48  Identities=23%  Similarity=0.681  Sum_probs=39.5

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCC-Ccccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT-FCPVCRHEIRRST  202 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~~~~  202 (214)
                      ..|.+|++    .+....++|+|.||.+|+..-+..... .||+||..+....
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            68999999    347789999999999999998876544 4999999876554

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.05  E-value=0.0076  Score=47.78  Aligned_cols=51  Identities=18%  Similarity=0.480  Sum_probs=39.6

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ....|||...+|........| ||||+|.+.+++..- ... .||+|-.++...
T Consensus       112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~-~Cp~c~~~f~~~  163 (260)
T PF04641_consen  112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSK-KCPVCGKPFTEE  163 (260)
T ss_pred             ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccc-cccccCCccccC
Confidence            667999999999665555444 799999999999962 223 499999887644

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

Probab=95.82  E-value=0.0075  Score=49.52  Aligned_cols=46  Identities=17%  Similarity=0.358  Sum_probs=40.0

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC--CCcccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG--TFCPVC  194 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~--~~CP~C  194 (214)
                      +-..|||=-+.-.++..+..|.|||+..++=+.+..+...  ..||+|
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYC  380 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYC  380 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCC
Confidence            4468999888888888999999999999999999877665  379999

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

Probab=95.78  E-value=0.0041  Score=49.09  Aligned_cols=46  Identities=33%  Similarity=0.629  Sum_probs=38.2

Q ss_pred             CcccccccccccCCC-ceEEecCCCccChhhHHHHHHhCCCCcccccc
Q 028085          150 ETLCSICLEDYREGE-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRH  196 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~  196 (214)
                      +..|+||.+.+.... .+..++|||.-|..|+......+ -+||+|..
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence            345999999877664 56788999999999999988776 56999977

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

Probab=95.78  E-value=0.0041  Score=55.55  Aligned_cols=42  Identities=26%  Similarity=0.665  Sum_probs=31.9

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      ..|..|-..+.-+  .+...|||.||.+|+.   .. ...||-|+-.+
T Consensus       841 skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~-~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DK-EDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccc--eeeeecccHHHHHhhc---cC-cccCCccchhh
Confidence            5899998887743  3566799999999998   23 33599998743

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

Probab=95.69  E-value=0.005  Score=55.36  Aligned_cols=36  Identities=25%  Similarity=0.570  Sum_probs=29.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHH
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLI  185 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~  185 (214)
                      .++.|.+|.-.+... .-..-||||.||++|+.+-..
T Consensus       816 p~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  816 PQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             CccchHHhcchhhcC-cceeeeccchHHHHHHHHHHH
Confidence            456899999988766 667889999999999987664

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.67  E-value=0.016  Score=33.86  Aligned_cols=43  Identities=26%  Similarity=0.798  Sum_probs=33.3

Q ss_pred             CcccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCccc--cccc
Q 028085          150 ETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPV--CRHE  197 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~--Cr~~  197 (214)
                      ...|++|-+.|.++|.+.+-| ||-.+|++|.+.    ... |-.  |..+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~-C~~~~c~~~   50 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGG-CINYSCGTG   50 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCc-eEeccCCCC
Confidence            357999999999888888888 999999999643    343 655  5443

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

Probab=95.57  E-value=0.0095  Score=43.44  Aligned_cols=51  Identities=27%  Similarity=0.686  Sum_probs=33.9

Q ss_pred             ccccccccccCC----CceEEecCCCccChhhHHHHHHhC----CC------Ccccccccccccc
Q 028085          152 LCSICLEDYREG----ENLRVLPCRHEFHSSCVDSWLIRW----GT------FCPVCRHEIRRST  202 (214)
Q Consensus       152 ~C~ICl~~~~~~----~~~~~l~C~H~FH~~Ci~~Wl~~~----~~------~CP~Cr~~i~~~~  202 (214)
                      .|.||+..--+|    +..--..||.-||.-|+..||+.-    ++      .||.|-.++.-+.
T Consensus       167 ~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  167 ACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             cccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            466666443333    122334699999999999999642    11      5999988886543

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

Probab=95.40  E-value=0.0052  Score=48.71  Aligned_cols=30  Identities=33%  Similarity=0.894  Sum_probs=22.5

Q ss_pred             EEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          167 RVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       167 ~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      |..||+|+||.+|...  ...+ .||.|-..+.
T Consensus       105 RmIPCkHvFCl~CAr~--~~dK-~Cp~C~d~Vq  134 (389)
T KOG2932|consen  105 RMIPCKHVFCLECARS--DSDK-ICPLCDDRVQ  134 (389)
T ss_pred             cccccchhhhhhhhhc--Cccc-cCcCcccHHH
Confidence            7889999999999754  2223 4999966553

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.38  E-value=0.011  Score=47.54  Aligned_cols=53  Identities=21%  Similarity=0.502  Sum_probs=36.6

Q ss_pred             CCcccccccccccCCCce-EEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENL-RVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~-~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +++-|+.|++++...|+- .-.|||-..|.-|...--+.-+-.||-||+.....
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            445699999998877643 34568987777776554433333699999976543

>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=95.10  E-value=0.0072  Score=33.82  Aligned_cols=42  Identities=24%  Similarity=0.654  Sum_probs=22.8

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHhCCC-Ccccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT-FCPVC  194 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~-~CP~C  194 (214)
                      |.+|-+-...|..-..-.|+=.+|..|++.++..++. .||.|
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            5677777666632111238888999999999987664 49987

; PDB: 3NW0_A 2CT0_A.

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

Probab=95.00  E-value=0.0083  Score=45.75  Aligned_cols=41  Identities=39%  Similarity=0.840  Sum_probs=30.6

Q ss_pred             cccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccc
Q 028085          153 CSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      |-.|-+.-.   .+..+||.|. +|..|-.. +   + .||+|+......
T Consensus       161 Cr~C~~~~~---~VlllPCrHl~lC~~C~~~-~---~-~CPiC~~~~~s~  202 (207)
T KOG1100|consen  161 CRKCGEREA---TVLLLPCRHLCLCGICDES-L---R-ICPICRSPKTSS  202 (207)
T ss_pred             ceecCcCCc---eEEeecccceEeccccccc-C---c-cCCCCcChhhce
Confidence            777777644   7899999885 99999754 2   3 399999876543

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

Probab=94.90  E-value=0.014  Score=46.94  Aligned_cols=42  Identities=29%  Similarity=0.596  Sum_probs=33.3

Q ss_pred             CcccccccccccCCCceEEecC--CCccChhhHHHHHHhCCCCccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPC--RHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C--~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      -.+|+||.+.+...    ...|  ||+-|..|-.+   ..+ .||.||-++.
T Consensus        48 lleCPvC~~~l~~P----i~QC~nGHlaCssC~~~---~~~-~CP~Cr~~~g   91 (299)
T KOG3002|consen   48 LLDCPVCFNPLSPP----IFQCDNGHLACSSCRTK---VSN-KCPTCRLPIG   91 (299)
T ss_pred             hccCchhhccCccc----ceecCCCcEehhhhhhh---hcc-cCCccccccc
Confidence            35899999999865    5667  89999999764   223 4999999886

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

Probab=94.70  E-value=0.017  Score=51.22  Aligned_cols=40  Identities=33%  Similarity=0.663  Sum_probs=28.4

Q ss_pred             ccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccc
Q 028085          152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPV  193 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~  193 (214)
                      .|+||--... +.......|+|+-|.+|...|+..+.. ||.
T Consensus      1030 ~C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~-Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDV-CPS 1069 (1081)
T ss_pred             eeeeEeeEee-ccchhhccccccccHHHHHHHHhcCCc-CCC
Confidence            3444443333 224456679999999999999999876 985

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

Probab=94.31  E-value=0.011  Score=51.34  Aligned_cols=43  Identities=28%  Similarity=0.647  Sum_probs=33.0

Q ss_pred             cccccccccccCCC-ceEEecCCCccChhhHHHHHHhCCCCccccccc
Q 028085          151 TLCSICLEDYREGE-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHE  197 (214)
Q Consensus       151 ~~C~ICl~~~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~  197 (214)
                      ..|.||+..|.... ..+.|-|||..|..|+..-.  +.+ || |+++
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~s-cp-~~~D   55 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NAS-CP-TKRD   55 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hcc-CC-CCcc
Confidence            46999998887653 55677799999999998754  345 99 7654

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

Probab=93.68  E-value=0.059  Score=42.55  Aligned_cols=49  Identities=31%  Similarity=0.636  Sum_probs=36.7

Q ss_pred             cccccccc-ccCCC-ceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          152 LCSICLED-YREGE-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       152 ~C~ICl~~-~~~~~-~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .|+.|-.+ |...+ .+..-+|+|-.|.+|++..+..+...||-|-..+..
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk   52 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRK   52 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhh
Confidence            58999876 33443 233337999999999999998877689999776543

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

Probab=93.35  E-value=0.026  Score=52.90  Aligned_cols=46  Identities=30%  Similarity=0.743  Sum_probs=37.5

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      ...|.||++.....-  .+..|||.++..|...|+..+.. ||+|+...
T Consensus      1153 ~~~c~ic~dil~~~~--~I~~cgh~~c~~c~~~~l~~~s~-~~~~ksi~ 1198 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQG--GIAGCGHEPCCRCDELWLYASSR-CPICKSIK 1198 (1394)
T ss_pred             ccchHHHHHHHHhcC--CeeeechhHhhhHHHHHHHHhcc-Ccchhhhh
Confidence            348999999988321  56779999999999999988666 99998543

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.34  E-value=0.036  Score=42.89  Aligned_cols=51  Identities=29%  Similarity=0.632  Sum_probs=36.5

Q ss_pred             CCcccccccccccCCCce-EEecC-----CCccChhhHHHHHHhCC-------CCccccccccc
Q 028085          149 RETLCSICLEDYREGENL-RVLPC-----RHEFHSSCVDSWLIRWG-------TFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~-~~l~C-----~H~FH~~Ci~~Wl~~~~-------~~CP~Cr~~i~  199 (214)
                      .+..|-||+..-+++-.- -+-||     .|=-|..|+..|+..++       ..||-|+....
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            667899999886655221 23465     36689999999997653       27999988653

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

Probab=92.58  E-value=0.046  Score=45.79  Aligned_cols=38  Identities=29%  Similarity=0.620  Sum_probs=29.0

Q ss_pred             CcccccccccccCC-CceEEecCCCccChhhHHHHHHhC
Q 028085          150 ETLCSICLEDYREG-ENLRVLPCRHEFHSSCVDSWLIRW  187 (214)
Q Consensus       150 ~~~C~ICl~~~~~~-~~~~~l~C~H~FH~~Ci~~Wl~~~  187 (214)
                      ..+|.||..+.... +......|+|.||.+|..+.+..+
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            45899999555444 444456799999999999998754

>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=92.46  E-value=0.18  Score=36.32  Aligned_cols=33  Identities=30%  Similarity=0.713  Sum_probs=21.8

Q ss_pred             CcccccccccccCCCceEEec------------CCCc-cChhhHHHHHH
Q 028085          150 ETLCSICLEDYREGENLRVLP------------CRHE-FHSSCVDSWLI  185 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~------------C~H~-FH~~Ci~~Wl~  185 (214)
                      +..|+||||---+.   +.|-            |+.. =|..|+++.-+
T Consensus         2 d~~CpICme~PHNA---VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCce---EEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            45799999874422   3443            4333 47899999865

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.

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0

Probab=91.97  E-value=0.13  Score=35.85  Aligned_cols=50  Identities=30%  Similarity=0.634  Sum_probs=38.0

Q ss_pred             CcccccccccccCCCceEEe-c---CCCccChhhHHHHHHhCCC--Ccccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVL-P---CRHEFHSSCVDSWLIRWGT--FCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l-~---C~H~FH~~Ci~~Wl~~~~~--~CP~Cr~~i~~~~  202 (214)
                      -.+|.||-|...+.   +.| |   ||-..|--|....++.-+.  .||.|+.+.-...
T Consensus        80 lYeCnIC~etS~ee---~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   80 LYECNICKETSAEE---RFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             ceeccCcccccchh---hcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            36899999997755   455 3   8998999888887766543  6999999876544

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=91.51  E-value=0.14  Score=40.94  Aligned_cols=46  Identities=17%  Similarity=0.301  Sum_probs=37.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCC--Ccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT--FCPVC  194 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~--~CP~C  194 (214)
                      +-..||+=-+.-.+...+..|.|||+.-++-++..-++...  .||.|
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYC  382 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYC  382 (396)
T ss_pred             ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCC
Confidence            34689998888888889999999999999999986655422  69999

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.44  E-value=0.098  Score=41.36  Aligned_cols=31  Identities=29%  Similarity=0.661  Sum_probs=23.5

Q ss_pred             CCCccChhhHHHHHHhCC------------CCccccccccccc
Q 028085          171 CRHEFHSSCVDSWLIRWG------------TFCPVCRHEIRRS  201 (214)
Q Consensus       171 C~H~FH~~Ci~~Wl~~~~------------~~CP~Cr~~i~~~  201 (214)
                      |+..+|.+|+.+|+..++            -.||+||+...-.
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~  367 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR  367 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence            577788999999986432            2699999987543

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=91.31  E-value=0.091  Score=43.86  Aligned_cols=35  Identities=31%  Similarity=0.771  Sum_probs=29.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHh
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR  186 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~  186 (214)
                      ++..|+||..-|+   ++.+|||+|..|.-|...-+..
T Consensus         3 eelkc~vc~~f~~---epiil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    3 EELKCPVCGSFYR---EPIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             ccccCceehhhcc---CceEeecccHHHHHHHHhhccc
Confidence            4578999999999   5589999999999999876643

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

Probab=91.27  E-value=0.15  Score=42.15  Aligned_cols=30  Identities=27%  Similarity=0.747  Sum_probs=22.9

Q ss_pred             CCCccChhhHHHHHHhCC------------CCcccccccccc
Q 028085          171 CRHEFHSSCVDSWLIRWG------------TFCPVCRHEIRR  200 (214)
Q Consensus       171 C~H~FH~~Ci~~Wl~~~~------------~~CP~Cr~~i~~  200 (214)
                      |+-.+|.+|+-+|+..++            ..||+||+.+.-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            466678899999997543            269999998653

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

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

Probab=91.24  E-value=0.1  Score=42.48  Aligned_cols=52  Identities=29%  Similarity=0.731  Sum_probs=37.4

Q ss_pred             CcccccccccccCCCc-eEEecCC-----CccChhhHHHHHHhCCC-Cccccccccccc
Q 028085          150 ETLCSICLEDYREGEN-LRVLPCR-----HEFHSSCVDSWLIRWGT-FCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~-~~~l~C~-----H~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~~~  201 (214)
                      +..|-||.++...... ....||.     +..|..|++.|+..... .|..|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            3679999998664422 4567762     45799999999985544 699998865443

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

Probab=90.96  E-value=0.069  Score=46.65  Aligned_cols=42  Identities=24%  Similarity=0.721  Sum_probs=27.1

Q ss_pred             Cccccccccc-----ccCCCceEEecCCCccChhhHHHHHHhCCCCccccc
Q 028085          150 ETLCSICLED-----YREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCR  195 (214)
Q Consensus       150 ~~~C~ICl~~-----~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr  195 (214)
                      ...|.+|-..     |+.....+...|+++||+.|+..    .+..||.|-
T Consensus       511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r----~s~~CPrC~  557 (580)
T KOG1829|consen  511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR----KSPCCPRCE  557 (580)
T ss_pred             eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc----cCCCCCchH
Confidence            3567777322     44333445566999999999754    233499993

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

Probab=90.94  E-value=0.17  Score=44.59  Aligned_cols=47  Identities=28%  Similarity=0.869  Sum_probs=38.3

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccC
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTS  203 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~  203 (214)
                      ..+.|.+|+++.    ..+..+|.   |..|+..|+..+.. ||+|+..+..+..
T Consensus       478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~-~pl~~~~~~~~~~  524 (543)
T KOG0802|consen  478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEV-CPLCHTYMKEDDF  524 (543)
T ss_pred             ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccc-cCCCchhhhcccc
Confidence            556899999998    44788888   89999999988776 9999887765543

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

Probab=90.77  E-value=0.21  Score=45.05  Aligned_cols=52  Identities=27%  Similarity=0.633  Sum_probs=39.1

Q ss_pred             CCcccccccccccCCCceEEecC---CC--ccChhhHHHHHHhCCC-Cccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPC---RH--EFHSSCVDSWLIRWGT-FCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C---~H--~FH~~Ci~~Wl~~~~~-~CP~Cr~~i~~~  201 (214)
                      ++..|-||..+=..++++ .-||   |-  -.|.+|+.+|+..... .|-+|+.++.-+
T Consensus        11 d~~~CRICr~e~~~d~pL-fhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk   68 (1175)
T COG5183          11 DKRSCRICRTEDIRDDPL-FHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFK   68 (1175)
T ss_pred             cchhceeecCCCCCCCcC-cccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeee
Confidence            557899999887766544 4565   33  3899999999987654 699999877544

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=90.43  E-value=0.2  Score=28.98  Aligned_cols=42  Identities=26%  Similarity=0.675  Sum_probs=21.5

Q ss_pred             cccccccccCCC------ceEEec-CCCccChhhHHHHHHhCCCCccccc
Q 028085          153 CSICLEDYREGE------NLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCR  195 (214)
Q Consensus       153 C~ICl~~~~~~~------~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr  195 (214)
                      |.-|+..|..+.      ....-| |++.|+.+| |..+-..-..||-|.
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC-D~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDC-DVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHH-HHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCc-ChhhhccccCCcCCC
Confidence            556677766542      334445 999999999 455433333699884

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=89.73  E-value=0.22  Score=37.97  Aligned_cols=42  Identities=31%  Similarity=0.826  Sum_probs=28.6

Q ss_pred             CCccccccccc-----ccCCCceEEecCCCccChhhHHHHHHhCCCCcccccc
Q 028085          149 RETLCSICLED-----YREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRH  196 (214)
Q Consensus       149 ~~~~C~ICl~~-----~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~  196 (214)
                      ....|-+|-++     |..+...+--.|+-+||+.|..     ++. ||-|.+
T Consensus       151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~-CpkC~R  197 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKS-CPKCAR  197 (202)
T ss_pred             CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCC-CCCcHh
Confidence            34578888754     4443344444599999999986     244 999954

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=89.68  E-value=0.15  Score=39.23  Aligned_cols=50  Identities=28%  Similarity=0.652  Sum_probs=37.2

Q ss_pred             CCcccccccccc-cCCC-ceEEec-CCCccChhhHHHHHHhCCCCcc--cccccc
Q 028085          149 RETLCSICLEDY-REGE-NLRVLP-CRHEFHSSCVDSWLIRWGTFCP--VCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~-~~~~-~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP--~Cr~~i  198 (214)
                      .+..||+|-.+. -..| .+.+-| |-|-.|.+|+++-+......||  -|..-+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            445899999773 3443 334446 9999999999999987766799  786544

>KOG3356 consensus Predicted membrane protein [Function unknown]

Probab=89.46  E-value=2.3  Score=28.89  Aligned_cols=42  Identities=21%  Similarity=0.374  Sum_probs=32.0

Q ss_pred             EEEEEeC-CCCCCeeeeeCCCCCeeeEEEEchh-hHHHHHHHhh
Q 028085           22 AAIVYAL-RKKSPLIYMTYPEGANVPAFYVTLE-TGAYLKEHAR   63 (214)
Q Consensus        22 aviv~~~-~~~~~~~~m~~~~~~~Ip~v~v~~~-~g~~L~~~~~   63 (214)
                      +-+|||. .+.+...+|.+..+...|++|+++. .|+++.+.+.
T Consensus        45 ~g~iydvivepp~igs~~d~~g~~rpv~fla~rvngqyimegla   88 (147)
T KOG3356|consen   45 GGIIYDVIVEPPSIGSMTDEHGHQRPVAFLAGRVNGQYIMEGLA   88 (147)
T ss_pred             ccEEEEEEecCCCCCcccccCCcCcceEEEeccccceeeehhhc
Confidence            4567885 3434678888888889999999887 6888887665

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.28  E-value=0.1  Score=29.39  Aligned_cols=33  Identities=24%  Similarity=0.640  Sum_probs=21.3

Q ss_pred             EecC-CCccChhhHHHHHHhCCCCccccccccccc
Q 028085          168 VLPC-RHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       168 ~l~C-~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ...| .|..|-.|+...+.... .||+|..+++++
T Consensus        15 Li~C~dHYLCl~CLt~ml~~s~-~C~iC~~~LPtk   48 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLSRSD-RCPICGKPLPTK   48 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-SSSS-EETTTTEE----
T ss_pred             eeeecchhHHHHHHHHHhcccc-CCCcccCcCccc
Confidence            5568 59999999999886644 599999998754

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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=89.19  E-value=0.074  Score=47.13  Aligned_cols=51  Identities=27%  Similarity=0.662  Sum_probs=39.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCC--Ccccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT--FCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~--~CP~Cr~~i~~~~  202 (214)
                      ...+|+||+..+...   ..+.|-|.|+..|+..-+...+.  .||+|++.+....
T Consensus        20 k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s   72 (684)
T KOG4362|consen   20 KILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRS   72 (684)
T ss_pred             hhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhh
Confidence            346899999999955   67889999999998876665442  5999998765443

>KOG0269 consensus WD40 repeat-containing protein [Function unknown]

Probab=89.12  E-value=0.37  Score=43.13  Aligned_cols=39  Identities=28%  Similarity=0.609  Sum_probs=30.0

Q ss_pred             cccccccccccCCCceEEec--CCCccChhhHHHHHHhCCCCccc
Q 028085          151 TLCSICLEDYREGENLRVLP--CRHEFHSSCVDSWLIRWGTFCPV  193 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~--C~H~FH~~Ci~~Wl~~~~~~CP~  193 (214)
                      -.|.+|-..+.   .+...+  |||.-|.+|+.+|+..... ||.
T Consensus       780 ~~CtVC~~vi~---G~~~~c~~C~H~gH~sh~~sw~~~~s~-ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIR---GVDVWCQVCGHGGHDSHLKSWFFKASP-CAK  820 (839)
T ss_pred             cCceeecceee---eeEeecccccccccHHHHHHHHhcCCC-Ccc
Confidence            36888877766   223333  9999999999999988766 876

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.49  E-value=0.19  Score=29.00  Aligned_cols=44  Identities=23%  Similarity=0.432  Sum_probs=20.6

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCC----CCccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG----TFCPVCRHE  197 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~----~~CP~Cr~~  197 (214)
                      ..|++....+..  .+|...|.|.-+ --++.|+..+.    -.||+|+++
T Consensus         3 L~CPls~~~i~~--P~Rg~~C~H~~C-FDl~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGKNCKHLQC-FDLESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEETT--SS---EEHHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCCcCcccce-ECHHHHHHHhhccCCeECcCCcCc
Confidence            358888777662  456666999743 23445665432    269999764

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 entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]

Probab=88.43  E-value=0.42  Score=38.52  Aligned_cols=68  Identities=22%  Similarity=0.476  Sum_probs=42.1

Q ss_pred             HHHHhcCCceeeeccccccCCCCCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccc
Q 028085          127 RSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRH  196 (214)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~  196 (214)
                      +..---.|-..|.+....... .+..|-.|.++.......+.-.|.|.||.+| +..+-..-..||-|..
T Consensus       308 RSyhhL~PL~~F~Eip~~~~~-~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldC-Dv~iHesLh~CpgCeh  375 (378)
T KOG2807|consen  308 RSYHHLFPLKPFVEIPETEYN-GSRFCFACQGELLSSGRYRCESCKNVFCLDC-DVFIHESLHNCPGCEH  375 (378)
T ss_pred             HHHHhhcCCcchhhccccccC-CCcceeeeccccCCCCcEEchhccceeeccc-hHHHHhhhhcCCCcCC
Confidence            333333444444443333222 3345999988877776666666999999999 4555443336999964

>smart00249 PHD PHD zinc finger

Probab=88.42  E-value=0.12  Score=28.77  Aligned_cols=30  Identities=30%  Similarity=0.686  Sum_probs=20.7

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHH
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDS  182 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~  182 (214)
                      |.+|-.....++.+.--.|...||..|+..
T Consensus         2 C~~C~~~~~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             cccCCCcCCCCCEEECCCCCchhhhhhCCC
Confidence            778887764443333335899999999854

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

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

Probab=87.57  E-value=0.26  Score=44.30  Aligned_cols=44  Identities=30%  Similarity=0.635  Sum_probs=33.3

Q ss_pred             Cccccccccccc-CC---CceEEecCCCccChhhHHHHHHhCCCCccccc
Q 028085          150 ETLCSICLEDYR-EG---ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCR  195 (214)
Q Consensus       150 ~~~C~ICl~~~~-~~---~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr  195 (214)
                      +..|.-|.+..- .+   +.+..+.|||.||+.|+..-..+++  |-.|.
T Consensus       784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~  831 (846)
T KOG2066|consen  784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES  831 (846)
T ss_pred             hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence            347999987754 22   5788999999999999998887654  65553

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

Probab=86.10  E-value=0.57  Score=42.25  Aligned_cols=50  Identities=12%  Similarity=0.239  Sum_probs=35.3

Q ss_pred             CCcccccccccccCC-CceEEec---CCCccChhhHHHHHHhCC-----CCcccccccc
Q 028085          149 RETLCSICLEDYREG-ENLRVLP---CRHEFHSSCVDSWLIRWG-----TFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~-~~~~~l~---C~H~FH~~Ci~~Wl~~~~-----~~CP~Cr~~i  198 (214)
                      ..+.|.+|.-++.++ |..-.+|   |+|-||..||..|...-.     ..|++|..-+
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            335677777776652 3344556   999999999999997531     2589998755

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

Probab=85.78  E-value=1.1  Score=32.57  Aligned_cols=23  Identities=22%  Similarity=0.403  Sum_probs=19.7

Q ss_pred             cHHHHHHHHHHcCCcEEEEEeCC
Q 028085            7 NFSYKIQNAQAAGYDAAIVYALR   29 (214)
Q Consensus         7 ~f~~K~~~a~~~ga~aviv~~~~   29 (214)
                      .+..|.+.|+++||.|+|+.++.
T Consensus        80 ~~~~K~~~A~~~GA~gvi~v~~~  102 (157)
T cd04821          80 RWTYKYEEAARQGAAGALIVHET  102 (157)
T ss_pred             cHHHHHHHHHHCCCeEEEEEeCC
Confidence            35679999999999999999654

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

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=85.54  E-value=0.084  Score=30.43  Aligned_cols=44  Identities=25%  Similarity=0.649  Sum_probs=28.6

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHhC-----CCCcccccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW-----GTFCPVCRH  196 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~-----~~~CP~Cr~  196 (214)
                      |.||...-..++.+.--.|+..||..|+..=....     .-.||.|+.
T Consensus         2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             BTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             CcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            88898854444333333489999999987654311     226988863

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 entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.21  E-value=0.76  Score=35.76  Aligned_cols=51  Identities=12%  Similarity=0.272  Sum_probs=36.6

Q ss_pred             CCcccccccccccCCCceEE-ecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRV-LPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~-l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ....|+|---++.....-.. .+|||+|-..-+.+.-   .+.|++|.+.+...+
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQEDD  161 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHhh---hccccccCCcccccC
Confidence            45689987777665544433 4699999999988742   335999999876554

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=82.48  E-value=0.64  Score=24.78  Aligned_cols=25  Identities=28%  Similarity=0.703  Sum_probs=15.6

Q ss_pred             ccccccccccCCCc--------eEEecCCCccC
Q 028085          152 LCSICLEDYREGEN--------LRVLPCRHEFH  176 (214)
Q Consensus       152 ~C~ICl~~~~~~~~--------~~~l~C~H~FH  176 (214)
                      +|+=|...|..+|+        ++-..|+|+|+
T Consensus         4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~   36 (36)
T PF13717_consen    4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF   36 (36)
T ss_pred             ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence            57788877765542        33334778774

>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length

Probab=82.26  E-value=0.86  Score=27.66  Aligned_cols=13  Identities=23%  Similarity=0.813  Sum_probs=9.4

Q ss_pred             ccChhhHHHHHHh
Q 028085          174 EFHSSCVDSWLIR  186 (214)
Q Consensus       174 ~FH~~Ci~~Wl~~  186 (214)
                      -||+.|+..|+..
T Consensus        11 gFCRNCLskWy~~   23 (68)
T PF06844_consen   11 GFCRNCLSKWYRE   23 (68)
T ss_dssp             S--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3999999999964

The function of this family is unknown.; PDB: 2O35_A 3FYB_B.

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=82.22  E-value=0.67  Score=22.77  Aligned_cols=22  Identities=27%  Similarity=0.688  Sum_probs=11.1

Q ss_pred             ccccccccccCCCceEEec-CCCcc
Q 028085          152 LCSICLEDYREGENLRVLP-CRHEF  175 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~-C~H~F  175 (214)
                      .|+-|-......  .+.-| |||.|
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCC
Confidence            356665554422  23444 66665

Several members are annotated as putative helicases.

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

Probab=82.06  E-value=1.3  Score=23.32  Aligned_cols=36  Identities=25%  Similarity=0.577  Sum_probs=24.1

Q ss_pred             cccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       153 C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      |+.|-..+..++. ....=+..||.+|+         .|..|+.++
T Consensus         2 C~~C~~~i~~~~~-~~~~~~~~~H~~Cf---------~C~~C~~~L   37 (39)
T smart00132        2 CAGCGKPIRGGEL-VLRALGKVWHPECF---------KCSKCGKPL   37 (39)
T ss_pred             ccccCCcccCCcE-EEEeCCccccccCC---------CCcccCCcC
Confidence            7788888776532 23334778998885         277777665

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=81.69  E-value=0.76  Score=39.44  Aligned_cols=37  Identities=30%  Similarity=0.651  Sum_probs=31.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW  187 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~  187 (214)
                      ...+|-||.+.+..  .+..+.|||.|+..|....+.++
T Consensus        69 ~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~k  105 (444)
T KOG1815|consen   69 GDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTK  105 (444)
T ss_pred             ccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhhe
Confidence            55789999999885  56778899999999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	214
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-09
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		9e-09
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-08
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		3e-07
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-06
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-05
1fbv_A	388	Structure Of A Cbl-Ubch7 Complex: Ring Domain Funct		6e-04
4a4c_A	391	Structure Of Phosphotyr371-C-Cbl-Ubch5b-Zap-70 Comp		6e-04
4a4b_A	391	Structure Of Modified Phosphotyr371-C-Cbl-Ubch5b-Za		6e-04
2y1m_A	389	Structure Of Native C-Cbl Length = 389		6e-04
4a49_A	84	Structure Of Phosphotyr371-C-Cbl-Ubch5b Complex Len		6e-04
2k4d_A	83	E2-C-Cbl Recognition Is Necessary But Not Sufficien		8e-04

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 133 LPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCP 192
           LPS+ F+          +TLC +C+ D+   + LRVLPC HEFH+ CVD WL +    CP
Sbjct: 9   LPSYRFNPNNH---QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWL-KANRTCP 64
Query: 193 VCRHE 197
           +CR +
Sbjct: 65  ICRAD 69

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 26/53 (49%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE 205
           C+ICL    EGE++R LPC H FH  CVD WLI     CP+CR +I     +E
Sbjct: 17  CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT-NKKCPICRVDIEAQLPSE 68

>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 = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 127 RSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR 186
           + +++ALP  + +        G+E  C IC  +Y +G+    LPC H FH  CV  WL +
Sbjct: 19  KESIDALPEILVTEDHGAV--GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQK 76
Query: 187 WGTFCPVCR 195
            GT CPVCR
Sbjct: 77  SGT-CPVCR 84

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C +C EDY  GE++R LPC H FH SC+  WL +  + CPVCR  +
Sbjct: 18  CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRKSL 62

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 153 CSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCR 195
           C++CL +  +GE  R LP C H FH+ CVD WL    T CP+CR
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCR 50

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWL-IRWGTFCPVCRHEI 198
           LC++CLED++  + L + PC+H FH  C+  WL +R    CP+C   +
Sbjct: 17  LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR--KVCPLCNMPV 62

>pdb|1FBV|A Chain A, Structure Of A Cbl-Ubch7 Complex: Ring Domain Function In Ubiquitin-Protein Ligases Length = 388

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           LC IC E+    +++++ PC H   +SC+ SW    G  CP CR EI+
Sbjct: 334 LCKICAEN---DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 378

>pdb|4A4C|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b-Zap-70 Complex Length = 391

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           LC IC E+    +++++ PC H   +SC+ SW    G  CP CR EI+
Sbjct: 336 LCKICAEN---DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 380

>pdb|4A4B|A Chain A, Structure Of Modified Phosphotyr371-C-Cbl-Ubch5b-Zap-70 Complex Length = 391

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           LC IC E+    +++++ PC H   +SC+ SW    G  CP CR EI+
Sbjct: 336 LCKICAEN---DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 380

>pdb|2Y1M|A Chain A, Structure Of Native C-Cbl Length = 389

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           LC IC E+    +++++ PC H   +SC+ SW    G  CP CR EI+
Sbjct: 334 LCKICAEN---DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 378

>pdb|4A49|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b Complex Length = 84

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           LC IC E+ +   ++++ PC H   +SC+ SW    G  CP CR EI+
Sbjct: 29  LCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 73

>pdb|2K4D|A Chain A, E2-C-Cbl Recognition Is Necessary But Not Sufficient For Ubiquitination Activity Length = 83

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           LC IC E+ +   ++++ PC H   +SC+ SW    G  CP CR EI+
Sbjct: 26  LCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	214
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	8e-27
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-24
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-23
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-22
2ect_A	78	Ring finger protein 126; metal binding protein, st	5e-22
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	4e-18
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	6e-15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-12
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-11
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-11
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-10
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-10
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	5e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-08
1xf1_A	926	C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {St	2e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	3e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	4e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	6e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	8e-07
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	8e-07
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	9e-07
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	1e-06
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-06
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-06
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-06
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	5e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	7e-06
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	1e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	1e-05
2ek8_A	421	Aminopeptidase; metalloproteinase, hydrolase; 1.80	2e-05
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	3e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	6e-05
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	9e-05
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-04
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	1e-04
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	2e-04
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	2e-04
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-04
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	2e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	3e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	3e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	5e-04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	6e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	7e-04
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	8e-04

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

 Score = 97.0 bits (242), Expect = 8e-27
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 127 RSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR 186
             +   LPS+ F+          +TLC +C+ D+   + LRVLPC HEFH+ CVD WL  
Sbjct: 3   SGSSGQLPSYRFNPNNH---QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA 59

Query: 187 WGTFCPVCRHEIRRST 202
             T CP+CR +   S+
Sbjct: 60  NRT-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 = 91.6 bits (228), Expect = 1e-24
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 125 LPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWL 184
             + +++ALP  + +             C IC  +Y +G+    LPC H FH  CV  WL
Sbjct: 17  ASKESIDALPEILVTEDHGAVGQEMC--CPICCSEYVKGDVATELPCHHYFHKPCVSIWL 74

Query: 185 IRWGTFCPVCRHEI 198
            + GT CPVCR   
Sbjct: 75  QKSGT-CPVCRCMF 87

>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 = 88.6 bits (220), Expect = 1e-23
 Identities = 27/59 (45%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 147 HGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE 205
              E  C+ICL    EGE++R LPC H FH  CVD WLI     CP+CR +I     +E
Sbjct: 11  EDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDIEAQLPSE 68

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

 Score = 86.4 bits (214), Expect = 1e-22
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNE 208
             LC++CLED++  + L + PC+H FH  C+  WL      CP+C   + +     G  
Sbjct: 15  HELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKV-CPLCNMPVLQLAQLSGPS 72

>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 = 84.8 bits (210), Expect = 5e-22
 Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 148 GRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGN 207
           G    C +C EDY  GE++R LPC H FH SC+  WL +  + CPVCR  +    +    
Sbjct: 13  GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRKSLTGQNTATNP 71

Query: 208 EQVHVSG 214
             +   G
Sbjct: 72  PGLTGVG 78

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

 Score = 73.8 bits (182), Expect = 4e-18
 Identities = 22/47 (46%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 153 CSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C++CL +  +GE  R LP C H FH+ CVD WL    T CP+CR  +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLTV 53

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

 Score = 74.0 bits (182), Expect = 6e-18
 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 138 FSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHE 197
             S   V+    E  C IC++    G    +LPC H F   C+D W  R    CP+CR +
Sbjct: 3   SGSSGRVKQLTDEEECCICMD----GRADLILPCAHSFCQKCIDKWSDRHRN-CPICRLQ 57

Query: 198 IRRSTSNEGNE 208
           +  +  + G  
Sbjct: 58  MTGANESSGPS 68

>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 = 65.8 bits (161), Expect = 6e-15
 Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 150 ETLCSICLEDYREGENL-RVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
            + C ICLED      +  VLPC H  H +C +  L      CP+C    
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYR-CPLCSGPS 53

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

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQ 209
           C ICLED         LPC H F   C+  W+ +  T CP+C+  +        ++ 
Sbjct: 8   CPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPT-CPLCKVPVESVVHTIESDS 61

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

 Score = 58.8 bits (142), Expect = 3e-12
 Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 5/50 (10%)

Query: 153 CSICLEDYRE----GENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C IC++ Y E    G  +    C H F S C+   L    T CP CR +I
Sbjct: 18  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKI 66

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 5/58 (8%)

Query: 148 GRETLCSICLEDYRE----GENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           G    C IC++ Y E    G  +    C H F S C+   L    T CP CR +I   
Sbjct: 1   GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHK 57

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

 Score = 56.1 bits (135), Expect = 5e-11
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 150 ETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
              C  C  + ++ + + V   C H FH+ C+  W+ +    CP+C+ + 
Sbjct: 26  MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNR-CPLCQQDW 74

>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 = 59.0 bits (142), Expect = 1e-10
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 5/96 (5%)

Query: 108 LYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLR 167
           L+P    R   P+ T     +  + +                  LC IC E+ +   +++
Sbjct: 292 LFP--DGRNQNPDLTGLCEPTPQDHIKVTQEQYELYCEMGSTFQLCKICAENDK---DVK 346

Query: 168 VLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTS 203
           + PC H   +SC+ SW    G  CP CR EI+ +  
Sbjct: 347 IEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP 382

>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 = 53.7 bits (129), Expect = 3e-10
 Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 5/53 (9%)

Query: 153 CSICLEDYRE----GENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           C IC++ Y E    G  +    C H F S C+   L    T CP CR +I   
Sbjct: 13  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHK 64

>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 = 52.9 bits (126), Expect = 5e-09
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 3   RGQ-CNFSYKIQNAQAAGYDAAIVYALRKKS-PLIYMTYPEGANVPAFYVTLETGAYLKE 60
           RG  C F+ KI  A   G   A+++        +I M++P   ++ A  +    G  + +
Sbjct: 112 RGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAVDIVAIMIGNLKGTKILQ 171

Query: 61  HAR 63
             +
Sbjct: 172 SIQ 174

>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 = 4e-08
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 2/49 (4%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           C IC+E  R+        C      SC+  WL      CP CR  ++  
Sbjct: 25  CFICMEKLRD--ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR 71

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

 Score = 49.7 bits (118), Expect = 2e-07
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 3   RGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHA 62
           RG  +F  KI  A+ AG    ++Y    +     +  P    +PA +++ + G  LK++ 
Sbjct: 288 RGDIDFKDKIAKAKKAGAVGVLIY--DNQDKGFPIELPNVDQMPAAFISRKDGLLLKDNP 345

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 22/102 (21%), Positives = 29/102 (28%), Gaps = 21/102 (20%)

Query: 134 PSFVFSSVTSVRCHGRETLCSICLEDYREGEN---------------LRVLPCRHEFHSS 178
           P  V    T       E  C IC+E                       R+  C H FH  
Sbjct: 9   PEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLL 68

Query: 179 CVDSWLIR----WGTFCPVCRHE--IRRSTSNEGNEQVHVSG 214
           C+ +            CP C+     +  T   G  +V  SG
Sbjct: 69  CLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWGKMEVFRSG 110

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

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C+ICL+          LPC+H F   CV       G  C +CR EI
Sbjct: 18  CAICLQTCVHP---VSLPCKHVFCYLCVKGASWL-GKRCALCRQEI 59

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

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 12/46 (26%), Positives = 16/46 (34%), Gaps = 4/46 (8%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C IC + ++      V  CRH F  SC           C +C    
Sbjct: 18  CFICRQAFQNP---VVTKCRHYFCESCALEHFRATPR-CYICDQPT 59

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

 Score = 47.9 bits (113), Expect = 6e-07
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 15/71 (21%)

Query: 153 CSICLEDYREGENLRV-----LPCRHEFHSSCVDSWLIRWGTF----------CPVCRHE 197
           C+IC     +G  + +       C  + H+ C++ W                 CP C+ +
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 198 IRRSTSNEGNE 208
           +  S +   N+
Sbjct: 371 LSTSFAALLND 381

>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 = 45.7 bits (108), Expect = 8e-07
 Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
              C  C E            C+H     C+D         CP CR+++ RS
Sbjct: 52  TFQCICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRS 100

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

 Score = 44.7 bits (106), Expect = 8e-07
 Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 153 CSICLEDYREGENL-RVLPCRHEFHSSCVDSWLIRWGTF--CPVCRHEIR 199
           C IC+E + E +   ++L C H     C++  L        CP C    R
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITR 67

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

 Score = 43.5 bits (103), Expect = 9e-07
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 7/47 (14%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           C  C  + +     ++LPC H   S C+++  ++    CP+C+    
Sbjct: 9   CQQCQAEAKC---PKLLPCLHTLCSGCLEASGMQ----CPICQAPWP 48

>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 = 45.3 bits (107), Expect = 1e-06
 Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 5/53 (9%)

Query: 149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           +   CS C    RE   + +  C H F S+CV       GT CPVC       
Sbjct: 21  KLLRCSRCTNILREP--VCLGGCEHIFCSNCVSDC---IGTGCPVCYTPAWIQ 68

>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 = 44.1 bits (104), Expect = 1e-06
 Identities = 17/71 (23%), Positives = 22/71 (30%), Gaps = 9/71 (12%)

Query: 143 SVRCHGRETL------CSICLEDYREGENLRVLPCRHEFHSSCVDSWL-IRWGTFCPVCR 195
           S    GRET       C+IC     +G++     C    H  CV  +        CP C 
Sbjct: 2   SSGSSGRETYPDAVKICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCN 59

Query: 196 HEIRRSTSNEG 206
                     G
Sbjct: 60  DYWPHEIPKSG 70

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

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 11/49 (22%), Positives = 16/49 (32%), Gaps = 3/49 (6%)

Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR 200
            C  C          +   C H F  SC+ + L      C  C+  I +
Sbjct: 17  KCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVK 62

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

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 3/49 (6%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           CSIC     +     +  C H F  SC+          CP C   + ++
Sbjct: 18  CSICKGYLID--ATTITECLHTFCKSCIVRHFYYSNR-CPKCNIVVHQT 63

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 10/56 (17%), Positives = 25/56 (44%), Gaps = 3/56 (5%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE 205
             +C +C   + +     ++ C H F  +C+  +L     +CP+C  ++ ++    
Sbjct: 15  HLMCVLCGGYFID--ATTIIECLHSFCKTCIVRYL-ETSKYCPICDVQVHKTRPLL 67

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 7/99 (7%)

Query: 106 RKLYPIDSPRRHRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGEN 165
           +    I   +    EQT++            +      +     E  C IC E + E   
Sbjct: 23  KDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLE---NELQCIICSEYFIEA-- 77

Query: 166 LRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSN 204
              L C H F S C++ W+ R    CP+CR +I+  T +
Sbjct: 78  -VTLNCAHSFCSYCINEWMKRKIE-CPICRKDIKSKTYS 114

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 43.6 bits (102), Expect = 5e-06
 Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 5/55 (9%)

Query: 150 ETLCSICLEDYREGENLR----VLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR 200
              C IC++ Y E            C H F S C+   L    T CP CR +I  
Sbjct: 7   TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINH 60

>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 = 5e-06
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
             +C  C E   +        C H     C+          CP CRH++ ++
Sbjct: 78  SFMCVCCQELVYQP---VTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 126

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

 Score = 43.0 bits (101), Expect = 7e-06
 Identities = 18/63 (28%), Positives = 22/63 (34%), Gaps = 3/63 (4%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEGNEQ 209
           E  C IC+E   E      LPC H     C  S + +    CP CR  +   T       
Sbjct: 15  ECQCGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHTRRN 71

Query: 210 VHV 212
             V
Sbjct: 72  SLV 74

>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 = 41.1 bits (96), Expect = 1e-05
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 150 ETLCSICLEDYREGENLRVL--PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           +  C  C        +L+++   C H    SCVD   +R    CP C   +R+S
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS 56

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

 Score = 41.2 bits (96), Expect = 1e-05
 Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 1/50 (2%)

Query: 150 ETLCSICLEDYRE-GENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
              C +C+E       N     C ++    C           CP CR   
Sbjct: 11  PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 60

>2ek8_A Aminopeptidase; metalloproteinase, hydrolase; 1.80A {Aneurinibacillus SP} PDB: 2ek9_A* Length = 421

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 16/66 (24%), Positives = 28/66 (42%)

Query: 1   MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKE 60
           + RG  +F+ K++NA   G  A I+Y          +   + + V A  +T + G  L  
Sbjct: 120 IQRGNISFADKVRNAAKQGAKAVIIYNNTDGKLNGTLGGSDASFVAAVGITKQEGDALAA 179

Query: 61  HARGEA 66
           + R   
Sbjct: 180 NLRAGE 185

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 5/64 (7%)

Query: 139 SSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCV-DSWLIRWGTF-CPVCRH 196
           +S   V     E +C ICL+  ++      + C H F   C+        G F CP+C+ 
Sbjct: 9   ASGQFVNKLQEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKT 65

Query: 197 EIRR 200
            +R+
Sbjct: 66  SVRK 69

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 39.3 bits (92), Expect = 6e-05
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 5/51 (9%)

Query: 152 LCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTF-CPVCRHEIRR 200
           LC IC +   +     V+P C + +   C+ + L+      CP C      
Sbjct: 17  LCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS 64

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 39.4 bits (92), Expect = 9e-05
 Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
              C IC E +     +    C H + S C+  +L      CP C   +   
Sbjct: 22  LLRCGICFEYFNIAMII--PQCSHNYCSLCIRKFLSYKTQ-CPTCCVTVTEP 70

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 15/75 (20%), Positives = 22/75 (29%), Gaps = 16/75 (21%)

Query: 138 FSSVTSVRCHGRETLCSICL---------------EDYREGENLRVLPCRHEFHSSCVDS 182
           +++V           C+IC                    E   +    C H FH  C+  
Sbjct: 25  WNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISR 84

Query: 183 WLIRWGTFCPVCRHE 197
           WL      CP+   E
Sbjct: 85  WLKTRQV-CPLDNRE 98

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 14/60 (23%), Positives = 18/60 (30%), Gaps = 16/60 (26%)

Query: 153 CSICL---------------EDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHE 197
           C+IC                    E   +    C H FH  C+  WL      CP+   E
Sbjct: 51  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDNRE 109

>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 = 1e-04
 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 152 LCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTF-CPVCRHE 197
           LC IC +      +  V+P C + +   C+ + L+      CP C   
Sbjct: 15  LCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 59

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 16/57 (28%), Positives = 19/57 (33%), Gaps = 8/57 (14%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWL-----IRWGTFCPVCRHEIRRS 201
           E  C ICLE  +E        C H F  +C+               CPVCR      
Sbjct: 19  EVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG 72

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            C ICL   RE       PC H F  +C+   +   G  CPV    +  +
Sbjct: 20  ECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN 66

>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 = 38.7 bits (90), Expect = 2e-04
 Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 3/53 (5%)

Query: 149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           +   C IC     +        C+H F   C+   L   G++CP CR+    +
Sbjct: 22  KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT 71

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 3/47 (6%)

Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           LCS C    R         C H + S C+ S L      C  C HE 
Sbjct: 33  LCSACRNVLRRP---FQAQCGHRYCSFCLASILSSGPQNCAACVHEG 76

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 5/54 (9%)

Query: 149 RETLCSICLEDYREGENLRVLPCRHEFHSSCV-DSWLIRWGTF-CPVCRHEIRR 200
           +   C ICLE  +E        C H F   C+      + G   CP+C+++I +
Sbjct: 20  KILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
            C ICL   RE       PC H F  +C+   +   G  CPV    +  +
Sbjct: 20  ECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN 66

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 36.5 bits (85), Expect = 5e-04
 Identities = 15/57 (26%), Positives = 19/57 (33%), Gaps = 9/57 (15%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWL------IRWGTFCPVCRHEIRR 200
           E  C ICLE   E      L C H    +C+          +   + CPVC      
Sbjct: 12  EVTCPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF 65

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 36.8 bits (85), Expect = 6e-04
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 150 ETLCSICLEDYREGENLRVLPCR-----HEFHSSCVDSWL-IRWGTFCPVCRHEIRRST 202
           + +C IC  +  +   L + PC      H  H +C+  W+       C +C++E    T
Sbjct: 15  QDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET 72

>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 = 38.0 bits (88), Expect = 7e-04
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           E +C ICL+  +    +    C H F + C+ + L      CP CR ++
Sbjct: 54  ELMCPICLDMLKNT--MTTKECLHRFCADCIITALRSGNKECPTCRKKL 100

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 35.8 bits (83), Expect = 8e-04
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 139 SSVTSVRCHGRETLCSICLEDYREGENLRV-LPCRHEFHSSCV-DSWLIRWGTF-CPVC 194
           +S   V     E +C ICL+  ++     V + C H F   C+        G F CP+C
Sbjct: 9   ASGQFVNKLQEEVICPICLDILQK----PVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	214
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.8
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.78
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.73
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.72
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.71
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.71
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	99.7
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.68
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.66
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.66
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.63
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.62
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.61
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.61
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.6
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.57
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.57
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.57
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.56
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.55
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.54
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.53
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.53
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.52
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.51
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.5
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.48
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.48
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.47
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.46
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.46
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.43
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.43
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.42
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.42
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.42
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.41
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.4
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.39
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.38
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.38
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.36
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.36
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.36
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.35
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.35
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.32
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.31
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.31
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.28
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.28
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.28
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.27
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.22
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.2
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.18
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.16
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.15
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.13
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.11
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.1
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.1
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.08
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.06
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.02
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.02
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.99
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.98
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.81
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.8
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.79
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.75
2ek8_A	421	Aminopeptidase; metalloproteinase, hydrolase; 1.80	98.66
3fed_A	707	Glutamate carboxypeptidase III; metallopeptidase,	98.29
3nw0_A	238	Non-structural maintenance of chromosomes element	98.16
3kas_A	640	Transferrin receptor protein 1; transferrin recept	98.09
3iib_A	444	Peptidase M28; YP_926796.1, structural genomics, J	97.95
1y9z_A	441	Alkaline serine protease; subtilisin-like alpha/be	97.63
1xf1_A	926	C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {St	97.56
3i6s_A	649	Subtilisin-like protease; PA-domain, FN3-domain, h	97.45
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.33
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.19
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.84
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	94.45
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	92.94
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	92.9
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	92.36
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	92.29
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	92.04
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	91.89
2yt5_A	66	Metal-response element-binding transcription facto	91.77
1we9_A	64	PHD finger family protein; structural genomics, PH	91.19
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	91.04
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	91.01
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	90.74
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	90.57
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	90.12
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	90.11
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	89.85
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	89.44
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	88.16
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	87.71
1z60_A	59	TFIIH basal transcription factor complex P44 subun	87.62
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	86.89
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	86.69
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	86.55
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	85.62
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	84.83
3vta_A	621	Cucumisin; subtilisin-like fold, serine protease,	84.56
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	84.45
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	84.28
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	84.06
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	83.75
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	82.12
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	81.67
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	81.6
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	81.41
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	80.27

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

Probab=99.80  E-value=7.9e-20  Score=120.73  Aligned_cols=79  Identities=34%  Similarity=0.762  Sum_probs=66.2

Q ss_pred             CCcCCCCCHHHHhcCCceeeeccccccCCCCCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccc
Q 028085          119 PEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI  198 (214)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i  198 (214)
                      ....+++.++.++.+|...+.......  +.+..|+||++.|..++.++.+||||.||..||+.|+..+.. ||+||..+
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~--~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~-CP~Cr~~~   87 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAV--GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGT-CPVCRCMF   87 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSS--SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCB-CTTTCCBS
T ss_pred             CcCCCCCCHHHHHhCCCeeeccccccc--CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCc-CcCcCccC
Confidence            345588999999999998887654322  255789999999999989999999999999999999987664 99999988


Q ss_pred             cc
Q 028085          199 RR  200 (214)
Q Consensus       199 ~~  200 (214)
                      ..
T Consensus        88 ~~   89 (91)
T 2l0b_A           88 PP   89 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

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

Probab=99.78  E-value=5.1e-20  Score=117.37  Aligned_cols=70  Identities=43%  Similarity=0.936  Sum_probs=56.6

Q ss_pred             HHhcCCceeeeccccccCCCCCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          129 TVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .++.+|..+++......   .+..|+||++.|..++.++.+||+|.||..|+.+|++.+.. ||+||+++....
T Consensus         5 ~i~~lp~~~~~~~~~~~---~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~-CP~Cr~~~~~~~   74 (75)
T 1x4j_A            5 SSGQLPSYRFNPNNHQS---EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRT-CPICRADSGPSS   74 (75)
T ss_dssp             CCSSCCCEEBCSSSCSS---SCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSS-CTTTCCCCCCCC
T ss_pred             hHhhCCcEEecCccccC---CCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCc-CcCcCCcCCCCC
Confidence            34567777776533222   45789999999999999999999999999999999988665 999999987543

>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=99.73  E-value=4.4e-18  Score=106.55  Aligned_cols=53  Identities=49%  Similarity=1.048  Sum_probs=47.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++.|..++.++.++|||.||..|+.+|+..+.. ||+||..+....
T Consensus        13 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~~   65 (69)
T 2kiz_A           13 TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDIEAQL   65 (69)
T ss_dssp             CCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSB-CTTTCSBSCSCC
T ss_pred             CCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCC-CcCcCccccCcC
Confidence            55789999999998888999999999999999999988665 999999987654

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

Probab=99.72  E-value=7e-18  Score=107.08  Aligned_cols=54  Identities=33%  Similarity=0.920  Sum_probs=47.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccC
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTS  203 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~  203 (214)
                      .+..|+||++.+..++.++.++|+|.||..|+.+|++.+.. ||+||.++.....
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~-CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKV-CPLCNMPVLQLAQ   67 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSB-CTTTCCBCSSCCS
T ss_pred             CCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCc-CCCcCcccccccc
Confidence            45789999999999989999999999999999999988765 9999999875543

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.71  E-value=6.9e-18  Score=108.23  Aligned_cols=56  Identities=41%  Similarity=0.971  Sum_probs=48.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccCCC
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE  205 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~  205 (214)
                      .+..|+||++.|..++.++.++|+|.||..||.+|++.+.. ||+||..+......+
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           14 SGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS-CPVCRKSLTGQNTAT   69 (78)
T ss_dssp             SSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCS-CTTTCCCCCCSCSCC
T ss_pred             CCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCc-CcCcCCccCCcccCC
Confidence            55789999999999888899999999999999999987655 999999997665443

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

Probab=99.71  E-value=3e-18  Score=102.45  Aligned_cols=50  Identities=44%  Similarity=1.062  Sum_probs=44.7

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      ++.+|+||++++.+++.+..++ |||.||.+|+.+|++.+.. ||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~-CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCS-CSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCc-CcCCCCEeE
Confidence            4568999999999998899998 9999999999999987655 999999864

>3icu_A E3 ubiquitin-protein ligase RNF128; E3 ligase, energy, PA domain, transmembrane,protein turnover conjugation pathway; HET: NAG; 2.10A {Homo sapiens}

Probab=99.70  E-value=4.1e-17  Score=120.75  Aligned_cols=74  Identities=22%  Similarity=0.338  Sum_probs=61.8

Q ss_pred             Ccccc-ccHHHHHHHHHHcCCcEEEEEeCC-CCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhh-cCCCceEEecc
Q 028085            1 MIRGQ-CNFSYKIQNAQAAGYDAAIVYALR-KKSPLIYMTYPEGANVPAFYVTLETGAYLKEHAR-GEAGECCIFPL   74 (214)
Q Consensus         1 v~rg~-C~f~~K~~~a~~~ga~aviv~~~~-~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~-~~~~~~~~~p~   74 (214)
                      |+||+ |+|.+|+++||++||+||||||+. +++.+++|......+||++||++.+|+.|++.+. +..+.+.+...
T Consensus       110 V~RG~~CsF~~Kv~nAq~aGA~avIIyNn~~~g~~~~~m~~~~~~~IPsv~Is~~~G~~L~~~L~~G~~Vtvti~vg  186 (194)
T 3icu_A          110 IQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAVDIVAIMIGNLKGTKILQSIQRGIQVTMVIEVG  186 (194)
T ss_dssp             EESCTTCCHHHHHHHHHHTTCSEEEEECCTTCTTCCCCCCCTTCCSSEEEEECHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             EECCCCcCHHHHHHHHHHCCCcEEEEEeCCCCCCceeeecCCCCCceeEEEECHHHHHHHHHHHHCCCeEEEEEECC
Confidence            58999 999999999999999999999975 4446788886566789999999999999999885 44566655544

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

Probab=99.68  E-value=1.4e-17  Score=107.40  Aligned_cols=52  Identities=25%  Similarity=0.703  Sum_probs=41.2

Q ss_pred             CCcccccccccccC-----------CCceEEec-CCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYRE-----------GENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~-----------~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .++.|+||+++|.+           ++.++.++ |+|.||.+||++|++.+++ ||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~-CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNR-CPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCB-CTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCC-CCCcCCCcchh
Confidence            34568888887753           45567776 9999999999999988665 99999987644

>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=99.66  E-value=7.7e-17  Score=110.84  Aligned_cols=60  Identities=25%  Similarity=0.453  Sum_probs=46.3

Q ss_pred             CCcccccccccccCCC---------------ceEEecCCCccChhhHHHHHHh----CCCCccccccccccccCCCCCc
Q 028085          149 RETLCSICLEDYREGE---------------NLRVLPCRHEFHSSCVDSWLIR----WGTFCPVCRHEIRRSTSNEGNE  208 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~---------------~~~~l~C~H~FH~~Ci~~Wl~~----~~~~CP~Cr~~i~~~~~~~~~~  208 (214)
                      .+..|+||++.|..+.               .++.++|+|.||..||..|+..    .+.+||+||+.+....++.+..
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~g  102 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWG  102 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCCC
Confidence            3468999999997643               3457899999999999999963    2336999999997776655443

>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=99.66  E-value=7.8e-17  Score=96.18  Aligned_cols=50  Identities=34%  Similarity=0.695  Sum_probs=42.9

Q ss_pred             CCcccccccccccCC-CceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREG-ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~-~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      ++..|+||++.+.++ +.++.++|||.||..|+.+|+..+.. ||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYR-CPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCC-CTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCc-CCCCCCcCC
Confidence            456899999999754 35788899999999999999998755 999998864

>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=99.63  E-value=1.2e-16  Score=107.70  Aligned_cols=50  Identities=26%  Similarity=0.553  Sum_probs=41.9

Q ss_pred             CCcccccccccccCC---------------CceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREG---------------ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~---------------~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .++.|+||++.|...               ..++.++|+|.||..||++||..+.+ ||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~-CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSB-CSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCc-CcCCCCcce
Confidence            457899999998854               13677899999999999999988555 999999854

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.62  E-value=1.9e-16  Score=99.55  Aligned_cols=53  Identities=32%  Similarity=0.681  Sum_probs=44.7

Q ss_pred             CCcccccccccccCC----CceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREG----ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++..|+||++.+.+.    +.+..++|||.||..|+.+|+..+.. ||+||.++....
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~~   65 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHKR   65 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSB-CTTTCCBCCCCS
T ss_pred             CCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCC-CCCCCCccChhh
Confidence            557899999998753    45688999999999999999988665 999999987553

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

Probab=99.61  E-value=3.2e-16  Score=97.89  Aligned_cols=51  Identities=33%  Similarity=0.708  Sum_probs=43.2

Q ss_pred             CCcccccccccccCC----CceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREG----ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .+..|+||++.+.+.    +.+..++|||.||..|+..|+..+.. ||+||..+..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSS-CTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCC-CCCCCCccCc
Confidence            557899999999853    34588999999999999999988665 9999998764

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=6.1e-16  Score=98.90  Aligned_cols=57  Identities=26%  Similarity=0.688  Sum_probs=46.6

Q ss_pred             CCcccccccccccCCCceEEecCC-----CccChhhHHHHHHhCC-CCccccccccccccCCCC
Q 028085          149 RETLCSICLEDYREGENLRVLPCR-----HEFHSSCVDSWLIRWG-TFCPVCRHEIRRSTSNEG  206 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~-----H~FH~~Ci~~Wl~~~~-~~CP~Cr~~i~~~~~~~~  206 (214)
                      .+..|+||++++.+++.+ .+||+     |.||.+||++|+..++ .+||+||..+......++
T Consensus        14 ~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~~P   76 (80)
T 2d8s_A           14 SQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLSG   76 (80)
T ss_dssp             TSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCSCC
T ss_pred             CCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcccCC
Confidence            456899999999887665 69996     9999999999998865 369999999876554433

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

Probab=99.60  E-value=3.1e-16  Score=96.47  Aligned_cols=52  Identities=33%  Similarity=0.685  Sum_probs=43.8

Q ss_pred             CCcccccccccccCC----CceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREG----ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ++.+|+||++.+.+.    +.+..++|||.||.+|+.+|+..+.. ||+||.++...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSB-CTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCC-CCCCCccCCcc
Confidence            456899999999753    45688999999999999999988555 99999998754

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

Probab=99.57  E-value=6.2e-16  Score=97.19  Aligned_cols=50  Identities=32%  Similarity=0.608  Sum_probs=42.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++.+.   ....++|||.||..|+..|+..+.. ||+||..+....
T Consensus        14 ~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~-CP~Cr~~~~~~~   63 (71)
T 2d8t_A           14 TVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKR-CALCRQEIPEDF   63 (71)
T ss_dssp             SCCBCSSSSSBCS---SEEEETTTEEEEHHHHHHCTTCSSB-CSSSCCBCCHHH
T ss_pred             CCCCCccCCcccC---CCEEccCCCHHHHHHHHHHHHCCCc-CcCcCchhCHhh
Confidence            4568999999997   4578899999999999999987654 999999987554

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

Probab=99.57  E-value=2.1e-15  Score=93.90  Aligned_cols=50  Identities=34%  Similarity=0.802  Sum_probs=42.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+  .+..+||||.||..|+..|+..+.. ||+||.++...
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPT-CPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCS-TTTTCCCCCCE
T ss_pred             CCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcCc-CcCCChhhHhh
Confidence            45689999999873  3578999999999999999988665 99999988643

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

Probab=99.57  E-value=3.4e-15  Score=94.00  Aligned_cols=50  Identities=26%  Similarity=0.578  Sum_probs=42.0

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++.+.+   ...+ +|||.||..||..|+..+.. ||+||..+....
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~-CP~Cr~~~~~~~   64 (72)
T 2djb_A           14 PYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNR-CPKCNIVVHQTQ   64 (72)
T ss_dssp             GGGSCTTTSSCCSS---CEECSSSCCEECHHHHHHHHHHCSS-CTTTCCCCCSSC
T ss_pred             CCCCCCCCChHHHC---cCEECCCCCHHHHHHHHHHHHcCCc-CCCcCcccCccc
Confidence            45789999999984   3555 99999999999999987555 999999987654

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

Probab=99.56  E-value=1.4e-15  Score=95.27  Aligned_cols=49  Identities=35%  Similarity=0.935  Sum_probs=42.0

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++.+.+    ..+||||.||..|+..|+.... .||+||..+....
T Consensus        14 ~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHR-NCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCS-SCHHHHHCTTCCC
T ss_pred             CCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcC-cCCCcCCcccCCC
Confidence            45689999999884    7899999999999999998655 4999999987543

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

Probab=99.55  E-value=4.8e-15  Score=96.99  Aligned_cols=53  Identities=28%  Similarity=0.669  Sum_probs=45.0

Q ss_pred             CCcccccccccccCCCc-eEEecCCCccChhhHHHHHHhC--CCCccccccccccc
Q 028085          149 RETLCSICLEDYREGEN-LRVLPCRHEFHSSCVDSWLIRW--GTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~-~~~l~C~H~FH~~Ci~~Wl~~~--~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.|.+++. ++.++|||.||..|+..|+..+  ...||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             CCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            45789999999997654 7889999999999999999875  23599999988654

>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=99.54  E-value=4.5e-16  Score=106.30  Aligned_cols=50  Identities=28%  Similarity=0.597  Sum_probs=1.1

Q ss_pred             CCcccccccccccCC-------------C--ceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREG-------------E--NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~-------------~--~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .++.|+||+++|.+.             +  .+..++|+|.||..||++||..+.+ ||+||++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~-CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDNREWE  111 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCc-CCCCCCeee
Confidence            457899999999752             2  3344689999999999999988665 999999854

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

Probab=99.53  E-value=4.3e-15  Score=91.91  Aligned_cols=50  Identities=22%  Similarity=0.473  Sum_probs=41.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+.   ..++|||.||..|+..|+...+..||+||..+..+
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           14 DKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCEECTTTCCEESSC---CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             cCCCCCCCChHhcCe---eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            557899999999854   45899999999999999964444699999998654

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.53  E-value=9.7e-15  Score=92.39  Aligned_cols=51  Identities=25%  Similarity=0.643  Sum_probs=42.3

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCC-CCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWG-TFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~-~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++.+.+   .+.++ |||.||..||..|+.... ..||+||+.+...+
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           14 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             GGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            45789999999984   47799 999999999999998753 35999999865443

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

Probab=99.52  E-value=8.3e-15  Score=94.39  Aligned_cols=47  Identities=26%  Similarity=0.504  Sum_probs=40.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .+..|+||++.+.+   ...++|||.||..|+..|+..... ||+||..+.
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~-CP~Cr~~~~   60 (81)
T 2csy_A           14 IPFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRATPR-CYICDQPTG   60 (81)
T ss_dssp             CCSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHHCSB-CSSSCCBCC
T ss_pred             CCCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHCCCc-CCCcCcccc
Confidence            45689999999973   467999999999999999987555 999999985

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=9.6e-15  Score=92.17  Aligned_cols=50  Identities=26%  Similarity=0.638  Sum_probs=41.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHh--CCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR--WGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~--~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.   ....++|||.||..|+..|+..  ....||+||..+..+
T Consensus        19 ~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           19 EEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCBCTTTCSBCS---SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             cCCEeccCCcccC---CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            5578999999998   4577899999999999999973  233699999998654

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.50  E-value=1.1e-14  Score=89.71  Aligned_cols=52  Identities=35%  Similarity=0.675  Sum_probs=42.2

Q ss_pred             Ccccccccc-cccCCCc-eEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLE-DYREGEN-LRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~-~~~~~~~-~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +..|+||++ .+.+... +..++|||.||..|+++|+......||+||..+..+
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            468999999 7776543 356799999999999999876555699999998654

>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=99.48  E-value=1.4e-14  Score=97.03  Aligned_cols=50  Identities=30%  Similarity=0.672  Sum_probs=42.4

Q ss_pred             CCcccccccccccCCCceEE-ecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRV-LPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~-l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.   ..+. ++|||.||..||..|+...+..||+||.++...
T Consensus        21 ~~~~C~IC~~~~~---~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           21 EVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCccCCcccc---CccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            3468999999998   3466 899999999999999998744599999998654

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.48  E-value=9.2e-15  Score=103.73  Aligned_cols=48  Identities=38%  Similarity=0.888  Sum_probs=41.4

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +..|+||++.|.   .++.+||||.||..|+..|+..+.. ||+||.++...
T Consensus        53 ~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIE-CPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSB-CTTTCCBCCCE
T ss_pred             cCCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCc-CCCCCCcCCCC
Confidence            357999999998   4578999999999999999987655 99999998643

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.47  E-value=2.4e-14  Score=91.50  Aligned_cols=50  Identities=18%  Similarity=0.387  Sum_probs=42.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.   ....++|||.||+.||..|+..++.+||+||..+...
T Consensus         7 ~~~~C~IC~~~~~---~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            7 EYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCCCcccccc---CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            4578999999998   4578899999999999999986445699999998654

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=7.1e-14  Score=85.53  Aligned_cols=43  Identities=28%  Similarity=0.637  Sum_probs=36.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHh--CCCCcccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR--WGTFCPVC  194 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~--~~~~CP~C  194 (214)
                      .+..|+||++.+.+   .+.++|||.||..||..|++.  ....||+|
T Consensus        19 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            55789999999984   478899999999999999985  23369998

>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=99.46  E-value=3.3e-14  Score=99.08  Aligned_cols=51  Identities=25%  Similarity=0.441  Sum_probs=43.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      .+..|+||++.+.   ....++|||.||..|+..|+..+...||+||..+....
T Consensus        51 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~  101 (124)
T 3fl2_A           51 ETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSY  101 (124)
T ss_dssp             HHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTC
T ss_pred             cCCCCCcCChHHc---CcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCCCC
Confidence            3468999999999   45788999999999999999865546999999997633

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.43  E-value=8e-14  Score=91.94  Aligned_cols=50  Identities=26%  Similarity=0.656  Sum_probs=41.9

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCC-CCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWG-TFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~-~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.|.+   .+.++ |||.||..||..|+.... ..||+||..+...
T Consensus        12 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   63 (92)
T 3ztg_A           12 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   63 (92)
T ss_dssp             TTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCT
T ss_pred             cCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCc
Confidence            56789999999984   47899 999999999999997654 3699999987433

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=1.5e-13  Score=89.10  Aligned_cols=50  Identities=32%  Similarity=0.581  Sum_probs=42.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC-----CCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW-----GTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~-----~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+.   ..++|||.||..|+..|+...     ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           18 EEVTCPICLELLKEP---VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTTSCTTTCSCCSSC---EECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             cCCCCcCCChhhCcc---eeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            457899999999844   689999999999999999883     33699999998754

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.42  E-value=4.7e-14  Score=99.26  Aligned_cols=53  Identities=32%  Similarity=0.681  Sum_probs=44.7

Q ss_pred             CCcccccccccccCC----CceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREG----ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++.+|+||++.|.+.    +.++.++|||.||.+|+.+|++.+.. ||+||..+....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSB-CTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCC-CCCCCCcCcccc
Confidence            557899999999753    45689999999999999999987665 999999887554

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=1.3e-13  Score=89.44  Aligned_cols=50  Identities=32%  Similarity=0.651  Sum_probs=41.7

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC-----CCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW-----GTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~-----~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+   ...++|||.||..|+..|+...     ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           18 EEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             CCCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            45789999999984   3668999999999999999871     33599999998754

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=1.2e-13  Score=86.39  Aligned_cols=52  Identities=21%  Similarity=0.511  Sum_probs=41.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC-CCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG-TFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~-~~CP~Cr~~i~~~~  202 (214)
                      ...+|+||.+.+..++.  -..|+|.||..||.+|++.+. .+||+||++...+.
T Consensus        14 ~i~~C~IC~~~i~~g~~--C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQS--CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSCBCSSSCCBCSSSEE--CSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCCcCcchhhHcccCCc--cCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            44689999999997753  337999999999999998762 35999999876443

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=1.1e-13  Score=83.20  Aligned_cols=43  Identities=37%  Similarity=0.906  Sum_probs=35.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHh--CCCCcccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR--WGTFCPVC  194 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~--~~~~CP~C  194 (214)
                      .+..|+||++.+.+.   +.++|||.||..|+..|+..  .+..||+|
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKEP---VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSSC---CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCcc---EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            457899999999854   56899999999999999754  33369998

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.40  E-value=3.1e-14  Score=91.18  Aligned_cols=50  Identities=30%  Similarity=0.538  Sum_probs=41.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC------CCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW------GTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~------~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+.   +.++|||.||..|+..|+...      ...||+||..+...
T Consensus        11 ~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           11 EEVTCPICLELLTEP---LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCEETTTTEECSSC---CCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cCCCCcCCCcccCCe---eECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            557899999999843   568999999999999999863      33699999998754

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.39  E-value=1.3e-13  Score=92.13  Aligned_cols=49  Identities=24%  Similarity=0.629  Sum_probs=40.9

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+   ...+ +|||.||..|+..|+..+. .||+||..+...
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~   70 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKT-QCPTCCVTVTEP   70 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCC-BCTTTCCBCCGG
T ss_pred             CCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCC-CCCCCCCcCChh
Confidence            34689999999984   4566 8999999999999998755 499999988753

>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=99.38  E-value=1.9e-13  Score=98.08  Aligned_cols=49  Identities=22%  Similarity=0.499  Sum_probs=42.6

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +..|+||++.+.   ....++|||.||..||..|+......||+||..+...
T Consensus        78 ~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhc---CCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            468999999998   4477999999999999999987654699999998765

>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=99.38  E-value=2e-13  Score=92.74  Aligned_cols=49  Identities=20%  Similarity=0.716  Sum_probs=41.2

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.+   ...+ +|||.||..|+..|+..+. .||+||..+...
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            45689999999983   4566 9999999999999998765 499999998754

>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=99.36  E-value=3.1e-13  Score=92.96  Aligned_cols=53  Identities=25%  Similarity=0.520  Sum_probs=43.9

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccCCC
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE  205 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~  205 (214)
                      +..|+||++.+.   ....++|||.||..|+..|+......||+||.++......+
T Consensus        23 ~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           23 SISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (116)
T ss_dssp             HTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             CCCCCCCCcHhc---CcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhccc
Confidence            468999999998   44679999999999999999874446999999987655333

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.36  E-value=2.5e-13  Score=95.50  Aligned_cols=53  Identities=32%  Similarity=0.681  Sum_probs=44.5

Q ss_pred             CCcccccccccccCC----CceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREG----ENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~----~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      +...|+||++.+.+.    ..+..++|||.||..|+++|++..++ ||+||.++..+.
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-CP~Cr~~~~~~~  127 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHKR  127 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSB-CTTTCCBCCGGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCC-CCCCCCcCChhc
Confidence            457899999998752    34578899999999999999988665 999999987653

>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=99.36  E-value=2.3e-13  Score=99.39  Aligned_cols=50  Identities=28%  Similarity=0.656  Sum_probs=41.2

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.|.+   ...+ +|||.||..|+..|+......||+||..+...
T Consensus        53 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           53 SELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHHBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCCcccChHhhC---cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            34589999999984   3555 99999999999999987455699999998543

>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=99.35  E-value=3.8e-13  Score=92.79  Aligned_cols=50  Identities=28%  Similarity=0.552  Sum_probs=43.1

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.   ..+.++|||.||..|+..|+......||+||.++...
T Consensus        17 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           17 SKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCcCChhhc---CeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            4568999999998   4477899999999999999988764699999998764

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

Probab=99.35  E-value=4.1e-13  Score=85.38  Aligned_cols=53  Identities=19%  Similarity=0.532  Sum_probs=41.7

Q ss_pred             CCcccccccccccCCCceEEec--CCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP--CRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~--C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++..|+||++.+...+ +..+|  |||.||..|+..|+......||.||+++....
T Consensus        10 ~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A           10 DPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            5578999999986543 23444  99999999999998654457999999987554

>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=99.32  E-value=6.3e-13  Score=90.79  Aligned_cols=50  Identities=30%  Similarity=0.621  Sum_probs=41.4

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCC--CCcccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG--TFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~--~~CP~Cr~~i~~~~  202 (214)
                      ...|+||++.+.+.   ..++|||.||..|+..|+..+.  ..||+||..+....
T Consensus        21 ~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CCCCcccChhhcCe---EECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhh
Confidence            45899999999844   5689999999999999998653  25999999987543

>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=99.31  E-value=7.1e-13  Score=81.19  Aligned_cols=48  Identities=27%  Similarity=0.460  Sum_probs=39.5

Q ss_pred             CCcccccccccccCCCceEEe--cCCCc-cChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL--PCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l--~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      ++..|+||++...   ....+  ||||. |+.+|+..|...+.. ||+||+++..
T Consensus         7 ~~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~-CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPK---NGCIVHGKTGHLMACFTCAKKLKKRNKP-CPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCS---CEEEEETTEEEEEECHHHHHHHHHTTCC-CTTTCCCCCE
T ss_pred             CcCCCCcCCCCCC---CEEEECCCCCChhhHHHHHHHHHHcCCc-CCCcCcchhc
Confidence            4468999999977   33555  99999 899999999987665 9999998853

>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=99.31  E-value=2.3e-13  Score=93.47  Aligned_cols=49  Identities=31%  Similarity=0.702  Sum_probs=42.0

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .+..|+||++.+.   ..+.++|||.||..|+..|+......||+||..+..
T Consensus        14 ~~~~C~iC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCS---SCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccC---ceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3468999999998   457889999999999999997655569999999864

>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=99.28  E-value=1.1e-12  Score=80.08  Aligned_cols=48  Identities=23%  Similarity=0.465  Sum_probs=39.1

Q ss_pred             CCcccccccccccCCCceEEe--cCCCc-cChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL--PCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l--~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .+..|.||++...+   ...+  ||||. |+..|+..|.+.+.. ||+||+++..
T Consensus         6 ~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~-CPiCR~~i~~   56 (63)
T 2vje_B            6 LLKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKAGAS-CPICKKEIQL   56 (63)
T ss_dssp             GGSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHTTCB-CTTTCCBCCE
T ss_pred             cCCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHhCCc-CCCcCchhhc
Confidence            45689999998763   3455  99998 999999999977554 9999998853

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

Probab=99.28  E-value=5.9e-13  Score=79.34  Aligned_cols=47  Identities=26%  Similarity=0.663  Sum_probs=38.7

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++..|+||++.|.+   .+.|||||.||..|+..|    ...||+||+.+..+.
T Consensus         5 ~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            5 QFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCS
T ss_pred             cCCCceEeCCccCC---eEEcCCCCcccHHHHccC----CCCCCcCCcEeecCC
Confidence            55789999999984   478999999999999884    335999999987553

>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=99.28  E-value=2.5e-12  Score=104.58  Aligned_cols=51  Identities=37%  Similarity=0.855  Sum_probs=42.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ....|+||++.+.   .+..+||||.||..|+..|+......||+||.++....
T Consensus       331 ~~~~C~ICle~~~---~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          331 TFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSSBCTTTSSSBC---CEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCCccCcCCC---CeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            3468999999987   56889999999999999999844446999999987653

>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=99.27  E-value=1.2e-12  Score=92.99  Aligned_cols=48  Identities=31%  Similarity=0.490  Sum_probs=41.3

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      .+..|+||++.+.+   .+.++|||.||..||..|+......||+||.++.
T Consensus        30 ~~~~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           30 AKYLCSACRNVLRR---PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             cCcCCCCCChhhcC---cEECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            56789999999984   4779999999999999999876546999999864

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=99.22  E-value=6.4e-12  Score=81.36  Aligned_cols=49  Identities=16%  Similarity=0.048  Sum_probs=42.7

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++-+.   .++.++|||.|++.||..|+..+. +||+||.++...
T Consensus        13 ~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~-~cP~~~~~l~~~   61 (85)
T 2kr4_A           13 DEFRDPLMDTLMT---DPVRLPSGTVMDRSIILRHLLNSP-TDPFNRQMLTES   61 (85)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHCS-BCTTTCCBCCGG
T ss_pred             hheECcccCchhc---CCeECCCCCEECHHHHHHHHhcCC-CCCCCcCCCChH
Confidence            4578999999999   558999999999999999998754 599999988654

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.20  E-value=3.5e-12  Score=80.43  Aligned_cols=45  Identities=29%  Similarity=0.708  Sum_probs=38.2

Q ss_pred             CCcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ++..|+||++.+.   .+..+||||. ||..|+..|    . .||+||.++...
T Consensus        23 ~~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~~~   68 (74)
T 4ic3_A           23 EEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEAV----D-KCPMCYTVITFK   68 (74)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCCBCCCHHHHTTC----S-BCTTTCCBCSEE
T ss_pred             cCCCCCCCCCCCC---CEEEcCCCChhHHHHhhhcC----c-cCCCcCcCccCc
Confidence            3468999999987   5688999999 999999998    3 499999988654

>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=99.18  E-value=7.5e-12  Score=83.45  Aligned_cols=49  Identities=16%  Similarity=0.067  Sum_probs=42.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++-|.   .++.++|||.|++.||..|+... .+||+||.++...
T Consensus        28 ~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~-~~cP~~~~~l~~~   76 (100)
T 2kre_A           28 DEFRDPLMDTLMT---DPVRLPSGTIMDRSIILRHLLNS-PTDPFNRQTLTES   76 (100)
T ss_dssp             TTTBCTTTCSBCS---SEEEETTTEEEEHHHHHHHTTSC-SBCSSSCCBCCTT
T ss_pred             HhhCCcCccCccc---CCeECCCCCEEchHHHHHHHHcC-CCCCCCCCCCChh
Confidence            4578999999999   55899999999999999999864 4599999998654

>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=99.16  E-value=1.4e-11  Score=81.85  Aligned_cols=49  Identities=20%  Similarity=0.122  Sum_probs=42.5

Q ss_pred             CCcccccccccccCCCceEEecCC-CccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCR-HEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~-H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++-|.   .++.++|| |.|++.||..|+..+. +||+||.++...
T Consensus        21 ~~~~CpI~~~~m~---dPV~~~cG~htf~r~cI~~~l~~~~-~cP~~~~~l~~~   70 (98)
T 1wgm_A           21 DEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQ-TDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSC-BCTTTCSBCCTT
T ss_pred             HhcCCcCcccccc---CCeECCCCCeEECHHHHHHHHHhCC-CCCCCCCCCChh
Confidence            4578999999999   45889999 9999999999998754 599999998654

>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=99.15  E-value=5.6e-12  Score=86.77  Aligned_cols=46  Identities=35%  Similarity=0.572  Sum_probs=38.9

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .+..|+||++.|.+   ++.+ +|||.||..||..|+.  . .||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~-~CP~Cr~~~~~   67 (117)
T 1jm7_B           21 KLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--T-GCPVCYTPAWI   67 (117)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--T-BCSSSCCBCSC
T ss_pred             hCCCCCCCChHhhC---ccEeCCCCCHHHHHHHHHHhc--C-CCcCCCCcCcc
Confidence            34689999999984   4677 9999999999999986  3 49999999853

>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=99.13  E-value=2.4e-11  Score=89.07  Aligned_cols=50  Identities=30%  Similarity=0.570  Sum_probs=43.1

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ++..|+||++.+.+   ++.++|||.||..|+..|+......||+||.++...
T Consensus        17 ~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcC---cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            45789999999984   477999999999999999987664699999998764

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=5e-11  Score=73.69  Aligned_cols=45  Identities=33%  Similarity=0.817  Sum_probs=37.6

Q ss_pred             CCcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ++..|.||++...   .+..+||||. ||..|+..    .. .||+||..+...
T Consensus        14 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~----~~-~CP~CR~~i~~~   59 (68)
T 2ea5_A           14 NSKDCVVCQNGTV---NWVLLPCRHTCLCDGCVKY----FQ-QCPMCRQFVQES   59 (68)
T ss_dssp             CSSCCSSSSSSCC---CCEETTTTBCCSCTTHHHH----CS-SCTTTCCCCCCE
T ss_pred             CCCCCCCcCcCCC---CEEEECCCChhhhHHHHhc----CC-CCCCCCcchhce
Confidence            5678999999977   5689999999 99999983    24 499999998654

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

Probab=99.10  E-value=1.8e-11  Score=96.90  Aligned_cols=54  Identities=24%  Similarity=0.632  Sum_probs=41.9

Q ss_pred             CCcccccccccccCCCceE-----EecCCCccChhhHHHHHHhCC----------CCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLR-----VLPCRHEFHSSCVDSWLIRWG----------TFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~-----~l~C~H~FH~~Ci~~Wl~~~~----------~~CP~Cr~~i~~~~  202 (214)
                      ...+|+||++.+.+++++-     ..+|+|.||..|+.+|++...          ..||+||+++..+-
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf  375 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSF  375 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGG
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccH
Confidence            5678999999998743332     246999999999999997631          15999999987653

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=99.10  E-value=5.1e-11  Score=71.58  Aligned_cols=48  Identities=29%  Similarity=0.678  Sum_probs=37.3

Q ss_pred             CCcccccccccccCCCceEEecCC--C---ccChhhHHHHHHhC-CCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCR--H---EFHSSCVDSWLIRW-GTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~--H---~FH~~Ci~~Wl~~~-~~~CP~Cr~~i~  199 (214)
                      +...|.||+++.  ++++ .+||.  |   .||.+|+++|+... +.+||+||..+.
T Consensus         5 ~~~~CrIC~~~~--~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEEC--SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCC--CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            456899999983  3344 68964  5   89999999999864 346999998864

>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=99.08  E-value=5.1e-11  Score=94.00  Aligned_cols=50  Identities=22%  Similarity=0.315  Sum_probs=43.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ....|+||++-+.   .++.+||||.||+.||..|+..+..+||+||.++...
T Consensus       207 ~~~~c~i~~~~~~---dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~  256 (281)
T 2c2l_A          207 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE  256 (281)
T ss_dssp             STTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             cccCCcCcCCHhc---CCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchh
Confidence            5578999999999   5588999999999999999987555599999998654

>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=99.06  E-value=7.9e-11  Score=77.68  Aligned_cols=49  Identities=22%  Similarity=0.545  Sum_probs=40.1

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhC-----CCCccc--cccc-ccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRW-----GTFCPV--CRHE-IRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~-----~~~CP~--Cr~~-i~~  200 (214)
                      .+..|+||++.|.   .++.++ |||.|++.||..|+..+     ..+||+  |+.. +..
T Consensus         6 ~~~~CPI~~~~~~---dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            6 SGFTCPITKEEMK---KPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SCCBCTTTCSBCS---SEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             cEeECcCcCchhc---CCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            4578999999999   457886 99999999999999875     236999  9866 543

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.02  E-value=6.3e-11  Score=74.84  Aligned_cols=44  Identities=30%  Similarity=0.721  Sum_probs=35.9

Q ss_pred             CcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +..|+||++.+.   .+..+||||. ||..|+..    .. .||+||.++...
T Consensus        25 ~~~C~IC~~~~~---~~~~~pCgH~~~C~~C~~~----~~-~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNI---AIVFVPCGHLVTCKQCAEA----VD-KCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCC---CBCCSSSCCCCBCHHHHHH----CS-BCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCC---CEEEecCCCHHHHHHHhhC----CC-CCccCCceecCc
Confidence            457999999987   4578999999 99999964    23 499999998653

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.02  E-value=1.3e-10  Score=85.03  Aligned_cols=50  Identities=22%  Similarity=0.307  Sum_probs=43.1

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ....|+||++-+.   .++.+||||.|+..||..|+..+..+||+||.++...
T Consensus       105 ~~f~CPI~~elm~---DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          105 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             HhhcccCccccCC---CCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            5578999999999   4588899999999999999987544699999988654

>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=98.99  E-value=9.2e-11  Score=74.73  Aligned_cols=44  Identities=34%  Similarity=0.767  Sum_probs=37.4

Q ss_pred             CcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      +..|+||++.+.   .+..+||||. |+..|+..|    . .||+||.++...
T Consensus        18 ~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEI---NSTFCPCGHTVCCESCAAQL----Q-SCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBC---CEEEETTCBCCBCHHHHTTC----S-BCTTTCCBCCEE
T ss_pred             CCEeEEeCcccC---cEEEECCCCHHHHHHHHHhc----C-cCCCCCchhhCe
Confidence            458999999987   5688999999 999999876    2 499999988654

>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=98.98  E-value=1.5e-10  Score=76.33  Aligned_cols=49  Identities=20%  Similarity=0.590  Sum_probs=39.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC-------CCCccc--cccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW-------GTFCPV--CRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~-------~~~CP~--Cr~~  197 (214)
                      ...+|+||++++...+.+..++|||.||.+|+..++...       ...||.  ||..
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            456899999999876555555799999999999999752       126999  9987

>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=98.81  E-value=9.5e-10  Score=88.83  Aligned_cols=45  Identities=29%  Similarity=0.768  Sum_probs=38.5

Q ss_pred             CCcccccccccccCCCceEEecCCCc-cChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHE-FHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~-FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      .+..|+||++.+.   .+..+||||. ||..|+..|    . .||+||.++...
T Consensus       294 ~~~~C~IC~~~~~---~~v~lpCgH~~fC~~C~~~~----~-~CP~CR~~i~~~  339 (345)
T 3t6p_A          294 EERTCKVCMDKEV---SVVFIPCGHLVVCQECAPSL----R-KCPICRGIIKGT  339 (345)
T ss_dssp             TTCBCTTTSSSBC---CEEEETTCCEEECTTTGGGC----S-BCTTTCCBCCEE
T ss_pred             CCCCCCccCCcCC---ceEEcCCCChhHhHHHHhcC----C-cCCCCCCCccCe
Confidence            4568999999998   5688999999 999999988    3 499999998654

>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=98.80  E-value=1.4e-09  Score=83.41  Aligned_cols=52  Identities=23%  Similarity=0.496  Sum_probs=41.3

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC-CCccc--ccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG-TFCPV--CRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~-~~CP~--Cr~~i~~~~  202 (214)
                      .+..|+||++.|.  +.|+.+.|||.|++.||..|+..+. ..||+  ||..+....
T Consensus       180 ~el~CPIcl~~f~--DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~d  234 (267)
T 3htk_C          180 IELTCPITCKPYE--APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRD  234 (267)
T ss_dssp             CCSBCTTTSSBCS--SEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGG
T ss_pred             eeeECcCccCccc--CCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhh
Confidence            4568999999998  3444458999999999999997643 36999  999876543

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.79  E-value=4.2e-09  Score=68.29  Aligned_cols=49  Identities=24%  Similarity=0.572  Sum_probs=39.4

Q ss_pred             ccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      -|++|--.+.  ...|.+||+|+||.+|+..|.++....||+||.++..-+
T Consensus         3 fC~~C~~Pi~--iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCS--EEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCeE--EEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeeeeE
Confidence            4777776655  345899999999999999999776567999999886543

>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=98.75  E-value=3.8e-09  Score=63.61  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=42.6

Q ss_pred             cccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCccccccccccccCC
Q 028085          151 TLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSN  204 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~  204 (214)
                      ..|+||++-+.+   ...+ +|||+|.+.||.+|++.+.. ||+.+.++......
T Consensus         4 ~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~~~~-cP~t~~~L~~~~Li   54 (61)
T 2bay_A            4 MLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGN-DPITNEPLSIEEIV   54 (61)
T ss_dssp             CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSB-CTTTCCBCCGGGCE
T ss_pred             EEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHhCCC-CcCCcCCCChhhcE
Confidence            579999999993   4777 89999999999999988766 99999998766543

>2ek8_A Aminopeptidase; metalloproteinase, hydrolase; 1.80A {Aneurinibacillus SP} PDB: 2ek9_A*

Probab=98.66  E-value=5e-08  Score=81.30  Aligned_cols=62  Identities=24%  Similarity=0.280  Sum_probs=50.5

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHh
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHA   62 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~   62 (214)
                      |+||+|+|.+|+++|+++||.|+||||+.+......+.......||++.|+.++++.|.+.+
T Consensus       120 v~~g~~~~~~k~~~A~~~GA~gvIi~~~~~~~~~g~~~~~~~~~IP~~~Is~~~a~~L~~~l  181 (421)
T 2ek8_A          120 IQRGNISFADKVRNAAKQGAKAVIIYNNTDGKLNGTLGGSDASFVAAVGITKQEGDALAANL  181 (421)
T ss_dssp             EECCSSCHHHHHHHHHHTTCSEEEEECSSSSCCCCBCSSCCTTCCEEEEECHHHHHHHHHHH
T ss_pred             EeCCCCCHHHHHHHHHHCCCeEEEEEeCCCcccccccCCCCCCCccEEEeCHHHHHHHHHHh
Confidence            46899999999999999999999999986542222333334578999999999999998876

>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=98.29  E-value=5.8e-07  Score=79.08  Aligned_cols=63  Identities=17%  Similarity=0.156  Sum_probs=46.9

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCC-----C-----------------CCeee---eeCC---------------
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRK-----K-----------------SPLIY---MTYP---------------   40 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~-----~-----------------~~~~~---m~~~---------------   40 (214)
                      |+||+|+|.+|+++|+++||.||||||+..     +                 ..+..   .+++               
T Consensus       160 v~~G~~~~~~Kv~~A~~~GA~gviiy~dp~d~~~~g~~~yP~~~~~p~~~vqrGsv~~~~~~GDp~TPG~ps~~~~~r~~  239 (707)
T 3fed_A          160 ARYGKIFRGNKVKNAMLAGAIGIILYSDPADYFAPEVQPYPKGWNLPGTAAQRGNVLNLNGAGDPLTPGYPAKEYTFRLD  239 (707)
T ss_dssp             EECCSSCHHHHHHHHHHTTCSEEEEECCHHHHCCTTCCBTTTSSBCCTTCCCCCCCCCCTTCCSTTCTTSCCCTTCCCCC
T ss_pred             EECCCCCHhHHHHHHHHCCCEEEEEEcCchhccccccccCCCCccCCCccccccceecccCCCCCCCCCCcccCCCcccC
Confidence            468999999999999999999999998621     0                 00100   0100               


Q ss_pred             -----CCCeeeEEEEchhhHHHHHHHhh
Q 028085           41 -----EGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus        41 -----~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                           ....||++.|++.+|+.|+..+.
T Consensus       240 ~~~~~~~p~IP~~pIS~~da~~Ll~~l~  267 (707)
T 3fed_A          240 VEEGVGIPRIPVHPIGYNDAEILLRYLG  267 (707)
T ss_dssp             GGGCTTCCSSCEEEECHHHHHHHHHTBC
T ss_pred             hhhccCCCCCCeEecCHHHHHHHHHHhc
Confidence                 12589999999999999998764

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=98.16  E-value=2.1e-06  Score=65.86  Aligned_cols=50  Identities=22%  Similarity=0.526  Sum_probs=40.0

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCC-CCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWG-TFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~-~~CP~Cr~~i~~~  201 (214)
                      ....|+||.+-...+   ..-+ |+|.||..|+..|++.+. ..||.|+.+....
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            356899999999876   3333 999999999999998754 3699999986544

>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=98.09  E-value=3.1e-06  Score=73.75  Aligned_cols=63  Identities=17%  Similarity=0.202  Sum_probs=47.0

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCCe--------e----------eee-------------CCCCCeeeEEE
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPL--------I----------YMT-------------YPEGANVPAFY   49 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~--------~----------~m~-------------~~~~~~Ip~v~   49 (214)
                      |+||+|+|.+|+++|+++||+||||||+..+.+.        .          +.+             ......||++.
T Consensus       137 v~~g~~~~~~K~~~A~~~GA~gvii~~~~~~~~~~~~~~~~~G~~~~~~Gdp~tpg~ps~~~~~~~~~~~~~~p~IP~~~  216 (640)
T 3kas_A          137 VRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQT  216 (640)
T ss_dssp             EESCSSCHHHHHHHHHTTTCSEEEEECCTTTCCCSCTTCCCCEECCSSSSCSCCCSSCC---CCCCCCSSCCCCSSCEEE
T ss_pred             EecCCCCHHHHHHHHHHCCCeEEEEEeccccccccccccccccccccCCCCCCCCCcccccccccccccccCCCCCCEEe
Confidence            4689999999999999999999999997532111        0          000             00124799999


Q ss_pred             EchhhHHHHHHHhh
Q 028085           50 VTLETGAYLKEHAR   63 (214)
Q Consensus        50 v~~~~g~~L~~~~~   63 (214)
                      |+.++++.|.+.+.
T Consensus       217 Is~~~a~~Ll~~l~  230 (640)
T 3kas_A          217 ISRAAAEKLFGNME  230 (640)
T ss_dssp             CCHHHHHHHHTTEE
T ss_pred             cCHHHHHHHHHHcc
Confidence            99999999987653

>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=97.95  E-value=3.2e-05  Score=64.79  Aligned_cols=63  Identities=10%  Similarity=0.001  Sum_probs=45.9

Q ss_pred             cccccc---------HHHH----HHHHHHcCCcEEEEEeCCCCCC----eeeee-CCCCCeeeEEEEchhhHHHHHHHhh
Q 028085            2 IRGQCN---------FSYK----IQNAQAAGYDAAIVYALRKKSP----LIYMT-YPEGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus         2 ~rg~C~---------f~~K----~~~a~~~ga~aviv~~~~~~~~----~~~m~-~~~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                      .||.|.         |..|    +.+|+++||+|+|+||+.+...    ...|. ......||++.|+.++|+.|...+.
T Consensus       135 ~~~~~~~~~~~~y~~~~~kr~~~a~~A~~aGA~avIi~~~~~~~~~~~~tg~~~~~~~~~~IP~~~Is~~da~~L~~~l~  214 (444)
T 3iib_A          135 DAKTERHRDGKGYGQTASGRSRGAVAAAEKGAVGIIIRSIGTDHDRMAHTGMMRYEEGVTAIPAAAISNPDADLINAMLK  214 (444)
T ss_dssp             CCCCCCCTTCHHHHHHHHHHHHHHHHHHHTTCSEEEEECSCSCCSSCCCCCBCCCCTTSCCCCEEEECHHHHHHHHHHHT
T ss_pred             eCCCCCCcccccccchhhhhhhHHHHHHHCCCeEEEEEccCCcccccccCCccccCCCCCCCCeEEecHHHHHHHHHHHh
Confidence            577774         6666    4679999999999999754321    11222 2234689999999999999998775


Q ss_pred             c
Q 028085           64 G   64 (214)
Q Consensus        64 ~   64 (214)
                      .
T Consensus       215 ~  215 (444)
T 3iib_A          215 R  215 (444)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=97.63  E-value=7.9e-05  Score=62.33  Aligned_cols=62  Identities=23%  Similarity=0.184  Sum_probs=48.4

Q ss_pred             ccccc-----cHHHHHHHHHHcCCcEEEEEeCCCCCCe---eeeeCCCCCeeeEEEEchhhHHHHHHHhh
Q 028085            2 IRGQC-----NFSYKIQNAQAAGYDAAIVYALRKKSPL---IYMTYPEGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus         2 ~rg~C-----~f~~K~~~a~~~ga~aviv~~~~~~~~~---~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                      +||.|     +|.+|+++|+++||.++|+||+.+....   +.+.......+|+++|+.++|+.|+.++.
T Consensus       280 ~rg~~~~~~~~~~~~~~~~~~aGa~gvii~~~~~~~g~~~~~~~~~~~~~~~p~~~v~~~~g~~l~~~~~  349 (441)
T 1y9z_A          280 ERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSVDRATGLALKAKLG  349 (441)
T ss_dssp             ECCSCSSSSCTHHHHHHHHHHTTCSEEEEECCTTSCSCCCCEEECTTCCCCSCEEEECHHHHHHHHTTTT
T ss_pred             eccccCcccccHHHHHHHHHhcCCeEEEEEeCCCccccccccccccccCccccEEEEeHHHHHHHHHHhc
Confidence            46655     8999999999999999999987643221   22333445689999999999999998775

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

Probab=97.56  E-value=0.00013  Score=66.38  Aligned_cols=57  Identities=30%  Similarity=0.490  Sum_probs=47.7

Q ss_pred             ccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHH
Q 028085            2 IRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKE   60 (214)
Q Consensus         2 ~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~   60 (214)
                      +||.|+|.+|+.+|+++||.|+|+||+..+...+.+  .....+|+++|+.++|..|+.
T Consensus       287 ~rg~~~~~~k~~~~~~~Ga~gvi~~n~~~~~~~~~~--~~~~~iP~~~i~~~~g~~l~~  343 (926)
T 1xf1_A          287 ERGDIDFKDKIAKAKKAGAVGVLIYDNQDKGFPIEL--PNVDQMPAAFISRKDGLLLKD  343 (926)
T ss_dssp             ECCSSCHHHHHHHHHHTTCSEEEEECSSTTCCCEEC--CCSTTCCEEEECHHHHHHHHH
T ss_pred             ECCCCCHHHHHHHHHhCCCcEEEEEecCCCCccccc--CccccccEEEEeHHHHHHHHh
Confidence            689999999999999999999999997655333332  345689999999999998875

>3i6s_A Subtilisin-like protease; PA-domain, FN3-domain, hydrolase; HET: NAG FUC; 2.50A {Solanum lycopersicum} PDB: 3i74_A*

Probab=97.45  E-value=0.00015  Score=63.53  Aligned_cols=57  Identities=9%  Similarity=-0.119  Sum_probs=48.4

Q ss_pred             ccccccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhhc
Q 028085            2 IRGQCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHARG   64 (214)
Q Consensus         2 ~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~~   64 (214)
                      +||.|+|.+|..+++++||.|+|+||+..  .+.    .....+|+++|+.++|+.|++++..
T Consensus       290 ~~g~~~~~~k~~~~~~~Ga~g~i~~n~~~--~~~----~~~~~~P~~~v~~~~g~~i~~yi~s  346 (649)
T 3i6s_A          290 DDNGDFSDQMRIITRARLKAAIFISEDPG--VFR----SATFPNPGVVVNKKEGKQVINYVKN  346 (649)
T ss_dssp             CCCSCHHHHHHHHHHHTCSEEEEECCCGG--GGG----CCCCCSCEEEECHHHHHHHHHHHHT
T ss_pred             eCCCccHHHHHHHHHhcCceEEEEecCcc--ccc----cccCcCCEEEEcHHHHHHHHHHHhc
Confidence            68999999999999999999999998662  221    2446899999999999999998864

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.33  E-value=0.0022  Score=42.05  Aligned_cols=34  Identities=18%  Similarity=0.523  Sum_probs=26.4

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHH
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSW  183 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~W  183 (214)
                      +..|.||++++.......-+.|+|.|+..|+..+
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            4689999987543334445899999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=96.19  E-value=0.0029  Score=38.13  Aligned_cols=47  Identities=21%  Similarity=0.434  Sum_probs=32.2

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCC---CCcccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG---TFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~---~~CP~Cr~~i  198 (214)
                      .+..|.||.+.   ++-+.--.|...||..|+++.+..--   -.||.|+...
T Consensus        11 ~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            44679999753   33332224899999999998875432   2799997643

>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=94.45  E-value=0.025  Score=35.24  Aligned_cols=31  Identities=23%  Similarity=0.838  Sum_probs=22.6

Q ss_pred             CCcccccccccccCCCceEEec---CCCccChhhHHHH
Q 028085          149 RETLCSICLEDYREGENLRVLP---CRHEFHSSCVDSW  183 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~---C~H~FH~~Ci~~W  183 (214)
                      .|..|.||-. +..++   .+|   |+-+||..|+.+-
T Consensus        14 ~D~~C~VC~~-~t~~~---l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           14 NDEMCDVCEV-WTAES---LFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTTCC-CCSSC---CSSCSSSSSCCCHHHHHHH
T ss_pred             CCcccCcccc-ccccc---eeccccccccccHhhcccc
Confidence            5678999963 33332   455   7899999999985

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.94  E-value=0.04  Score=34.99  Aligned_cols=47  Identities=23%  Similarity=0.470  Sum_probs=30.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i  198 (214)
                      .+..|.+|.+.   ++-+.--.|.-.||..|+++=+..-   ...||.|+..-
T Consensus        24 n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           24 SATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             SSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            55689999964   3322222378889999997755331   12799997653

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=92.90  E-value=0.033  Score=32.82  Aligned_cols=45  Identities=24%  Similarity=0.648  Sum_probs=29.9

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRH  196 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~  196 (214)
                      .+..|.+|.+.   ++-+.--.|...||..|+.+=+...   .-.||.|+.
T Consensus        10 ~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           10 HQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            45689999873   3322222488899999998754321   227999965

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.36  E-value=0.013  Score=33.88  Aligned_cols=45  Identities=31%  Similarity=0.704  Sum_probs=29.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRH  196 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~  196 (214)
                      .+..|.+|.+.   ++-+.--.|...||..|+.+=+...   .-.||.|+.
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            55689999874   3333333488899999998644321   226999964

>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=92.29  E-value=0.019  Score=33.88  Aligned_cols=47  Identities=26%  Similarity=0.613  Sum_probs=30.3

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i  198 (214)
                      .+..|.+|-+.   ++-+.--.|...||..|+.+-+...   .-.||.|+...
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            45679999853   3322222378899999998644321   22799997653

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=92.04  E-value=0.015  Score=34.17  Aligned_cols=49  Identities=29%  Similarity=0.678  Sum_probs=32.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i~~  200 (214)
                      .+..|.+|...   ++-+.--.|...||..|+.+=+...   .-.||.|+.....
T Consensus         4 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~   55 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLK   55 (60)
T ss_dssp             CCSSCTTTCCC---SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHH
T ss_pred             CCCCCcCCCCC---CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhc
Confidence            45679999874   3333333488999999998644321   2279999776543

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=91.89  E-value=0.043  Score=30.96  Aligned_cols=45  Identities=22%  Similarity=0.538  Sum_probs=28.3

Q ss_pred             ccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccc
Q 028085          152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRH  196 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~  196 (214)
                      .|.+|...-..++-+.--.|...||..|+++=+...   .-.||.|+.
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            488888764433322223488899999997533221   226999965

>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=91.77  E-value=0.033  Score=33.30  Aligned_cols=50  Identities=22%  Similarity=0.575  Sum_probs=33.0

Q ss_pred             CCcccccccccccC-CCceEEe-cCCCccChhhHHHHHHh------CCCCcccccccc
Q 028085          149 RETLCSICLEDYRE-GENLRVL-PCRHEFHSSCVDSWLIR------WGTFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~-~~~~~~l-~C~H~FH~~Ci~~Wl~~------~~~~CP~Cr~~i  198 (214)
                      .+..|.+|...... ++.+..- .|.-.||..|+.+=+..      ..-.||.|+...
T Consensus         5 ~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            55789999987533 2233333 38899999999864321      233799997643

>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=91.19  E-value=0.059  Score=31.95  Aligned_cols=49  Identities=29%  Similarity=0.505  Sum_probs=32.7

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHh----CCCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIR----WGTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~----~~~~CP~Cr~~  197 (214)
                      ++..|++|...+.+++..+.- .|..=||..|+.--...    ....||.|+..
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            456799999988655444333 37888999998643221    23379999764

>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=91.04  E-value=0.049  Score=36.23  Aligned_cols=47  Identities=21%  Similarity=0.513  Sum_probs=31.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHh---CCCCccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIR---WGTFCPVCR  195 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~---~~~~CP~Cr  195 (214)
                      .++.|.+|.+.-...+-+.--.|+..||..|+...+..   ....||.|+
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            56789999887433322444459999999999887642   122577664

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=91.01  E-value=0.035  Score=40.49  Aligned_cols=47  Identities=32%  Similarity=0.632  Sum_probs=31.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i  198 (214)
                      .++.|.+|.+.   |+-+..=.|.-.||..|+.+-+...   ...||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            45679999854   4322222388999999998766432   22799998743

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=90.74  E-value=0.044  Score=33.70  Aligned_cols=51  Identities=24%  Similarity=0.488  Sum_probs=33.3

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhC---CCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRW---GTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i~~  200 (214)
                      ....|.+|-.... ++.+..- .|.--||..|+..-....   ...||.|+..+..
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            3456999987754 3333333 388889999997644321   2379999877643

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=90.57  E-value=0.047  Score=40.64  Aligned_cols=45  Identities=29%  Similarity=0.718  Sum_probs=30.5

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhC---CCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRW---GTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~  197 (214)
                      .++.|.+|.+.   + .+..- .|...||..|+.+-+...   ...||.|+..
T Consensus         6 ~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~   54 (207)
T 3u5n_A            6 NEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI   54 (207)
T ss_dssp             SCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCc
Confidence            45679999743   3 33222 288899999998766432   2279999764

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=90.12  E-value=0.093  Score=33.37  Aligned_cols=50  Identities=20%  Similarity=0.468  Sum_probs=31.7

Q ss_pred             CCccccccccccc-CCCceEEec-CCCccChhhHHHHHHhC-CCCcccccccc
Q 028085          149 RETLCSICLEDYR-EGENLRVLP-CRHEFHSSCVDSWLIRW-GTFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~-~~~~~~~l~-C~H~FH~~Ci~~Wl~~~-~~~CP~Cr~~i  198 (214)
                      .+..|.||.+.-. +++.+..-. |.-.||..|+..-+.-. .-.||.|....
T Consensus        24 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~   76 (88)
T 2l43_A           24 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSR   76 (88)
T ss_dssp             CCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHT
T ss_pred             CCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCcc
Confidence            5578999997642 222333333 77889999997633221 22799997654

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=90.11  E-value=0.32  Score=32.32  Aligned_cols=46  Identities=26%  Similarity=0.493  Sum_probs=29.0

Q ss_pred             Cccccccccccc-----CCCceEE-ecCCCccChhhHHH------HHHhCCCCccccc
Q 028085          150 ETLCSICLEDYR-----EGENLRV-LPCRHEFHSSCVDS------WLIRWGTFCPVCR  195 (214)
Q Consensus       150 ~~~C~ICl~~~~-----~~~~~~~-l~C~H~FH~~Ci~~------Wl~~~~~~CP~Cr  195 (214)
                      ...|.+|+..-.     .++++.. -.|+..||..|+..      -+....-.||.|+
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            457999997631     2223333 34999999999953      2333344688885

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=89.85  E-value=0.059  Score=32.25  Aligned_cols=46  Identities=26%  Similarity=0.561  Sum_probs=30.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~  197 (214)
                      .+..|.+|.+.   ++-+.-=.|...||..|+.+=+...   .-.||.|...
T Consensus         7 ~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            7 NEDECAVCRDG---GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCCSBSSSSCC---SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCccCCCC---CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            55689999864   3322222488899999998644321   2279999764

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=89.44  E-value=0.088  Score=32.02  Aligned_cols=49  Identities=20%  Similarity=0.493  Sum_probs=31.7

Q ss_pred             CCcccccccccc-cCCCceEEe-cCCCccChhhHHHHHHhC-CCCccccccc
Q 028085          149 RETLCSICLEDY-REGENLRVL-PCRHEFHSSCVDSWLIRW-GTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~-~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~-~~~CP~Cr~~  197 (214)
                      .+..|.||.+.- .+++.+..- .|.-.||..|+..-..-. .-.||.|+..
T Consensus        15 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           15 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             SSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            556899998764 233343333 388899999997532211 2279999764

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=88.16  E-value=0.081  Score=33.64  Aligned_cols=50  Identities=18%  Similarity=0.519  Sum_probs=33.5

Q ss_pred             CcccccccccccC-CCceEEe-cCCCccChhhHHHHHHh-------CCCCccccccccc
Q 028085          150 ETLCSICLEDYRE-GENLRVL-PCRHEFHSSCVDSWLIR-------WGTFCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~~-~~~~~~l-~C~H~FH~~Ci~~Wl~~-------~~~~CP~Cr~~i~  199 (214)
                      +..|.+|...-.. ++.+..- .|...||..|+.+=+..       ....||.|+....
T Consensus        16 ~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~   74 (88)
T 1wev_A           16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             CCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhh
Confidence            4579999976432 2233333 38999999999876542       2237999977554

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=87.71  E-value=0.12  Score=33.58  Aligned_cols=46  Identities=22%  Similarity=0.312  Sum_probs=28.7

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhC--CCCcccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW--GTFCPVCRH  196 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~--~~~CP~Cr~  196 (214)
                      ...| ||-.....+.-+.-=.|.--||..|+..=+..-  ...||.|+.
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            3567 898776555322222388899999986522111  127999963

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=87.62  E-value=0.18  Score=29.33  Aligned_cols=43  Identities=21%  Similarity=0.531  Sum_probs=29.0

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVC  194 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~C  194 (214)
                      ..|--|...+.+....+--.|++.|+-+| |..+-..-..||-|
T Consensus        16 ~~C~~C~~~~~~~~~y~C~~C~~~FC~dC-D~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQHVYVCAVCQNVFCVDC-DVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTSEEECCTTTTCCBCHHH-HHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCCccEECCccCcCcccch-hHHHHhhccCCcCC
Confidence            46999999986442222334999999999 45543333369988

>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=86.89  E-value=0.2  Score=36.47  Aligned_cols=47  Identities=21%  Similarity=0.487  Sum_probs=32.3

Q ss_pred             cccccccccccCCCc---eEEec-CCCccChhhHHHH------HH----hCCCCccccccc
Q 028085          151 TLCSICLEDYREGEN---LRVLP-CRHEFHSSCVDSW------LI----RWGTFCPVCRHE  197 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~---~~~l~-C~H~FH~~Ci~~W------l~----~~~~~CP~Cr~~  197 (214)
                      ..|+||...|.+++.   ...-. |..=||..|..-=      +.    .....||.|+..
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~   63 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTER   63 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCC
Confidence            469999999988862   44443 8889999998431      11    013469999774

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=86.69  E-value=0.13  Score=34.17  Aligned_cols=45  Identities=31%  Similarity=0.702  Sum_probs=29.2

Q ss_pred             ccccccccccCCCceEEe-cCCCccChhhHHHHHHhC---CCCcccccc
Q 028085          152 LCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRW---GTFCPVCRH  196 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~  196 (214)
                      .|.+|.+.-.+++++..- .|...||..|+++-|..-   .-.||.|+.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            588888653333344333 389999999997655332   127999974

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=86.55  E-value=0.22  Score=33.20  Aligned_cols=45  Identities=22%  Similarity=0.519  Sum_probs=28.2

Q ss_pred             cccccccccccC------CCc-eEEecCCCccChhhHHHHH------HhCCCCccccc
Q 028085          151 TLCSICLEDYRE------GEN-LRVLPCRHEFHSSCVDSWL------IRWGTFCPVCR  195 (214)
Q Consensus       151 ~~C~ICl~~~~~------~~~-~~~l~C~H~FH~~Ci~~Wl------~~~~~~CP~Cr  195 (214)
                      +.|.+|+..-..      +++ +.-..|+..||..|+....      ....-.||.|+
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   59 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECK   59 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCCHHHHHHHHHTTCCCGGGC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCChhhhhhccCCCccCccccC
Confidence            469999976421      123 3333489999999998652      23333677773

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=85.62  E-value=0.11  Score=38.15  Aligned_cols=46  Identities=24%  Similarity=0.481  Sum_probs=30.1

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHEI  198 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i  198 (214)
                      ++.|.+|.+.   ++-+..-.|...||..|+.+=+...   ...||.|+..-
T Consensus         2 ~~~C~~C~~~---g~ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---SSCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---CceeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            3579999854   4333333478899999997644321   22799998653

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.83  E-value=0.082  Score=33.91  Aligned_cols=48  Identities=21%  Similarity=0.436  Sum_probs=31.5

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHHhC---CCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRW---GTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~  197 (214)
                      .+..|.||...-..+ .+..- .|...||..|+.+=+..-   .-.||.|+..
T Consensus        15 ~~~~C~vC~~~~~~~-~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           15 DSYICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCSSSCCSGGGG-GCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCccCCCcCCCC-CEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            445799999775333 33333 389999999997533221   2269999764

>3vta_A Cucumisin; subtilisin-like fold, serine protease, hydrolase; HET: DFP NAG FUC BMA MAN; 2.75A {Cucumis melo}

Probab=84.56  E-value=1.7  Score=37.68  Aligned_cols=52  Identities=6%  Similarity=-0.023  Sum_probs=42.1

Q ss_pred             cccHHHHHHHHHHcCCcEEEEEeCCCCCCeeeeeCCCCCeeeEEEEchhhHHHHHHHhh
Q 028085            5 QCNFSYKIQNAQAAGYDAAIVYALRKKSPLIYMTYPEGANVPAFYVTLETGAYLKEHAR   63 (214)
Q Consensus         5 ~C~f~~K~~~a~~~ga~aviv~~~~~~~~~~~m~~~~~~~Ip~v~v~~~~g~~L~~~~~   63 (214)
                      .+.+..|..+++.+||.++|++++..+.       .....+|+++++..+|..+..+..
T Consensus       288 ~~~~~~~~~~~~~~Ga~gvi~~~~~~~~-------~~~~~lP~~~v~~~~g~~i~~~~~  339 (621)
T 3vta_A          288 EASFGPHEFFKSLDGAAGVLMTSNTRDY-------ADSYPLPSSVLDPNDLLATLRYIY  339 (621)
T ss_dssp             SSCCCHHHHHHHHTTCSEEEEECSCCSS-------CCCCSSSEEEECHHHHHHHHHHHH
T ss_pred             ecCCChhHHhhhhcceeEEEEEecCCCc-------ccccccceEEECHHHHHHHHHHHh
Confidence            4678889999999999999999865431       133578999999999999988664

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=84.45  E-value=0.2  Score=32.90  Aligned_cols=50  Identities=16%  Similarity=0.351  Sum_probs=33.6

Q ss_pred             CcccccccccccCCCceEEe--cCCCccChhhHHHHHH---------hCCCCccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVL--PCRHEFHSSCVDSWLI---------RWGTFCPVCRHEIR  199 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l--~C~H~FH~~Ci~~Wl~---------~~~~~CP~Cr~~i~  199 (214)
                      ...|.+|...+.+++....-  .|.-=||..|+.-=-.         .....||.|+..-.
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~   63 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKE   63 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCC
Confidence            35799999998776555544  3777799999852110         02237999987543

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=84.28  E-value=0.74  Score=31.93  Aligned_cols=45  Identities=22%  Similarity=0.485  Sum_probs=30.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHH----------hCCCCcccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLI----------RWGTFCPVCRH  196 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~----------~~~~~CP~Cr~  196 (214)
                      .++.|.+|-+.   |+-+--=.|-.+||..|+++=+.          .....||+|+.
T Consensus        62 ~~d~C~vC~~G---G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           62 MDEQCRWCAEG---GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             CBCSCSSSCCC---SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCeecccCCC---CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            56789999874   32222224888999999997652          11237999974

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=84.06  E-value=0.62  Score=42.30  Aligned_cols=50  Identities=16%  Similarity=0.207  Sum_probs=41.9

Q ss_pred             CCcccccccccccCCCceEEecCC-CccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCR-HEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~-H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++..|+|-++-+.   .++.+|-| +.|-+..|.+|+..+. +||.=|.++....
T Consensus       890 ~~F~cPIs~~lM~---DPVilpsG~~TydR~~I~~wl~~~~-tdP~Tr~~L~~~~  940 (968)
T 3m62_A          890 DEFLDPLMYTIMK---DPVILPASKMNIDRSTIKAHLLSDS-TDPFNRMPLKLED  940 (968)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCC-BCTTTCCBCCGGG
T ss_pred             HHhCCcchhhHHh---CCeEcCCCCEEECHHHHHHHHhcCC-CCCCCCCCCCccc
Confidence            5578999999999   45899997 5899999999998755 5999999887553

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=83.75  E-value=1.4  Score=29.96  Aligned_cols=45  Identities=29%  Similarity=0.590  Sum_probs=30.0

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHH------Hh----CCCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWL------IR----WGTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl------~~----~~~~CP~Cr~~  197 (214)
                      .++.|.+|-+-   + ++..- .|-.+||.+|+.+-+      +.    ..-.|++|+..
T Consensus        56 ~~~~C~vC~dG---G-~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           56 MDEQCRWCAEG---G-NLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             CBSSCTTTCCC---S-EEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCcCeecCCC---C-eeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            55679999964   3 33222 388999999999742      21    12379999654

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=82.12  E-value=1.1  Score=29.37  Aligned_cols=47  Identities=26%  Similarity=0.491  Sum_probs=29.8

Q ss_pred             CCcccccccccccCCCceEEec---CCCccChhhHHHHHHhC---CCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP---CRHEFHSSCVDSWLIRW---GTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~---C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i~~~  201 (214)
                      .++.|.+|.+   .+ ++..-.   |-..||..|+.  |...   .-.||.|+..+..+
T Consensus        14 ~~~~C~~C~~---~G-~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C~k   66 (107)
T 4gne_A           14 HEDYCFQCGD---GG-ELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDECSS   66 (107)
T ss_dssp             SCSSCTTTCC---CS-EEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTTCS
T ss_pred             CCCCCCcCCC---CC-cEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcCCC
Confidence            5567999983   23 443433   77899999997  4321   12699887655433

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.67  E-value=0.14  Score=31.61  Aligned_cols=44  Identities=20%  Similarity=0.511  Sum_probs=28.2

Q ss_pred             ccccccccccCCCceEEe-cCCCccChhhHHHHHHh---C-CCCcccccc
Q 028085          152 LCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIR---W-GTFCPVCRH  196 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~---~-~~~CP~Cr~  196 (214)
                      .|.+|...-..+ .+..- .|...||..|+++=|..   . .-.||.|+.
T Consensus        28 ~C~vC~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           28 SCRVCGGKHEPN-MQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SCSSSCCCCCST-TEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCcCcCCcCCCC-CEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            688998653333 33333 38899999999854432   1 226999964

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=81.60  E-value=3.8  Score=25.71  Aligned_cols=54  Identities=20%  Similarity=0.383  Sum_probs=37.1

Q ss_pred             CCcccccccccccCCC--ceEEe--cCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGE--NLRVL--PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~--~~~~l--~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ....|-||-++.-...  ++...  .|+--.|+.|++-=.+..+..||.|+....+.+
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr~k   72 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLR   72 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCT
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccccc
Confidence            3458999999954321  33222  377778999998766655557999999886533

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=81.41  E-value=0.41  Score=34.31  Aligned_cols=48  Identities=23%  Similarity=0.454  Sum_probs=31.1

Q ss_pred             CCcccccccccccCCCceEEe-cCCCccChhhHHHHHH----hCCCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLI----RWGTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~----~~~~~CP~Cr~~  197 (214)
                      ....| +|...+.++.....- .|..-||..|+.--..    .....||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            44679 999886544444333 3888899999953221    123379999764

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=80.27  E-value=4.4  Score=24.89  Aligned_cols=45  Identities=24%  Similarity=0.539  Sum_probs=33.9

Q ss_pred             CCcccccccccccCCCceEEec--CCCccChhhHHHHHHhCCC----Ccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP--CRHEFHSSCVDSWLIRWGT----FCPVC  194 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~--C~H~FH~~Ci~~Wl~~~~~----~CP~C  194 (214)
                      ....|.+|-+.+++.+ .++-|  =+|-||-.|-...++.+..    .||-=
T Consensus        14 a~l~CtlC~erLEdtH-FVQCPsv~~HkFCFpCsr~sIk~q~~~~EvyCPSG   64 (93)
T 2cs3_A           14 GPLCCTICHERLEDTH-FVQCPSVPSHKFCFPCSRESIKAQGATGEVYCPSG   64 (93)
T ss_dssp             CSCCCSSSCSCCSSTT-SEECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTS
T ss_pred             CeeEeecchhhhccCc-eeeCCCccCCeeeccccHHHHHhcCCCCcEECCCC
Confidence            4568999999999884 34555  3899999999999987532    46654

---

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	214
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-14
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-13
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-12
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	7e-11
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-09
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	7e-08
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	1e-07
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-07
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.004

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 63.7 bits (155), Expect = 1e-14
 Identities = 22/47 (46%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 153 CSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C++CL +  +GE  R LP C H FH+ CVD WL    T CP+CR  +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLTV 53

>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 = 60.8 bits (147), Expect = 3e-13
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTS 203
           LC IC E+ +   ++++ PC H   +SC+ SW    G  CP CR EI+ +  
Sbjct: 25  LCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP 73

>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 = 56.9 bits (137), Expect = 5e-12
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR 200
           C ICLED         LPC H F   C+  W+ +  T CP+C+  +  
Sbjct: 8   CPICLEDPSNYS--MALPCLHAFCYVCITRWIRQNPT-CPLCKVPVES 52

>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 = 55.9 bits (134), Expect = 1e-11
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 150 ETLCSICLEDYREGENLRVL--PCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           +  C  C        +L+++   C H    SCVD   +R    CP C   +R+S
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS 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 = 53.6 bits (128), Expect = 7e-11
 Identities = 10/47 (21%), Positives = 15/47 (31%), Gaps = 1/47 (2%)

Query: 153 CSICLEDYREGE-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEI 198
           C +C+E     + N     C ++    C           CP CR   
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 2e-09
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 7/47 (14%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIR 199
           C  C  + +     ++LPC H   S C+++  ++    CP+C+    
Sbjct: 9   CQQCQAEAKCP---KLLPCLHTLCSGCLEASGMQ----CPICQAPWP 48

>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 = 47.0 bits (110), Expect = 7e-08
 Identities = 18/104 (17%), Positives = 26/104 (25%), Gaps = 6/104 (5%)

Query: 117 HRPEQTRQLPRSTVNALPSFVFSSVTSVRCHGRETLCSICLEDYREGENLRVLPCRHEFH 176
             PEQ  +     +   P                       +        R+  C H FH
Sbjct: 7   GEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFH 66

Query: 177 SSCVDSWLIR----WGTFCPVCRHEIRRSTSN--EGNEQVHVSG 214
             C+ +            CP C+      T     G  +V  SG
Sbjct: 67  LLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWGKMEVFRSG 110

>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 = 45.8 bits (108), Expect = 1e-07
 Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGT--FCPVCRHEIRRS 201
           C ICLE  +E        C H F   C+   L +      CP+C+++I + 
Sbjct: 24  CPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

>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 = 2e-07
 Identities = 13/61 (21%), Positives = 18/61 (29%), Gaps = 16/61 (26%)

Query: 153 CSICLEDYREGE---------------NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHE 197
           C+IC     +                  +    C H FH  C+  WL      CP+   E
Sbjct: 24  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDNRE 82

Query: 198 I 198
            
Sbjct: 83  W 83

>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 = 45.3 bits (107), Expect = 2e-07
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           C IC        +     C+H F   C+   L   G++CP CR+    +
Sbjct: 26  CQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT 71

>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 = 4e-07
 Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 3/50 (6%)

Query: 153 CSICLEDYREGENL--RVLPCRHEFHSSCVDSWL-IRWGTFCPVCRHEIR 199
           C IC E+                  H SC+ +WL I   T C +C     
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWL---IRWGTF----CPVCR 195
           C +CL +Y   +   +  C+  F + C+  ++   I+ G      CP   
Sbjct: 8   CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>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 = 37.8 bits (87), Expect = 1e-04
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 5/49 (10%)

Query: 153 CSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           CS C    RE   + +  C H F S+CV   +   GT CPVC       
Sbjct: 25  CSRCTNILRE--PVCLGGCEHIFCSNCVSDCI---GTGCPVCYTPAWIQ 68

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.4 bits (73), Expect = 0.004
 Identities = 8/50 (16%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 152 LCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS 201
           LC+I  +  R          R  F  S ++ ++       P+    +   
Sbjct: 2   LCAISGKVPRRPVLSP--KSRTIFEKSLLEQYVKDT-GNDPITNEPLSIE 48

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	214
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.81
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.71
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.69
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.68
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.67
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.66
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.58
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.51
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.49
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.44
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.39
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.36
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.33
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.26
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.98
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.96
d1de4c2	193	Transferrin receptor ectodomain, apical domain {Hu	98.47
d3bi1a2	233	Glutamate carboxypeptidase II {Human (Homo sapiens	98.26
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	95.62
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.33
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	95.06
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	93.46
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	92.75
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	92.22
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	91.28
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	88.7
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	88.25
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	86.29
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	85.88
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	82.24
d2co8a2	36	Nedd9 interacting protein with calponin homology,	82.18
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	82.05

>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=99.81  E-value=4.6e-21  Score=112.43  Aligned_cols=50  Identities=44%  Similarity=1.062  Sum_probs=44.5

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEIR  199 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~  199 (214)
                      ++.+|+||+++|.+++.++.++ |+|.||.+|+++|++.++. ||+||+++.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~-CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST-CPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCS-CSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCc-CCCCCCEeE
Confidence            4467999999999999998886 9999999999999988665 999999874

>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=99.71  E-value=4.7e-19  Score=102.69  Aligned_cols=49  Identities=18%  Similarity=0.440  Sum_probs=41.9

Q ss_pred             ccccccccccCCCc-eEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          152 LCSICLEDYREGEN-LRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       152 ~C~ICl~~~~~~~~-~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      +|+||+++|..++. ++.++|||.||.+|+++|++.++.+||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            69999999987764 45568999999999999998766679999998754

>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=99.69  E-value=8.7e-18  Score=103.01  Aligned_cols=48  Identities=35%  Similarity=0.856  Sum_probs=41.4

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .++|+||++.+.+  .++.+||||.||.+|+.+|++.+++ ||+||+++..
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~~~~-CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPT-CPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCS-TTTTCCCCCC
T ss_pred             CCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHhCCc-CCCCCcchHh
Confidence            4579999999863  4577899999999999999998665 9999998854

>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=99.68  E-value=1.3e-17  Score=112.95  Aligned_cols=63  Identities=24%  Similarity=0.417  Sum_probs=48.3

Q ss_pred             CCcccccccccccC---------------CCceEEecCCCccChhhHHHHHHhCC----CCccccccccccccCCCCCcc
Q 028085          149 RETLCSICLEDYRE---------------GENLRVLPCRHEFHSSCVDSWLIRWG----TFCPVCRHEIRRSTSNEGNEQ  209 (214)
Q Consensus       149 ~~~~C~ICl~~~~~---------------~~~~~~l~C~H~FH~~Ci~~Wl~~~~----~~CP~Cr~~i~~~~~~~~~~~  209 (214)
                      .+..|+||++++..               .+.+..++|+|.||.+||+.|+..++    .+||+||+.+..+.++.++.+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~qP~~~  103 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWGK  103 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTSS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCCCCCc
Confidence            34579999998853               23467788999999999999998643    269999999877766655554


Q ss_pred             cc
Q 028085          210 VH  211 (214)
Q Consensus       210 ~~  211 (214)
                      ..
T Consensus       104 ~~  105 (114)
T d1v87a_         104 ME  105 (114)
T ss_dssp             CC
T ss_pred             ee
Confidence            43

>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=99.67  E-value=1.1e-17  Score=107.90  Aligned_cols=51  Identities=25%  Similarity=0.522  Sum_probs=41.9

Q ss_pred             CCcccccccccccCCC---------------ceEEecCCCccChhhHHHHHHhCCCCcccccccccc
Q 028085          149 RETLCSICLEDYREGE---------------NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~---------------~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~  200 (214)
                      .++.|+||++++.+..               .+..++|||+||.+||.+||+.+++ ||+||++..-
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~-CP~CR~~~~~   85 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDNREWEF   85 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSB-CSSSCSBCCE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCc-CCCCCCcccc
Confidence            4567999998876532               3678899999999999999998765 9999998653

>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=99.66  E-value=2.8e-17  Score=99.68  Aligned_cols=53  Identities=30%  Similarity=0.587  Sum_probs=42.0

Q ss_pred             CCcccccccccccCC-C-ceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREG-E-NLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~-~-~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ++..|+||++++..+ + .+..++|||.||.+||.+|+..++..||+||.++..+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            356899999986433 2 4566789999999999999977555699999988543

>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=99.65  E-value=5.8e-17  Score=102.09  Aligned_cols=50  Identities=38%  Similarity=0.874  Sum_probs=42.7

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ...|+||++.+.   .++.+||||.||.+||..|+..+...||+||..|....
T Consensus        23 ~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBC---CEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCC---CeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            356999999987   56899999999999999999865546999999997554

>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=99.58  E-value=4.3e-16  Score=99.03  Aligned_cols=54  Identities=24%  Similarity=0.500  Sum_probs=45.4

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccCCCC
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNEG  206 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~~  206 (214)
                      +..|+||++.+.   .++.++|||.||+.||.+|++.++..||+||.++......++
T Consensus        23 ~l~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~~P   76 (86)
T d1rmda2          23 SISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESP   76 (86)
T ss_dssp             HTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBCC
T ss_pred             CcCCccCCcchh---cceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhccCH
Confidence            357999999998   568899999999999999998766569999999876654443

>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=99.51  E-value=8e-16  Score=89.85  Aligned_cols=49  Identities=24%  Similarity=0.630  Sum_probs=40.1

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccccCCC
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTSNE  205 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~~~  205 (214)
                      ..+|+||++.+.+   .+.+||||.||..|+++|    +..||+||+++....+.+
T Consensus         6 ~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~~~~   54 (56)
T d1bora_           6 FLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGADTP   54 (56)
T ss_dssp             CSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCSSCC
T ss_pred             CCCCcccCcccCC---CEEecCCCHHhHHHHHcC----CCcCcCCCCcccCCCCCC
Confidence            3589999999984   478999999999999765    335999999998665544

>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=99.49  E-value=4e-15  Score=87.21  Aligned_cols=48  Identities=21%  Similarity=0.328  Sum_probs=41.2

Q ss_pred             ccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCccccccccccccC
Q 028085          152 LCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVCRHEIRRSTS  203 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~~  203 (214)
                      .|+||++.++   ....++ |||+||++||.+|+++++. ||+||+++...+-
T Consensus         2 ~C~Ic~~~~~---~Pv~~~~cGh~fc~~cI~~~l~~~~~-CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGN-DPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSB-CTTTCCBCCGGGC
T ss_pred             CCccCCchHH---hcCccCCCCCcccHHHHHHHHhhccC-CCccCCcCCHHhc
Confidence            5999999998   446775 9999999999999998776 9999999876543

>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=99.44  E-value=2e-14  Score=95.20  Aligned_cols=50  Identities=30%  Similarity=0.616  Sum_probs=41.6

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCC--CCcccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG--TFCPVCRHEIRRST  202 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~--~~CP~Cr~~i~~~~  202 (214)
                      ...|+||++.|.+   ++.++|||.||..||..|+...+  ..||+||.++....
T Consensus        21 ~l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          21 ILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CcCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            3579999999984   46789999999999999997754  26999999986543

>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=99.39  E-value=6.5e-14  Score=83.23  Aligned_cols=49  Identities=29%  Similarity=0.651  Sum_probs=38.0

Q ss_pred             CCcccccccccccCCCceEEecC-----CCccChhhHHHHHHhC-CCCcccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPC-----RHEFHSSCVDSWLIRW-GTFCPVCRHEIRR  200 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C-----~H~FH~~Ci~~Wl~~~-~~~CP~Cr~~i~~  200 (214)
                      +...|.||++++.+.   ...||     +|.||..||.+|+..+ +.+||+||+++..
T Consensus         5 d~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           5 DVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            556899999998754   23444     5999999999999764 3469999998753

>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=99.36  E-value=1.7e-13  Score=86.28  Aligned_cols=51  Identities=22%  Similarity=0.309  Sum_probs=43.8

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++..|+||++-|.   .++.++|||.|+..||.+|+..++..||.||.++....
T Consensus         6 ~~l~CpIc~~l~~---dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           6 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             STTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             ccccCcCcCchhh---hhcccCCcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            4578999999998   44789999999999999999876667999999886543

>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=99.33  E-value=2.7e-13  Score=84.92  Aligned_cols=50  Identities=18%  Similarity=0.387  Sum_probs=43.4

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ++..|+||++-|.   ..+.++|||.|++.||..|+..+...||.|+.++...
T Consensus         7 ~~l~CpIc~~~m~---dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           7 EYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCcCcCchhh---CceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            5678999999998   4478999999999999999987665699999988654

>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=99.26  E-value=4e-13  Score=87.77  Aligned_cols=47  Identities=32%  Similarity=0.541  Sum_probs=38.0

Q ss_pred             CcccccccccccCCCceEEecCCCccChhhHHHHHHhCCCCccccccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWGTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~  201 (214)
                      ...|+||++.|.+.  +..++|||.||.+||..|+.  +. ||.||.++...
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~CgH~fC~~Ci~~~~~--~~-CP~Cr~~~~~~   68 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGGCEHIFCSNCVSDCIG--TG-CPVCYTPAWIQ   68 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCSSSCCBCTTTGGGGTT--TB-CSSSCCBCSCS
T ss_pred             cCCCccCCchhhcC--ceeCCCCCchhHHHHHHHHh--cc-ccccCCcCchh
Confidence            45899999999843  34458999999999999983  34 99999987654

>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=98.98  E-value=6.7e-11  Score=76.48  Aligned_cols=48  Identities=19%  Similarity=0.472  Sum_probs=38.5

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC----CC---Ccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW----GT---FCPVCRH  196 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~----~~---~CP~Cr~  196 (214)
                      +..+|+||++++...+.+..++|+|.||.+|+..|++.+    ..   .||.|+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            456899999999877666667899999999999999743    11   5998653

>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=98.96  E-value=1.4e-10  Score=75.29  Aligned_cols=50  Identities=22%  Similarity=0.151  Sum_probs=42.1

Q ss_pred             CCcccccccccccCCCceEEecCC-CccChhhHHHHHHhCCCCcccccccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCR-HEFHSSCVDSWLIRWGTFCPVCRHEIRRST  202 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~-H~FH~~Ci~~Wl~~~~~~CP~Cr~~i~~~~  202 (214)
                      ++..|+||++-|.   .+++++|+ |.|++.||..|+..+.. ||.||.++....
T Consensus        21 ~~f~CPI~~~lm~---dPV~~~~~~~ty~r~~I~~~l~~~~~-~P~~~~~l~~~~   71 (98)
T d1wgma_          21 DEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQT-DPFNRSPLTMDQ   71 (98)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCB-CTTTCSBCCTTT
T ss_pred             HHhCCcCchhHHH---HHHhcccccchhhHHHHHHHHHhcCC-cccccccccchh
Confidence            4679999999999   55899965 58999999999987665 999999987543

>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=98.47  E-value=7.3e-08  Score=69.14  Aligned_cols=64  Identities=19%  Similarity=0.249  Sum_probs=47.6

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCCCCC----------eeeee--C-------------------CCCCeeeEEE
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRKKSP----------LIYMT--Y-------------------PEGANVPAFY   49 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~~~~----------~~~m~--~-------------------~~~~~Ip~v~   49 (214)
                      +++|+++|.+|+++|+++||.|+|||++..+.+          ...+.  +                   ..--+||++-
T Consensus        68 ~r~G~~~~~~Kv~~A~~~GA~gviiysDp~d~~~~~~~~~~~g~~~~~~GDPlTPg~ps~~~~~~~~~~~~~lP~IP~~P  147 (193)
T d1de4c2          68 VRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQT  147 (193)
T ss_dssp             EESCSSCHHHHHHHHHHTTCCCEEEECCTTTSCCSCTTCCCCEECCSSSSCTTSTTSCCCGGGTCCSCCCTTSCSSCEEE
T ss_pred             EeCCCCCHHHHHHHHHHcCceEEEEecCccccCCcCcccccccccccCCCCCCCCCcccccccccCccccCCCCcCCeee
Confidence            478999999999999999999999998642210          00000  0                   0113699999


Q ss_pred             EchhhHHHHHHHhhc
Q 028085           50 VTLETGAYLKEHARG   64 (214)
Q Consensus        50 v~~~~g~~L~~~~~~   64 (214)
                      |++++++.|++.+.+
T Consensus       148 IS~~dA~~lL~~L~G  162 (193)
T d1de4c2         148 ISRAAAEKLFGNMEG  162 (193)
T ss_dssp             CCHHHHHHHHTTBCS
T ss_pred             CCHHHHHHHHHHcCC
Confidence            999999999998864

>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=98.26  E-value=4.6e-07  Score=66.92  Aligned_cols=65  Identities=23%  Similarity=0.210  Sum_probs=47.8

Q ss_pred             CccccccHHHHHHHHHHcCCcEEEEEeCCC--------------------------------CCCeeeee----------
Q 028085            1 MIRGQCNFSYKIQNAQAAGYDAAIVYALRK--------------------------------KSPLIYMT----------   38 (214)
Q Consensus         1 v~rg~C~f~~K~~~a~~~ga~aviv~~~~~--------------------------------~~~~~~m~----------   38 (214)
                      +++|++++.+|+++|+++||+|||||++..                                ++++.+..          
T Consensus        86 ~ryG~~~~~~Kv~~A~~~GA~GviiysDP~d~~~~g~~~yP~~~~~p~~~vqrgsv~~~~~~GDplTPg~ps~~~~~r~~  165 (233)
T d3bi1a2          86 ARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRG  165 (233)
T ss_dssp             EECCSSCHHHHHHHHHHTTCSEEEEECCHHHHCCTTCCBTTSSSBCCTTCCCCEECCCCTTCCSTTCTTSCCCTTCCCCC
T ss_pred             EeCCCCchhHHHHHHHHcCceEEEEecChHHccCcccccccCCccCCCCceeEeeeeecCCCCCCCCCCCCCCCCCcccC
Confidence            367999999999999999999999998620                                00111000          


Q ss_pred             --CC-CCCeeeEEEEchhhHHHHHHHhhcC
Q 028085           39 --YP-EGANVPAFYVTLETGAYLKEHARGE   65 (214)
Q Consensus        39 --~~-~~~~Ip~v~v~~~~g~~L~~~~~~~   65 (214)
                        .. .--+||++-|+.++++.|++.+.+.
T Consensus       166 ~~~~~~lP~IP~~PIS~~dA~~lL~~L~G~  195 (233)
T d3bi1a2         166 IAEAVGLPSIPVHPIGYYDAQKLLEKMGGS  195 (233)
T ss_dssp             GGGCSSCCSSCEEEECHHHHHHHHTTBCBB
T ss_pred             hhHhcCCCCCceeccCHHHHHHHHHHcCCC
Confidence              00 1137999999999999999988644

>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=95.62  E-value=0.0016  Score=38.31  Aligned_cols=49  Identities=22%  Similarity=0.431  Sum_probs=30.8

Q ss_pred             cccccccccccCCCceEEecCCCccChhhHHHHHHhCC---CCcccccccccccc
Q 028085          151 TLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRWG---TFCPVCRHEIRRST  202 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~~---~~CP~Cr~~i~~~~  202 (214)
                      ..|.+|-+   .++-+.-=.|...||..|+.+.+....   -.||.|+..-....
T Consensus         8 ~~C~~C~~---~~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~~   59 (70)
T d1fp0a1           8 TICRVCQK---PGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKE   59 (70)
T ss_dssp             SCCSSSCS---SSCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCC
T ss_pred             CCCCCCCC---cCEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCccCc
Confidence            45666653   343322224899999999998764432   27999976544333

>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=95.33  E-value=0.0018  Score=35.45  Aligned_cols=44  Identities=25%  Similarity=0.604  Sum_probs=29.7

Q ss_pred             ccccccccccCCCceEEe-cCCCccChhhHHHHHHhCC---CCcccccc
Q 028085          152 LCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWG---TFCPVCRH  196 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~---~~CP~Cr~  196 (214)
                      .|.||-..-..+ .+..- .|...||..|+++-+....   -.||.||.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            488887664433 33333 3899999999988664321   27999975

>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=95.06  E-value=0.0021  Score=37.03  Aligned_cols=49  Identities=27%  Similarity=0.488  Sum_probs=33.8

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHH---h-CCCCccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLI---R-WGTFCPVCRHE  197 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~---~-~~~~CP~Cr~~  197 (214)
                      .+..|.+|...+.+++.++.-. |+.-||..|+..=..   . ....||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            4568999999887776544443 899999999963111   1 12379999753

>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=93.46  E-value=0.016  Score=34.30  Aligned_cols=31  Identities=26%  Similarity=0.896  Sum_probs=24.3

Q ss_pred             CCcccccccccccCCCceEEec---CCCccChhhHHHH
Q 028085          149 RETLCSICLEDYREGENLRVLP---CRHEFHSSCVDSW  183 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~---C~H~FH~~Ci~~W  183 (214)
                      .|..|.|| +-+...+   .+|   |+-+||..|+.+-
T Consensus        14 ~D~mC~vC-~v~t~~~---l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          14 NDEMCDVC-EVWTAES---LFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTT-CCCCSSC---CSSCSSSSSCCCHHHHHHH
T ss_pred             cCcccccc-Ccccccc---eecceeecchhhHHHHHHh
Confidence            56789999 6776664   446   6899999999885

>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=92.75  E-value=0.0072  Score=34.28  Aligned_cols=47  Identities=26%  Similarity=0.606  Sum_probs=30.3

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhHHHHHHhC---CCCcccccccc
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCVDSWLIRW---GTFCPVCRHEI  198 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci~~Wl~~~---~~~CP~Cr~~i  198 (214)
                      .++.|.+|.+   .++-+.-=.|.-.||..|+...+...   .-.||.|+..-
T Consensus         8 ~~~~C~~C~~---~g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKD---GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCC---CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCC---CCeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            3457999975   33322222488899999997655432   22799997653

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.22  E-value=0.022  Score=31.54  Aligned_cols=44  Identities=25%  Similarity=0.615  Sum_probs=30.6

Q ss_pred             CCcccccccccccCCCceEEec-CCCccChhhHHHHHHhCCCCcccc
Q 028085          149 RETLCSICLEDYREGENLRVLP-CRHEFHSSCVDSWLIRWGTFCPVC  194 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~~Wl~~~~~~CP~C  194 (214)
                      ....|--|...+.+. .+..-+ |++.|+-+| |-.+-..-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dC-D~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDC-DVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHH-HHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCcccccc-chhhhhhhcCCCCC
Confidence            346799999988755 334444 999999999 45443333369988

>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=91.28  E-value=0.053  Score=32.86  Aligned_cols=52  Identities=17%  Similarity=0.440  Sum_probs=32.0

Q ss_pred             CcccccccccccCC-CceEEe-cCCCccChhhHHHHH-----HhC--CCCccccccccccc
Q 028085          150 ETLCSICLEDYREG-ENLRVL-PCRHEFHSSCVDSWL-----IRW--GTFCPVCRHEIRRS  201 (214)
Q Consensus       150 ~~~C~ICl~~~~~~-~~~~~l-~C~H~FH~~Ci~~Wl-----~~~--~~~CP~Cr~~i~~~  201 (214)
                      ...|.||....... ..+..- .|+..||..|+.+.+     ...  ...||.|.......
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~~~   76 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRM   76 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCCS
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHhhh
Confidence            35699998654332 233333 389999999987432     111  23799997654433

>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=88.70  E-value=0.59  Score=27.32  Aligned_cols=47  Identities=26%  Similarity=0.486  Sum_probs=30.1

Q ss_pred             cccccccccccCCCceEEec-CCCccChhhHH--HHHHhC--CCCcccccccc
Q 028085          151 TLCSICLEDYREGENLRVLP-CRHEFHSSCVD--SWLIRW--GTFCPVCRHEI  198 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l~-C~H~FH~~Ci~--~Wl~~~--~~~CP~Cr~~i  198 (214)
                      .-| ||-..+..++..+.-. |.--||..|+.  ..-...  ...||.|+...
T Consensus        13 v~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          13 VYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             eEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            345 8988776555444443 88889999985  222111  23799998643

>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=88.25  E-value=0.062  Score=31.78  Aligned_cols=46  Identities=20%  Similarity=0.407  Sum_probs=29.6

Q ss_pred             CcccccccccccCCCceEEec---CCCccChhhHHH----HHHh----CCCCccccccc
Q 028085          150 ETLCSICLEDYREGENLRVLP---CRHEFHSSCVDS----WLIR----WGTFCPVCRHE  197 (214)
Q Consensus       150 ~~~C~ICl~~~~~~~~~~~l~---C~H~FH~~Ci~~----Wl~~----~~~~CP~Cr~~  197 (214)
                      ...| ||-.....+ ......   |..=||..|+.-    .-..    ....||.|+..
T Consensus        16 ~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T d1wewa_          16 KVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             ccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCc
Confidence            3568 899877655 444564   888899999831    1000    12379999764

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.29  E-value=0.038  Score=29.91  Aligned_cols=44  Identities=16%  Similarity=0.452  Sum_probs=27.9

Q ss_pred             ccccccccccCCCceEEe-cCCCccChhhHHHHHHhCCCCcccccc
Q 028085          152 LCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIRWGTFCPVCRH  196 (214)
Q Consensus       152 ~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~~~~~CP~Cr~  196 (214)
                      .|.+|-..|..-..-..- .||++|+.+|....-...+ .|..|.+
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~R-vC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPR-LCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CC-EEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCe-ECHhHhh
Confidence            488888888755432333 3899999999766543333 3888854

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {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 At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.88  E-value=0.054  Score=31.47  Aligned_cols=46  Identities=20%  Similarity=0.327  Sum_probs=28.9

Q ss_pred             cccccccccccCCCceEEe-cCCCccChhhHHHHHHh---CCCCccccccc
Q 028085          151 TLCSICLEDYREGENLRVL-PCRHEFHSSCVDSWLIR---WGTFCPVCRHE  197 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~~Wl~~---~~~~CP~Cr~~  197 (214)
                      ..| ||.....+++.+..- .|..-||..|+..-...   ....||.|+..
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            457 787766655543333 38888999997542111   12279999764

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.24  E-value=1.1  Score=25.30  Aligned_cols=46  Identities=24%  Similarity=0.530  Sum_probs=34.1

Q ss_pred             CCcccccccccccCCCceEEec--CCCccChhhHHHHHHhCCC----Cccccc
Q 028085          149 RETLCSICLEDYREGENLRVLP--CRHEFHSSCVDSWLIRWGT----FCPVCR  195 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~--C~H~FH~~Ci~~Wl~~~~~----~CP~Cr  195 (214)
                      ....|.+|-+.+++.+ .++-|  =+|-||-.|-...++.+..    .||-=+
T Consensus         7 ~~l~CtlC~erLEdtH-FVQCPsv~~HkFCFpCsr~sik~q~~~~evyCPSG~   58 (80)
T d2cs3a1           7 GPLCCTICHERLEDTH-FVQCPSVPSHKFCFPCSRESIKAQGATGEVYCPSGE   58 (80)
T ss_dssp             CSCCCSSSCSCCSSTT-SEECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTSS
T ss_pred             CceeeeeehhhhcCCc-eEeCCCCcCCceeccccHHHHHhcCCCCcEECCCCC
Confidence            4468999999999874 34445  3899999999999987532    566543

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.18  E-value=0.37  Score=23.65  Aligned_cols=30  Identities=37%  Similarity=0.597  Sum_probs=20.6

Q ss_pred             CCcccccccccccCCCceEEecCCCccChhhH
Q 028085          149 RETLCSICLEDYREGENLRVLPCRHEFHSSCV  180 (214)
Q Consensus       149 ~~~~C~ICl~~~~~~~~~~~l~C~H~FH~~Ci  180 (214)
                      ..+.|.+|-...-.-+  +..-=|++||+.|+
T Consensus         7 ~~~~C~~C~K~VY~~E--rl~a~g~~yHk~CF   36 (36)
T d2co8a2           7 AGDLCALCGEHLYVLE--RLCVNGHFFHRSCF   36 (36)
T ss_dssp             SSCBCSSSCCBCCTTT--BCCBTTBCCBTTTC
T ss_pred             CCCcccccCCEEeeee--EEEecCcEeccccC
Confidence            4568999987755333  22334899999994

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.05  E-value=0.91  Score=26.05  Aligned_cols=45  Identities=27%  Similarity=0.532  Sum_probs=27.0

Q ss_pred             cccccccccccCCCceEEe-cCCCccChhhHH------HHH--HhCCCCccccccc
Q 028085          151 TLCSICLEDYREGENLRVL-PCRHEFHSSCVD------SWL--IRWGTFCPVCRHE  197 (214)
Q Consensus       151 ~~C~ICl~~~~~~~~~~~l-~C~H~FH~~Ci~------~Wl--~~~~~~CP~Cr~~  197 (214)
                      ..| ||-....++ .+..- .|.--||..|+.      ...  ......||.|+..
T Consensus        17 ~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          17 LYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            457 887765544 33333 377889999982      111  1123479999654