Citrus Sinensis ID: 025608

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250
Protein Sequence
MIIFFIKETRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEcccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHccccHHHHHHHHHHHHHHHccccccEEccccccccEEEcccccccccccccccccccccccccccccccccHHHHHHccccccHHHHHHHHHHHcccccccccccccEEcccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEcHHHHHHHHHHHHHHHHccccccccccccccccccccEEEcccccHHHcccccccccHHHHHHHHHHHEEEHcccEEEEcccccccccccHHHHHHHccHHHHHHHHHHHHHHHccccccEEccccccccEEEEccccccccEEEcccccEEEEcccccccccccHHHHHHHHHccccccHHHHHHHHHccccccccccccEEEEccccccEEEEcccEEEEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
MIIFFIKETRKSLEFNFQELVRFSMtenemasstrsetsRSFVCEICVEtklrnesfsikgcshmycvDCTVKYVDSKLQEnvtsigcpvtdcggslepeycrdilpeeaFDKWGKALCESlipgaqkfycpfkdcsaLLIDDAGeairesecpnchrlfCAQCKVAWHAgiecadfqklhkdepesEDIILMKLAQnqkwnrcpnckfyvekkdgcsyircrcghafcyhcgvqlstvshgyycpscnk
Flexible Loop (DISEMBL)
miiffiketrkslefNFQELVRFSMTENEMasstrsetsrsfVCEICVETKlrnesfsikgcSHMYCVDCTVKYVDSKLQENVTsigcpvtdcgGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLaqnqkwnrcpNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
Low Complexity Region (SEG)
MIIFFIKETRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
Disordered region (IsUnstruct)
*IIFFIKETRKSLEFNFQELVRF*****************SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHK*****EDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCP****
Disordered Region (DISOPRED)
MIIFF**ETRKSLEFN***************************CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQK*************MKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
Disordered Region (DISEMBL)
MIIFFIKETRKSLEFNFQELVRFSMTE*************SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
Disordered Region (DISPRO)
MIIFFIKETRKSLEFNFQELVRFSMTENE**********RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIIFFIKETRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK
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	250	2.2.26 [Sep-21-2011]
P0CE10	1787	Putative uncharacterized	no	no	0.856	0.119	0.260	4e-16
A5PK27	304	E3 ubiquitin-protein liga	yes	no	0.824	0.677	0.261	6e-15
Q7Z419	303	E3 ubiquitin-protein liga	yes	no	0.748	0.617	0.271	2e-14
P50876	292	Probable E3 ubiquitin-pro	no	no	0.752	0.643	0.270	8e-14
Q4KLT0	282	Probable E3 ubiquitin-pro	N/A	no	0.724	0.641	0.27	2e-13
A4IIY1	292	Probable E3 ubiquitin-pro	no	no	0.752	0.643	0.270	3e-13
Q925F3	292	Probable E3 ubiquitin-pro	yes	no	0.752	0.643	0.265	5e-13
Q8BKD6	301	E3 ubiquitin-protein liga	no	no	0.744	0.617	0.267	7e-13
Q9LVX0	537	Probable E3 ubiquitin-pro	no	no	0.804	0.374	0.276	8e-13
Q9SKC3	543	Probable E3 ubiquitin-pro	no	no	0.736	0.338	0.276	1e-12

>sp|P0CE10|Y4102_ARATH Putative uncharacterized protein At4g01020, chloroplastic OS=Arabidopsis thaliana GN=At4g01020 PE=4 SV=1

 Score = 85.1 bits (209), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 106/230 (46%), Gaps = 16/230 (6%)

Query: 7    KETRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMY 66
            KE R+ ++    EL R      E       E      C IC+     ++ +S++GCSH++
Sbjct: 1530 KEMRQEVQKMVNELAREKSALGEKPDEIELE------CPICLSEV--DDGYSLEGCSHLF 1581

Query: 67   CVDCTVKYVDSKLQE-NVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPG 125
            C  C ++  ++ ++  +   I C   DCG  +     R +L +E  D+   A   + +  
Sbjct: 1582 CKACLLEQFEASMRNFDAFPILCSHIDCGAPIVVADMRALLSQEKLDELISASLSAFVTS 1641

Query: 126  A--QKFYCPFKDCSALL-IDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHK 182
            +  +  +C   DC ++  +    E+     C  CH   C +C + +H  I C  ++K   
Sbjct: 1642 SDGKLRFCSTPDCPSIYRVAGPQESGEPFICGACHSETCTRCHLEYHPLITCERYKKFK- 1700

Query: 183  DEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHC 232
               E+ D+ L   A+ +    CP CK  +EK DGC++++CRCG   C+ C
Sbjct: 1701 ---ENPDLSLKDWAKGKDVKECPICKSTIEKTDGCNHLQCRCGKHICWTC 1747

Arabidopsis thaliana (taxid: 3702)

>sp|A5PK27|R144B_BOVIN E3 ubiquitin-protein ligase RNF144B OS=Bos taurus GN=RNF144B PE=2 SV=1

 Score = 81.3 bits (199), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 57/218 (26%), Positives = 102/218 (46%), Gaps = 12/218 (5%)

Query: 23  FSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQEN 82
            +MT  E  +           C++C+  +  ++  +++ C  ++C  C  +Y+   ++E 
Sbjct: 10  LTMTAAENPTPGDLALVPLVTCKLCLCEQSLDKMTTLQECRCIFCTACLKQYMQLAIREG 69

Query: 83  VTS-IGCPVTDC--GGSLEPEYCRDILPEEAFDKWGKALCESLIP-GAQKFYCPFKDCSA 138
             S I CP   C   G+L+      ++P + F  + +   E  +     + +CP  DC  
Sbjct: 70  CGSPITCPDMVCLNHGTLQEAEIACLVPVDQFQLYQRLKFEREVHLDPCRTWCPVADCQT 129

Query: 139 L---LIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKL 195
           +      D G+ +   ECP+CH  FC+ CK AWHA + C D Q        +E   L   
Sbjct: 130 VCPVATSDPGQPVL-VECPSCHLKFCSCCKDAWHAEVSCRDSQ---PGILPTEHGTLFGT 185

Query: 196 AQNQKWNRCPNCKFYVEKKDGCSYIRCR-CGHAFCYHC 232
             +    +CP C+ Y+E+ +GC+ + C+ C H FC++C
Sbjct: 186 ETDAPIKQCPVCRVYIERNEGCAQMMCKNCKHTFCWYC 223

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7Z419|R144B_HUMAN E3 ubiquitin-protein ligase RNF144B OS=Homo sapiens GN=RNF144B PE=1 SV=1

 Score = 79.7 bits (195), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 54/199 (27%), Positives = 97/199 (48%), Gaps = 12/199 (6%)

Query: 42  FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTS-IGCPVTDC--GGSLE 98
             C++C+  +  ++  +++ C  ++C  C  +Y+   ++E   S I CP   C   G+L+
Sbjct: 28  ITCKLCLCEQSLDKMTTLQECQCIFCTACLKQYMQLAIREGCGSPITCPDMVCLNHGTLQ 87

Query: 99  PEYCRDILPEEAFDKWGKALCESLIP-GAQKFYCPFKDCSAL---LIDDAGEAIRESECP 154
                 ++P + F  + +   E  +     + +CP  DC  +      D G+ +   ECP
Sbjct: 88  EAEIACLVPVDQFQLYQRLKFEREVHLDPYRTWCPVADCQTVCPVASSDPGQPVL-VECP 146

Query: 155 NCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKK 214
           +CH  FC+ CK AWHA + C D Q +      +E   L          +CP C+ Y+E+ 
Sbjct: 147 SCHLKFCSCCKDAWHAEVSCRDSQPIVL---PTEHRALFGTDAEAPIKQCPVCRVYIERN 203

Query: 215 DGCSYIRCR-CGHAFCYHC 232
           +GC+ + C+ C H FC++C
Sbjct: 204 EGCAQMMCKNCKHTFCWYC 222

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P50876|R144A_HUMAN Probable E3 ubiquitin-protein ligase RNF144A OS=Homo sapiens GN=RNF144A PE=1 SV=2

 Score = 77.4 bits (189), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 53/196 (27%), Positives = 94/196 (47%), Gaps = 8/196 (4%)

Query: 44  CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV-TSIGCPVTDCG--GSLEPE 100
           C++C+      +  +I  C  ++C  C  +YV+  ++E + T+I CP   C   G L+  
Sbjct: 20  CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN 79

Query: 101 YCRDILPEEAFDKWGKALCE-SLIPGAQKFYCPFKDCSAL--LIDDAGEAIRESECPNCH 157
               ++  E   ++ K   E  ++    + +CP   C A+  L D   +  +  +C  C 
Sbjct: 80  EIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQLQDVGLQTPQPVQCKACR 139

Query: 158 RLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGC 217
             FC+ CK +WH G  C +   +     E+     M+   +    RCP CK Y+E+ +GC
Sbjct: 140 MEFCSTCKASWHPGQGCPETMPITFLPGETSAAFKME-EDDAPIKRCPKCKVYIERDEGC 198

Query: 218 SYIRCR-CGHAFCYHC 232
           + + C+ C HAFC++C
Sbjct: 199 AQMMCKNCKHAFCWYC 214

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q4KLT0|RN217_XENLA Probable E3 ubiquitin-protein ligase RNF217 OS=Xenopus laevis GN=rnf217 PE=2 SV=1

 Score = 76.3 bits (186), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 91/200 (45%), Gaps = 19/200 (9%)

Query: 44  CEICVETKLRNESFSIKG---CSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100
           C +C+E +      SIK    C    C +C  +Y+ S++Q     I CP+T+C   L+  
Sbjct: 3   CRVCLEDR------SIKPLPCCKKPVCDECLKRYLSSQVQLGQAEIQCPITECNKHLDES 56

Query: 101 YCRDILPEEAFDKWGKALCESLIPGAQK------FYCPFKDCSALLIDDAGEAIRESECP 154
                LP +   K+   L  S +  + K       +  FK  + +      E   + +CP
Sbjct: 57  TILYSLPHDDIIKYKYFLELSRMDSSTKPCPQCKHFTTFKRKTHIPNPTKSENKLKIQCP 116

Query: 155 NCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKK 214
           +C  ++C +C   WH G+ C +++K  K      + I       QK   CP CK ++++ 
Sbjct: 117 SCQFIWCFRCHAPWHEGVNCREYKKGDKLLRHWANEIEHGQRNAQK---CPRCKVHIQRT 173

Query: 215 DGCSYIRC-RCGHAFCYHCG 233
           +GC ++ C +C   FCY CG
Sbjct: 174 EGCDHMTCSQCNTNFCYRCG 193

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|A4IIY1|R144A_XENTR Probable E3 ubiquitin-protein ligase RNF144A OS=Xenopus tropicalis GN=rnf144a PE=2 SV=1

 Score = 75.9 bits (185), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/196 (27%), Positives = 91/196 (46%), Gaps = 8/196 (4%)

Query: 44  CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV-TSIGCPVTDCG--GSLEPE 100
           C++C+      +  +I  C  ++C  C  +YV+  ++E + T+I CP   C   G L+  
Sbjct: 20  CKLCLGEYTVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDASCPKRGHLQEN 79

Query: 101 YCRDILPEEAFDKWGKALCES-LIPGAQKFYCPFKDCSAL--LIDDAGEAIRESECPNCH 157
               ++  E   K+ K   E  ++    + +CP   C A+  L +   +  +  +C  C 
Sbjct: 80  EIECMVAAEIMQKYKKLQFEKEILLDPCRTWCPSSSCQAVCKLQEKGIQNPQLVQCSACD 139

Query: 158 RLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGC 217
             FC+ CK  WH G  C +   +    P         L  +    RCP CK Y+E+ +GC
Sbjct: 140 IEFCSACKANWHPGQGCPENMAI-TFLPGDSSSFFKSLEDDVPIKRCPKCKVYIERDEGC 198

Query: 218 SYIRCR-CGHAFCYHC 232
           + + C+ C HAFC++C
Sbjct: 199 AQMMCKNCKHAFCWYC 214

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes ube2l3 and ube2l6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q925F3|R144A_MOUSE Probable E3 ubiquitin-protein ligase RNF144A OS=Mus musculus GN=Rnf144a PE=1 SV=1

 Score = 75.1 bits (183), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 52/196 (26%), Positives = 93/196 (47%), Gaps = 8/196 (4%)

Query: 44  CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV-TSIGCPVTDCG--GSLEPE 100
           C++C+      +  +I  C  ++C  C  +YV+  ++E + T+I CP   C   G L+  
Sbjct: 20  CKLCLGEYPAEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN 79

Query: 101 YCRDILPEEAFDKWGKALCE-SLIPGAQKFYCPFKDCSAL--LIDDAGEAIRESECPNCH 157
               ++  E   ++ K   E  ++    + +CP   C A+  L D   +  +  +C  C 
Sbjct: 80  EIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQLQDIGLQTPQLVQCKACD 139

Query: 158 RLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGC 217
             FC+ CK  WH G  C +   +     E+     M+   +    RCP C+ Y+E+ +GC
Sbjct: 140 MEFCSACKARWHPGQGCPETMPITFLPGETSSAFKMEEG-DAPIKRCPKCRVYIERDEGC 198

Query: 218 SYIRCR-CGHAFCYHC 232
           + + C+ C HAFC++C
Sbjct: 199 AQMMCKNCKHAFCWYC 214

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8BKD6|R144B_MOUSE E3 ubiquitin-protein ligase RNF144B OS=Mus musculus GN=Rnf144b PE=2 SV=2

 Score = 74.3 bits (181), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 53/198 (26%), Positives = 93/198 (46%), Gaps = 12/198 (6%)

Query: 42  FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTS-IGCPVTDC--GGSLE 98
             C++C+  +  ++   ++ C  ++C  C  +Y+   ++E   S I CP   C   G+L+
Sbjct: 28  VTCKLCLCEQSLDKMTMLQECQCIFCTPCLKQYMVLSIREGCGSPITCPDMVCLNHGTLQ 87

Query: 99  PEYCRDILPEEAFDKWGKALCESLI-PGAQKFYCPFKDCSALLIDDAGEAIRES--ECPN 155
                 ++P + F  + +   E  +     + +CP  DC  +    AG+  +    ECP+
Sbjct: 88  ETEIACLVPLDEFQLYQRLKFEREVHMDPLRTWCPVADCQTVCHISAGDPGQPVLVECPS 147

Query: 156 CHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKD 215
           CH  FC+ CK AWH    C D Q         E   L     +    +CP C+ Y+E+ +
Sbjct: 148 CHLKFCSCCKDAWHEESSCRDSQSAM-----PEHGALFGTDADAPIKQCPVCRIYIERNE 202

Query: 216 GCSYIRCR-CGHAFCYHC 232
           GC+ + C+ C H FC++C
Sbjct: 203 GCAQMMCKNCKHTFCWYC 220

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9LVX0|ARI3_ARATH Probable E3 ubiquitin-protein ligase ARI3 OS=Arabidopsis thaliana GN=ARI3 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 97/210 (46%), Gaps = 9/210 (4%)

Query: 38  TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTS-IGCPVTDCGGS 96
           + ++  C++C+E  L +   +   C H +C DC + +   K+ E  +  I C   +C   
Sbjct: 115 SKKTMKCDVCMEDDLPSNVMTRMECGHRFCNDCWIGHFTVKINEGESKRILCMAHECKAI 174

Query: 97  LEPEYCRDILPEEAFDKWGKALCESLIPGAQKF-YCPFKD--CSALLIDDAGEAIRESEC 153
            + +  R ++  E  D++ + L ES +       +CP K    SA+   + G  + E  C
Sbjct: 175 CDEDVVRKLVSPELADRYDRFLIESYVEDNNMVKWCPSKPHCGSAIRKIEDGHDVVEVGC 234

Query: 154 PNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEK 213
            +C   FC  C    H+   C    KL K + E E   +  +  N K   CP C   ++K
Sbjct: 235 -SCGLQFCFSCLSESHSPCSCL-MWKLWKKKCEDESETVNWITVNTKL--CPKCSKPIQK 290

Query: 214 KDGCSYIRCRCGHAFCYHCGVQLSTVSHGY 243
           +DGC+ + C+CG  FC+ CG Q +   H Y
Sbjct: 291 RDGCNLMTCKCGQHFCWLCG-QATGRDHTY 319

Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9SKC3|ARI9_ARATH Probable E3 ubiquitin-protein ligase ARI9 OS=Arabidopsis thaliana GN=ARI9 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 90/195 (46%), Gaps = 11/195 (5%)

Query: 44  CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV--TSIGCPVTDCGGSLEPEY 101
           C IC E+  R E   +  C H YC  C   Y+ +K+++      + CP   C  ++  + 
Sbjct: 128 CGICFESYTREEIARV-SCGHPYCKTCWAGYITTKIEDGPGCLRVKCPEPSCSAAVGKDM 186

Query: 102 CRDILPEEAFDKWGKALCESLIPGAQKF-YCPFKDCSALLIDDAGEAIRESECPNCHRLF 160
             D+   +  +K+ + +  S +   +K  +CP   C   +     E+        C   F
Sbjct: 187 IEDVTETKVNEKYSRYILRSYVEDGKKIKWCPSPGCGYAVEFGGSESSSYDVSCLCSYRF 246

Query: 161 CAQCKVAWHAGIECADFQK-LHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSY 219
           C  C    H+ ++C    K + K++ ESE+   M LA ++    CP CK  +EK DGC++
Sbjct: 247 CWNCSEDAHSPVDCDTVSKWIFKNQDESENKNWM-LANSKP---CPECKRPIEKNDGCNH 302

Query: 220 IRCR--CGHAFCYHC 232
           + C   CGH FC+ C
Sbjct: 303 MTCSAPCGHEFCWIC 317

Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Arabidopsis thaliana (taxid: 3702)

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	250
297738503	329	unnamed protein product [Vitis vinifera]	0.924	0.702	0.604	7e-81
225444595	358	PREDICTED: probable E3 ubiquitin-protein	0.928	0.648	0.601	8e-81
224142755	307	predicted protein [Populus trichocarpa]	0.956	0.778	0.561	5e-76
255550303	400	zinc finger protein, putative [Ricinus c	0.844	0.527	0.620	5e-76
356530471	333	PREDICTED: putative uncharacterized prot	0.82	0.615	0.592	5e-68
356558463	685	PREDICTED: uncharacterized protein LOC10	0.828	0.302	0.566	3e-66
356522436	292	PREDICTED: probable E3 ubiquitin-protein	0.812	0.695	0.551	1e-65
297820104	322	zinc finger family protein [Arabidopsis	0.892	0.692	0.506	3e-65
356522438	303	PREDICTED: probable E3 ubiquitin-protein	0.824	0.679	0.538	8e-64
15231861	320	RING/U-box domain-containing protein [Ar	0.876	0.684	0.511	6e-63

>gi|297738503|emb|CBI27748.3| unnamed protein product [Vitis vinifera]

 Score =  306 bits (783), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 145/240 (60%), Positives = 172/240 (71%), Gaps = 9/240 (3%)

Query: 9   TRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCV 68
           TRK   F        S+TE    S+++ +   +FVCEIC++ K  N SFSIKGC H YC 
Sbjct: 97  TRKPFTFP-------SVTETGQPSNSKPDPPPTFVCEICIDPKPLNHSFSIKGCPHSYCS 149

Query: 69  DCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQK 128
           DC  KYV SKLQ+NV+ I CP  +C G LEP+ CR ILP   FD+WG ALCE+LI G+QK
Sbjct: 150 DCMTKYVASKLQDNVSRISCPAPNCTGVLEPQQCRPILPSHVFDRWGNALCEALILGSQK 209

Query: 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESE 188
           FYCP+KDCSALLI D GE I+ESECPNC RLFCAQC+V WH+GI+C +FQKL+KDE   E
Sbjct: 210 FYCPYKDCSALLIRDEGEVIKESECPNCRRLFCAQCEVPWHSGIDCGEFQKLNKDERGRE 269

Query: 189 DIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSC 248
           DI++M LA+   W RCP CKFYVEK  GC YIRCRCG AFCY+CG   ST+SH   CP C
Sbjct: 270 DILMMNLAKTNNWKRCPKCKFYVEKSFGCMYIRCRCGFAFCYNCGAPSSTISH--ICPHC 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444595|ref|XP_002277363.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-B-like [Vitis vinifera]

 Score =  305 bits (782), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 145/241 (60%), Positives = 173/241 (71%), Gaps = 9/241 (3%)

Query: 9   TRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCV 68
           TRK   F        S+TE    S+++ +   +FVCEIC++ K  N SFSIKGC H YC 
Sbjct: 97  TRKPFTFP-------SVTETGQPSNSKPDPPPTFVCEICIDPKPLNHSFSIKGCPHSYCS 149

Query: 69  DCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQK 128
           DC  KYV SKLQ+NV+ I CP  +C G LEP+ CR ILP   FD+WG ALCE+LI G+QK
Sbjct: 150 DCMTKYVASKLQDNVSRISCPAPNCTGVLEPQQCRPILPSHVFDRWGNALCEALILGSQK 209

Query: 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESE 188
           FYCP+KDCSALLI D GE I+ESECPNC RLFCAQC+V WH+GI+C +FQKL+KDE   E
Sbjct: 210 FYCPYKDCSALLIRDEGEVIKESECPNCRRLFCAQCEVPWHSGIDCGEFQKLNKDERGRE 269

Query: 189 DIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSC 248
           DI++M LA+   W RCP CKFYVEK  GC YIRCRCG AFCY+CG   ST+SH   CP C
Sbjct: 270 DILMMNLAKTNNWKRCPKCKFYVEKSFGCMYIRCRCGFAFCYNCGAPSSTISH--ICPHC 327

Query: 249 N 249
           +
Sbjct: 328 S 328

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142755|ref|XP_002324718.1| predicted protein [Populus trichocarpa] gi|222866152|gb|EEF03283.1| predicted protein [Populus trichocarpa]

 Score =  290 bits (741), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 141/251 (56%), Positives = 176/251 (70%), Gaps = 12/251 (4%)

Query: 2   IIFFIKE---TRKSLEFNFQELVRFSMTENEMASSTRSETSRSFVCEICVETKLRNESFS 58
           ++ F+ E   +RK  E  F E V       E   S+ S+    FVC+ICVE  +   SF 
Sbjct: 61  VLDFLPEVIPSRKQKEPTFIESVA------EKGQSSNSQIDPDFVCQICVEPTILKNSFL 114

Query: 59  IKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL 118
           IKGC+H YC +C VKYV SKLQEN+T I CPV DC G+LEPE CR +LPE  FD+WG AL
Sbjct: 115 IKGCTHAYCTECMVKYVSSKLQENITKICCPVPDCKGALEPEDCRSVLPENVFDRWGNAL 174

Query: 119 CESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQ 178
           CE++I G+QKFYCPFKDCSA+LIDD  E +RESECPNC R+FCAQCKV WH+ I C +++
Sbjct: 175 CEAVILGSQKFYCPFKDCSAMLIDDGEEVVRESECPNCWRMFCAQCKVPWHSQISCEEYK 234

Query: 179 KLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCG-VQLS 237
            LHKDE E +DI+LM LA+N+ W RCP C+ +VEK +GC Y++CRCG  FCY CG   L+
Sbjct: 235 MLHKDERERDDILLMNLAKNKNWRRCPKCRIFVEKIEGCRYMKCRCGTQFCYSCGSTDLN 294

Query: 238 TVSHGYYCPSC 248
            V+H  YC  C
Sbjct: 295 PVTH--YCYKC 303

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550303|ref|XP_002516202.1| zinc finger protein, putative [Ricinus communis] gi|223544688|gb|EEF46204.1| zinc finger protein, putative [Ricinus communis]

 Score =  290 bits (741), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 131/211 (62%), Positives = 159/211 (75%)

Query: 22  RFSMTENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQE 81
           RF  +  E   S+       FVCEICVE+K  +ES +I+GC+H YC DC  KYV SK+QE
Sbjct: 185 RFGFSVTEKGHSSEPNDHPQFVCEICVESKTADESLAIRGCTHAYCTDCMAKYVASKIQE 244

Query: 82  NVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLI 141
           N+T I CPV+ CGG LEPEYCR ILP+E FD+WG ALCE+L  G+QKFYCPFKDCSA+LI
Sbjct: 245 NITGIYCPVSGCGGLLEPEYCRSILPQEVFDRWGNALCEALNLGSQKFYCPFKDCSAMLI 304

Query: 142 DDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKW 201
           +D GE IRESECP+C RLFCA CKV WH+GI+C  FQ LHKDE E EDI+LMKLA+N+KW
Sbjct: 305 NDGGEVIRESECPHCRRLFCAHCKVPWHSGIDCNKFQTLHKDEREKEDIMLMKLAENKKW 364

Query: 202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHC 232
            RCP C+ YVE+ +GC Y++CR     C+ C
Sbjct: 365 RRCPICRIYVERTEGCRYMKCRYIFICCFVC 395

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530471|ref|XP_003533804.1| PREDICTED: putative uncharacterized protein At4g01020, chloroplastic-like [Glycine max]

 Score =  263 bits (672), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 122/206 (59%), Positives = 147/206 (71%), Gaps = 1/206 (0%)

Query: 38  TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL 97
            S SFVCEIC ETK   +SFSI GC H+YC  C  +YV+SKL+EN+ SI CPV  C G L
Sbjct: 122 NSASFVCEICTETKTARDSFSIIGCHHVYCNSCVAQYVESKLEENIVSIPCPVPGCRGLL 181

Query: 98  EPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEA-IRESECPNC 156
           E + CR+IL    FD+WGKALCE++I   +KFYCPF DCS +LI    E  IRE+ECPNC
Sbjct: 182 EADDCREILAPRVFDRWGKALCEAVIAAEEKFYCPFADCSVMLIRGIEENNIREAECPNC 241

Query: 157 HRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDG 216
            RLFCAQC+V WH  + C DFQKL+ DE + EDI+LM LA   +W RCP C+FYV K DG
Sbjct: 242 RRLFCAQCRVPWHDNMPCEDFQKLNADERDKEDIMLMNLANQMQWKRCPRCRFYVAKSDG 301

Query: 217 CSYIRCRCGHAFCYHCGVQLSTVSHG 242
           C Y++CRCG+AFCY+CG    T SH 
Sbjct: 302 CMYMKCRCGNAFCYNCGAPNLTSSHS 327

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558463|ref|XP_003547526.1| PREDICTED: uncharacterized protein LOC100803898 [Glycine max]

 Score =  257 bits (657), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 119/210 (56%), Positives = 153/210 (72%), Gaps = 3/210 (1%)

Query: 32  SSTRSETSRS--FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCP 89
           SS++ E S +  F+CEIC ETK   +SFSI GC H+YC  C  +YV+SKL++NV +I CP
Sbjct: 114 SSSKGECSSTAPFLCEICTETKTDRDSFSITGCRHVYCNSCVAQYVESKLEDNVVNIPCP 173

Query: 90  VTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEA-I 148
           V  C G LE +YCR+IL    FD+WG ALCE++I   +KFYCPF DCSA+LI  + +A I
Sbjct: 174 VPGCRGLLEADYCREILSPRVFDRWGNALCEAVIDAEEKFYCPFADCSAMLIRASEDADI 233

Query: 149 RESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCK 208
           RE ECPNC RLFCA C+V WH  I C +FQKL+ +E E EDI+LM LA+  +W RCP+C+
Sbjct: 234 RECECPNCRRLFCALCRVPWHENIPCEEFQKLNAEEREREDIMLMSLAKQMQWKRCPHCR 293

Query: 209 FYVEKKDGCSYIRCRCGHAFCYHCGVQLST 238
           FYV K +GC Y+RCRCG++FCY CG  + T
Sbjct: 294 FYVAKSEGCMYMRCRCGNSFCYKCGAPILT 323

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522436|ref|XP_003529852.1| PREDICTED: probable E3 ubiquitin-protein ligase ARI3-like [Glycine max]

 Score =  255 bits (651), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 112/203 (55%), Positives = 151/203 (74%)

Query: 36  SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95
            E SR   C IC++ K   E F  + CSH +C DC  +YV +K+QEN++ + CP   C G
Sbjct: 82  GECSRQVYCGICMDAKYGEEMFRNQNCSHSFCDDCIGRYVATKVQENISMVKCPHPKCKG 141

Query: 96  SLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPN 155
            +EP+YCR  +P+E FD+W  ALCE+L+PG+QKFYCPFKDCSA+LI+DA E +  SECP+
Sbjct: 142 VIEPQYCRSFIPKEVFDRWEDALCENLVPGSQKFYCPFKDCSAMLINDAEEIVTVSECPH 201

Query: 156 CHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKD 215
           C+RLFCAQCKV+WHAG+EC +FQ L + E E ED+++M+LA+N+ W RCP C FYVE+ D
Sbjct: 202 CNRLFCAQCKVSWHAGVECKEFQNLKEYEREREDLMVMELAKNKNWKRCPKCSFYVERID 261

Query: 216 GCSYIRCRCGHAFCYHCGVQLST 238
           GC++I CRCG+ FCY CG +  +
Sbjct: 262 GCTHISCRCGNEFCYACGSKWGS 284

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820104|ref|XP_002877935.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297323773|gb|EFH54194.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  254 bits (648), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 114/225 (50%), Positives = 158/225 (70%), Gaps = 2/225 (0%)

Query: 26  TENEMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTS 85
           T++     + S  + +F CEICVETK   E+F I GCSH YC DC  KY+ +KLQ+N+ S
Sbjct: 100 TKSLEKGQSSSSATVTFDCEICVETKSIIETFRIGGCSHFYCNDCVSKYIAAKLQDNILS 159

Query: 86  IGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAG 145
           I CPV+ C G LEP+ CR ILP E FD+WG ALCE+++  +++FYCP+KDCSALL  D  
Sbjct: 160 IECPVSGCSGRLEPDQCRQILPREVFDRWGDALCEAVVMRSKRFYCPYKDCSALLFMDES 219

Query: 146 EAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCP 205
           E +++SECP+CHR+ C +C   WH  + C +FQKL ++E   +DI+L  +A+ +KW RCP
Sbjct: 220 EVMKDSECPHCHRMVCVECGTKWHPEMTCEEFQKLAENERGRDDILLATMAKKKKWKRCP 279

Query: 206 NCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK 250
           +CKFY+EK  GC Y++CRCG AFCY+CG    +  H +YC +C +
Sbjct: 280 SCKFYIEKSHGCLYMKCRCGLAFCYNCGT--PSRDHSHYCYNCKR 322

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522438|ref|XP_003529853.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-like [Glycine max]

 Score =  249 bits (636), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 111/206 (53%), Positives = 150/206 (72%)

Query: 36  SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95
            E+S+   C IC++ K   E F  + CSH +C DC  +YV +K+QEN++ + CP   C G
Sbjct: 92  GESSQQVYCGICMDAKYGEEMFRNQNCSHSFCDDCIGRYVATKVQENISMVKCPHPKCKG 151

Query: 96  SLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPN 155
            +EP+YCR  +P+E FD+W  ALCE+L+ G+QKFYCPFKDCSA+LI+DA E +  SECP+
Sbjct: 152 VIEPQYCRSFIPKEVFDRWENALCENLVLGSQKFYCPFKDCSAVLINDAEEIVTVSECPH 211

Query: 156 CHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKD 215
           C+RLFCAQCKV+WHAG++C +FQ L + E E ED+++M+LA+N+ W RCP C FYVE+ D
Sbjct: 212 CNRLFCAQCKVSWHAGVDCKEFQNLKEYEREREDLMVMELAKNKSWKRCPKCIFYVERID 271

Query: 216 GCSYIRCRCGHAFCYHCGVQLSTVSH 241
           GC+ I CRCG+ FCY CG   S   H
Sbjct: 272 GCTRITCRCGNEFCYACGSSWSGGLH 297

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231861|ref|NP_190937.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|6729520|emb|CAB67676.1| putative protein [Arabidopsis thaliana] gi|21536688|gb|AAM61020.1| unknown [Arabidopsis thaliana] gi|332645607|gb|AEE79128.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  246 bits (628), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 114/223 (51%), Positives = 159/223 (71%), Gaps = 4/223 (1%)

Query: 29  EMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGC 88
           E   S+ S+T+ +F CEICV++K   ESF I GCSH YC DC  KY+ +KLQ+N+ SI C
Sbjct: 101 EKGQSSSSKTA-TFDCEICVDSKSIIESFRIGGCSHFYCNDCVSKYIAAKLQDNILSIEC 159

Query: 89  PVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEA- 147
           PV+ C G LEP+ CR ILP+E FD+WG ALCE+++  ++KFYCP+KDCSAL+  +  E  
Sbjct: 160 PVSGCSGRLEPDQCRQILPKEVFDRWGDALCEAVVMRSKKFYCPYKDCSALVFLEESEVK 219

Query: 148 IRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNC 207
           +++SECP+CHR+ C +C   WH  + C +FQKL  +E   +DI+L  +A+ +KW RCP+C
Sbjct: 220 MKDSECPHCHRMVCVECGTQWHPEMTCEEFQKLAANERGRDDILLATMAKQKKWKRCPSC 279

Query: 208 KFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK 250
           KFY+EK  GC Y++CRCG AFCY+CG    +  H +YC +C +
Sbjct: 280 KFYIEKSQGCLYMKCRCGLAFCYNCGT--PSRDHTHYCYNCKR 320

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	250
TAIR|locus:2084116	320	AT3G53690 [Arabidopsis thalian	0.876	0.684	0.511	7.2e-68
TAIR|locus:2091030	303	AT3G14250 [Arabidopsis thalian	0.888	0.732	0.471	1.5e-60
TAIR|locus:2085612	348	AT3G45540 [Arabidopsis thalian	0.832	0.597	0.328	1.3e-36
TAIR|locus:2151689	444	AT5G37560 [Arabidopsis thalian	0.82	0.461	0.344	1.2e-35
TAIR|locus:2143995	655	AT5G60250 [Arabidopsis thalian	0.752	0.287	0.343	7.8e-35
TAIR|locus:2085622	222	AT3G45470 [Arabidopsis thalian	0.76	0.855	0.353	1.3e-34
TAIR|locus:2133935	532	AT4G19670 [Arabidopsis thalian	0.756	0.355	0.364	2.8e-34
TAIR|locus:2040065	373	AT2G25360 [Arabidopsis thalian	0.848	0.568	0.318	2e-33
TAIR|locus:1006230127	384	AT2G26135 [Arabidopsis thalian	0.792	0.515	0.334	6.7e-33
TAIR|locus:2050100	468	AT2G21420 [Arabidopsis thalian	0.796	0.425	0.353	2.9e-32

TAIR|locus:2084116 AT3G53690 [Arabidopsis thaliana (taxid:3702)]

 Score = 689 (247.6 bits), Expect = 7.2e-68, P = 7.2e-68
 Identities = 114/223 (51%), Positives = 159/223 (71%)

Query:    29 EMASSTRSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGC 88
             E   S+ S+T+ +F CEICV++K   ESF I GCSH YC DC  KY+ +KLQ+N+ SI C
Sbjct:   101 EKGQSSSSKTA-TFDCEICVDSKSIIESFRIGGCSHFYCNDCVSKYIAAKLQDNILSIEC 159

Query:    89 PVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEA- 147
             PV+ C G LEP+ CR ILP+E FD+WG ALCE+++  ++KFYCP+KDCSAL+  +  E  
Sbjct:   160 PVSGCSGRLEPDQCRQILPKEVFDRWGDALCEAVVMRSKKFYCPYKDCSALVFLEESEVK 219

Query:   148 IRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNC 207
             +++SECP+CHR+ C +C   WH  + C +FQKL  +E   +DI+L  +A+ +KW RCP+C
Sbjct:   220 MKDSECPHCHRMVCVECGTQWHPEMTCEEFQKLAANERGRDDILLATMAKQKKWKRCPSC 279

Query:   208 KFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK 250
             KFY+EK  GC Y++CRCG AFCY+CG    +  H +YC +C +
Sbjct:   280 KFYIEKSQGCLYMKCRCGLAFCYNCGTP--SRDHTHYCYNCKR 320

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2091030 AT3G14250 [Arabidopsis thaliana (taxid:3702)]

 Score = 620 (223.3 bits), Expect = 1.5e-60, P = 1.5e-60
 Identities = 109/231 (47%), Positives = 158/231 (68%)

Query:    18 QELVRFSMTENEM-ASSTRSETSRSFVCEICVETKLRNESF-SIKGCSHMYCVDCTVKYV 75
             + LV     E E+ A +   E SR  +C IC++ K  ++ F     C+H YC DCTV+YV
Sbjct:    69 RNLVTLVKQEPEIKAENEPMEPSRR-LCMICMDEKPSSDIFRGTTNCTHAYCTDCTVRYV 127

Query:    76 DSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKD 135
              +K++EN + I CP  +C   +EP  CRD++P++ FD+W K LCESLI    KFYCPFKD
Sbjct:   128 ATKIKENASRIKCPDVECTRLIEPYTCRDLIPKDVFDRWEKILCESLISSWDKFYCPFKD 187

Query:   136 CSALLIDDA-GEA-IRESECPNCHRLFCAQCKVAWHAGIECADFQKL---HKDEPESEDI 190
             CSA+++++  G+A + ++EC +CHRLFC QCKV WHAGI C +FQ+     K   + +D 
Sbjct:   188 CSAMMVNNENGDANVTQTECRSCHRLFCVQCKVTWHAGIGCDEFQRFGNTKKKSSDEDDA 247

Query:   191 ILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSH 241
             +L+++A+N++W RCP+CKFYV+K +GC +I+CRCG+ FCY CG   S+ SH
Sbjct:   248 LLIQMAKNKQWRRCPSCKFYVDKVEGCQHIKCRCGYQFCYGCGSVWSS-SH 297

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2085612 AT3G45540 [Arabidopsis thaliana (taxid:3702)]

 Score = 394 (143.8 bits), Expect = 1.3e-36, P = 1.3e-36
 Identities = 71/216 (32%), Positives = 119/216 (55%)

Query:    37 ETSRSFVCEICVETKLR-NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95
             + +R   C+IC++  +  N+ F +  C H +C DC  ++++ +L E  + + CP   C  
Sbjct:    93 KATRKTTCKICLDDDINENQMFCVGKCRHRFCSDCMRRHIEVRLLEG-SVMRCPHYRCKT 151

Query:    96 SLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLID-DAGEAIRESE-- 152
             +L+   C ++L  +  + W + + E LIP   + YCP   CSAL+ + +   + +E E  
Sbjct:   152 TLKFGGCINLLTPKIREMWQQRIKEDLIPVTGRIYCPNSRCSALMSETELSISTKEDEVR 211

Query:   153 --CPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFY 210
               C  C ++FC +CKV+WH+ + C D++KL+   P   D  +  LA  ++W +C  C+  
Sbjct:   212 RCCFKCGQIFCIKCKVSWHSNLSCNDYKKLNP-YPTENDGKIKALANQKRWRQCGKCQHM 270

Query:   211 VEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCP 246
             +E   GC  ++CRCGH FCY CGVQ     HG+  P
Sbjct:   271 IELSKGCVQVKCRCGHKFCYRCGVQAGGCKHGHGLP 306

GO:0008270 "zinc ion binding" evidence=IEA

GO:0048446 "petal morphogenesis" evidence=RCA

TAIR|locus:2151689 AT5G37560 [Arabidopsis thaliana (taxid:3702)]

 Score = 385 (140.6 bits), Expect = 1.2e-35, P = 1.2e-35
 Identities = 75/218 (34%), Positives = 112/218 (51%)

Query:    35 RSETSRSFVCEICVETKLRNESFSIKG-CSHMYCVDCTVKYVDSKLQENVTSIGCPVTDC 93
             ++   +   C IC + K   E   +   C H +C  C  + V  KL+  +    C    C
Sbjct:   172 KATQEKPLTCSICSD-KTDAEHMLLNDKCLHRHCFSCVKQQVKVKLRSGIVP-PCLEDGC 229

Query:    94 GGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESE- 152
                L  E C  +L  +  + W + + E LIP A+K YCP++ CS L+     E  RE+E 
Sbjct:   230 KSELTLESCSMVLTPKLIEMWKRKMEEDLIPDAEKIYCPYRSCSMLM--SKTELSREAEQ 287

Query:   153 -----CPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNC 207
                  C  C  LFC  CKV WH+ + CAD++++H +   + D++L  LA +Q W +C  C
Sbjct:   288 SNVRACIKCSELFCIDCKVPWHSDLSCADYKRIHSERLVN-DMMLKVLANDQMWRQCSEC 346

Query:   208 KFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYC 245
             K  +E  +GC++I CRCG+ FCY CG +  T  H Y C
Sbjct:   347 KHMIELTEGCNHITCRCGYEFCYRCGHKW-TKYHHYSC 383

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2143995 AT5G60250 [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 7.8e-35, P = 7.8e-35
 Identities = 69/201 (34%), Positives = 104/201 (51%)

Query:    44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103
             C IC    +    FS+  C H +C  C  ++V+ KL   +    CP   C   L  + C 
Sbjct:   301 CAICFNDIVAEGMFSVDKCRHRFCFQCVKQHVEVKLLHGMAP-KCPHDGCKSELVIDACG 359

Query:   104 DILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALL----IDDAGEAIRE-------SE 152
              +L  +    W + L E+ IP  ++ YCP+  CSAL+    I ++ +++           
Sbjct:   360 KLLTPKLSKLWQQRLQENAIPVTERVYCPYPRCSALMSKTKISESAKSLLSLYPKSGVRR 419

Query:   153 CPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVE 212
             C  C  LFC  CKV WH  + C +++KLH  EP ++D+ L  LA N+ W +C  C+  +E
Sbjct:   420 CVECRGLFCVDCKVPWHGNLSCTEYKKLHP-EPPADDVKLKSLANNKMWRQCGKCQHMIE 478

Query:   213 KKDGCSYIRCRCGHAFCYHCG 233
                GC++I CRCGH FCY+CG
Sbjct:   479 LSQGCNHITCRCGHEFCYNCG 499

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2085622 AT3G45470 [Arabidopsis thaliana (taxid:3702)]

 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 69/195 (35%), Positives = 107/195 (54%)

Query:    44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103
             C IC+E    +  F +  C H +C  C  + V+ KL+ N T   C   +C   L  E C 
Sbjct:     6 CVICLEETKADRMFVMDKCLHRHCYPCVNQLVEVKLR-NGTVPTCLDYECKLKLSLENCF 64

Query:   104 DILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLID-DAGEAIRESE--CPNCHRLF 160
              +L  +  + W   + E  IP A++ YCP+ +CS L+   +   + + ++  C  C  L 
Sbjct:    65 KVLKPKVIELWKHMMKEESIPLAKRIYCPYINCSTLMSKTEISRSNKSNDRACIKCSGLV 124

Query:   161 CAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYI 220
             C  CKV WH+ + CA+++KLH D P  +D+ L  LA +QKW +C  C+  +E   GC+++
Sbjct:   125 CIDCKVPWHSDLSCAEYKKLHPD-PVLDDLTLKLLANDQKWRQCVKCRHLIELNQGCNHM 183

Query:   221 RCRCGHAFCYHCGVQ 235
              CRCG+ FCY CGV+
Sbjct:   184 TCRCGYQFCYKCGVE 198

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2133935 AT4G19670 [Arabidopsis thaliana (taxid:3702)]

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 75/206 (36%), Positives = 102/206 (49%)

Query:    44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103
             C IC E +      S+K C+H +C  C   YV+ K++ +   I CP   C   L    C+
Sbjct:   207 CSICCEDRQSEMMLSLK-CTHKFCSHCMKTYVEGKVKTSEVPIRCPQVQCKHYLSAAECK 265

Query:   104 DILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDD----AGEAIRES-------- 151
               LP   F  + +A   S   G  K YCP+ +CS LL       +G A   S        
Sbjct:   266 SFLPVTTFKSFEEANVCSKNNG--KIYCPYPNCSFLLDPQECLSSGRASSSSSTQSENSC 323

Query:   152 --ECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKF 209
               ECP C R  C  C V WHA + C +FQ L  DE   +DI L +LA+ ++W RC  C+ 
Sbjct:   324 CVECPVCERFVCVDCGVPWHASMSCEEFQILPVDERYPDDITLHRLARYKRWRRCQQCRI 383

Query:   210 YVEKKDGCSYIRCRCGHAFCYHCGVQ 235
              +E   GC+++ CRCGH FCY CG +
Sbjct:   384 MIELAQGCNHMTCRCGHEFCYSCGAE 409

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2040065 AT2G25360 [Arabidopsis thaliana (taxid:3702)]

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 70/220 (31%), Positives = 113/220 (51%)

Query:    21 VRFSMTENEMASSTRSETSRSFVCEICVE-TKLRNESFSIKGCSHMYCVDCTVKYVDSKL 79
             V F+      A  +R +  ++ +C IC E T+     F+ + C H +C  C  +YV+ KL
Sbjct:    68 VNFAFKLAREAIVSRDDV-KAEICSICFEETEGERMFFTTEKCVHRHCFPCVKQYVEVKL 126

Query:    80 QENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSAL 139
                     C    C   L  E C  +L  E  + W + + E  IP A++ YCP+ +CS L
Sbjct:   127 LSGTVPT-CLDDGCKFKLTLESCSKVLTLELIEMWKQKMKEDSIPAAERIYCPYPNCSML 185

Query:   140 L----IDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKL 195
             +    +    +   +  C  C  LFC  CKV  H+ + CA+++KLH D P  +++ L  L
Sbjct:   186 MSKTELSSESDLSNDRSCVKCCGLFCIDCKVPSHSDLSCAEYKKLHHD-PLVDELKLKSL 244

Query:   196 AQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQ 235
             A+++KW +C  C+  +E    C+++ CRCG+ FCY C V+
Sbjct:   245 AKDKKWRQCKMCRHMIELSHACNHMTCRCGYQFCYQCEVE 284

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:1006230127 AT2G26135 [Arabidopsis thaliana (taxid:3702)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 68/203 (33%), Positives = 101/203 (49%)

Query:    44 CEICVETKLRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102
             C IC +  +  +  F I  C HM+C +C  ++++  L +  + I CP   C   L    C
Sbjct:   153 CTICFDDDINADMMFYIDQCGHMFCSECVKRHIEVSLLQG-SLITCPSYRCKSKLTYGSC 211

Query:   103 RDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESE--CPNCHRLF 160
              +IL  +  + W + + E  IP   + YCP   CSAL+     + +  S+  C  C   F
Sbjct:   212 VNILTPKVKEMWIQRMGEDSIPVTDRVYCPNPTCSALMSVTELDQLTGSKRCCVKCGESF 271

Query:   161 CAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYI 220
             C +CKV WH  + C  ++KLH +   + D  L +LA  + W +C  CK  +E   GC  +
Sbjct:   272 CIKCKVPWHDNLSCKRYKKLHSNRT-TNDKQLNELANQESWRQCSKCKHMIELTQGCVRV 330

Query:   221 RCRCGHAFCYHCGVQLSTVSHGY 243
              CRCGH FCY CG      SHG+
Sbjct:   331 ICRCGHEFCYGCGADAGCCSHGH 353

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=ISS

TAIR|locus:2050100 AT2G21420 [Arabidopsis thaliana (taxid:3702)]

 Score = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 75/212 (35%), Positives = 104/212 (49%)

Query:    44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103
             C IC E    +  F  + C H  C  C  ++V   L   ++   C    C   L  E C 
Sbjct:   187 CCICRENTDADRMFFTENCFHRQCFSCVNRHVQRMLLCGISPT-CLHFPCNSELTFESCS 245

Query:   104 DILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESE------CPNCH 157
              +L     + W + + E L+P A K YCP++ CS L+   A    RE++      C  C 
Sbjct:   246 KVLTPNLIEFWKRKIEEDLVPAADKIYCPYRRCSMLMSKTA--LSRETDQSNVRACIKCC 303

Query:   158 RLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGC 217
             RLFC  CKV  HAG+ C D++KL+ D P   D+ L  LA  +KW +C  C   VE  +GC
Sbjct:   304 RLFCIDCKVPSHAGLSCVDYKKLNPD-P-LYDVKLKSLANKKKWRQCVQCSNLVELFEGC 361

Query:   218 SYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN 249
             ++I CRCG  FCY CG + +    G   P C+
Sbjct:   362 NHITCRCGFEFCYVCGKEWN--QRGCLSPGCD 391

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00016368001 SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (329 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	250
smart00647	64	smart00647, IBR, In Between Ring fingers	2e-09
pfam01485	63	pfam01485, IBR, IBR domain	5e-04

>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 112 DKWGKALCESLIP-GAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHA 170
           +K+ + L ES +       +CP  DCSA +I    E      CP C   FC +CKV WH+
Sbjct: 1   EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60

Query: 171 GIEC 174
            + C
Sbjct: 61  PVSC 64

the domains occurs between pairs og RING fingers. Length = 64

>gnl|CDD|216524 pfam01485, IBR, IBR domain

 Score = 37.2 bits (86), Expect = 5e-04
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 130 YCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIEC 174
           +CP  DC  ++    G + +   C  C   FC  CK  WH G+ C
Sbjct: 20  WCPTPDCGNIIEKTDGGS-QNVTCSKCGTEFCFSCKEPWHEGLTC 63

The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease. Length = 63

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	250
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	99.96
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	99.92
smart00647	64	IBR In Between Ring fingers. the domains occurs be	99.21
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	99.21
smart00647	64	IBR In Between Ring fingers. the domains occurs be	98.52
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.5
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.47
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	98.46
PF14634	44	zf-RING_5: zinc-RING finger domain	98.46
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.45
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.38
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.37
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.32
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.15
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	97.98
PHA02926	242	zinc finger-like protein; Provisional	97.85
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	97.8
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	97.75
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.74
PHA02929	238	N1R/p28-like protein; Provisional	97.69
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	97.62
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	97.57
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	97.48
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
KOG4367	699	consensus Predicted Zn-finger protein [Function un	97.33
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	97.24
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.21
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.1
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	96.75
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	96.72
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	96.56
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.45
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	96.43
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.4
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.23
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	96.1
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.05
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	95.7
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	95.36
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.06
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	94.85
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	94.82
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	94.73
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.61
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	94.39
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	94.26
PF14634	44	zf-RING_5: zinc-RING finger domain	93.82
KOG2660	331	consensus Locus-specific chromosome binding protei	93.52
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	93.5
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.34
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	93.31
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	93.28
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	93.22
KOG4739	233	consensus Uncharacterized protein involved in syna	93.14
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	93.01
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	92.86
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	92.67
COG5152	259	Uncharacterized conserved protein, contains RING a	92.35
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	92.29
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	92.25
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	92.13
PF12773	50	DZR: Double zinc ribbon	92.01
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	91.91
smart00661	52	RPOL9 RNA polymerase subunit 9.	91.83
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	91.73
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	91.67
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	91.5
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	91.47
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	91.38
PF13248	26	zf-ribbon_3: zinc-ribbon domain	91.21
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	90.98
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	90.93
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	90.73
PHA00626	59	hypothetical protein	90.6
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	90.45
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	90.41
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	89.91
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	89.88
PRK14714	1337	DNA polymerase II large subunit; Provisional	89.85
KOG3039	303	consensus Uncharacterized conserved protein [Funct	89.8
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	89.75
PRK04023	1121	DNA polymerase II large subunit; Validated	89.54
PRK00432	50	30S ribosomal protein S27ae; Validated	89.45
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	89.38
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	89.34
KOG0297	391	consensus TNF receptor-associated factor [Signal t	89.06
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	88.79
PLN03086	567	PRLI-interacting factor K; Provisional	88.65
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	88.21
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	87.98
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	87.84
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	87.59
KOG4445	368	consensus Uncharacterized conserved protein, conta	87.38
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	87.37
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	87.34
COG1198	730	PriA Primosomal protein N' (replication factor Y)	87.25
KOG2807	378	consensus RNA polymerase II transcription initiati	87.24
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	87.12
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	86.88
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	86.8
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	86.78
smart00661	52	RPOL9 RNA polymerase subunit 9.	86.77
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	86.6
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	86.46
PF14952	44	zf-tcix: Putative treble-clef, zinc-finger, Zn-bin	86.2
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	85.91
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	85.88
COG5175	480	MOT2 Transcriptional repressor [Transcription]	85.85
PF10601	73	zf-LITAF-like: LITAF-like zinc ribbon domain; Inte	85.66
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	85.65
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	85.33
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	85.33
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	85.26
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	85.23
PRK14559	645	putative protein serine/threonine phosphatase; Pro	85.04
PF03833	900	PolC_DP2: DNA polymerase II large subunit DP2; Int	84.97
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	84.6
PRK14873	665	primosome assembly protein PriA; Provisional	84.55
PF04641	260	Rtf2: Rtf2 RING-finger	84.53
PF15616	131	TerY-C: TerY-C metal binding domain	84.44
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	83.88
PHA03096	284	p28-like protein; Provisional	82.37
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	81.89
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	81.43
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	80.26
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	80.05

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

Probab=100.00  E-value=1.1e-36  Score=263.96  Aligned_cols=199  Identities=37%  Similarity=0.877  Sum_probs=169.6

Q ss_pred             CceecccCcccc-cCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHH
Q 025608           40 RSFVCEICVETK-LRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL  118 (250)
Q Consensus        40 ~~~~C~iC~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~  118 (250)
                      ...+|.||+.+. ..+.++....|+|.||.+|+++|++.+ ..+...++||..+|...++.+....+|++.+.++|.+.+
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~-~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~  223 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK-LLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRL  223 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh-hccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHH
Confidence            456899999554 444667678999999999999999998 445688999999999999999999999999999999999


Q ss_pred             HhhccCCCCeecCCCCCCCCceecCc---cCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHH
Q 025608          119 CESLIPGAQKFYCPFKDCSALLIDDA---GEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKL  195 (250)
Q Consensus       119 ~~~~~~~~~~~~Cp~~~C~~~~~~~~---~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~  195 (250)
                      .+.++...+.++||.|+|...+....   ........|+.|+..||.+|+.+||.+++|++++++....... +..+..+
T Consensus       224 ~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d-~~~~~~l  302 (384)
T KOG1812|consen  224 KEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVD-DITLKYL  302 (384)
T ss_pred             HHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCccccc-HHHHHHH
Confidence            99999988878999999998877653   2345667899999999999999999999999999987644322 2222333


Q ss_pred             HhcCCCccCCCCCcceeccCCCcceEEeccccccccccccccCCCCC
Q 025608          196 AQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHG  242 (250)
Q Consensus       196 ~~~~~~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~  242 (250)
                      +  ..|+.||+|+..|++.+|||||+|+||++|||.|+.+|.++.+.
T Consensus       303 a--~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~  347 (384)
T KOG1812|consen  303 A--KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGE  347 (384)
T ss_pred             H--HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCcc
Confidence            3  78899999999999999999999999999999999999866664

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

Probab=100.00  E-value=7.6e-36  Score=249.93  Aligned_cols=208  Identities=26%  Similarity=0.649  Sum_probs=169.4

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcC-cccccCCCCCCCCCCCHHHHhccCChHHHHHH
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQEN-VTSIGCPVTDCGGSLEPEYCRDILPEEAFDKW  114 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~  114 (250)
                      ......+.|.|||+......-+..++|+|.||+.|++.|+...|.+| ...++||+.+|+..-....++.+|+.+++++|
T Consensus       179 ~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arY  258 (445)
T KOG1814|consen  179 KFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARY  258 (445)
T ss_pred             HHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHH
Confidence            44566789999999998877788889999999999999999999997 58999999999999999999999999999999


Q ss_pred             HHHHHhhccCC-CCeecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHh--------hhccCCC
Q 025608          115 GKALCESLIPG-AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQ--------KLHKDEP  185 (250)
Q Consensus       115 ~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~--------~~~~~~~  185 (250)
                      ++++.+.++.. .+.++||.+.|+.+...+++  ...+.|..|+..||..|+..||++..|.--.        .+.....
T Consensus       259 e~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~--~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~  336 (445)
T KOG1814|consen  259 EKLMLQKTLELMSDVVYCPRACCQLPVKQDPG--RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADE  336 (445)
T ss_pred             HHHHHHHHHHhhcccccCChhhccCccccCch--hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCH
Confidence            99999888876 56679999999999855544  3668999999999999999999999996431        1111111


Q ss_pred             ch------------HHHHHHHHH----hcCCCccCCCCCcceeccCCCcceEE-ecccccccccccccc---CCCCCcCC
Q 025608          186 ES------------EDIILMKLA----QNQKWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLS---TVSHGYYC  245 (250)
Q Consensus       186 ~~------------~~~~~~~~~----~~~~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~---~~~h~~~~  245 (250)
                      .+            ...++++++    -..+.++||+|+++|+|++|||+|+| +|++.|||+|...+.   ++.|+.+=
T Consensus       337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~  416 (445)
T KOG1814|consen  337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP  416 (445)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence            10            011122222    12466999999999999999999999 999999999987773   56786543

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

Probab=99.96  E-value=1.7e-29  Score=224.77  Aligned_cols=203  Identities=27%  Similarity=0.593  Sum_probs=165.0

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcc-cccCCCCCCCCCCCHHHHhccCCh-HHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVT-SIGCPVTDCGGSLEPEYCRDILPE-EAFDKWGK  116 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~-~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~~  116 (250)
                      ....+|.||++..+.  ......|+|.||..||..|+...|.++.. .|+||..+|...+..+.|..++++ +..++|.+
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~  145 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQR  145 (444)
T ss_pred             CccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHH
Confidence            455789999998876  34456999999999999999999988632 399999999999999999999988 59999999


Q ss_pred             HHHhhccCCCC-eecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHH
Q 025608          117 ALCESLIPGAQ-KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKL  195 (250)
Q Consensus       117 ~~~~~~~~~~~-~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~  195 (250)
                      .+..+++.... ..|||+|+|+..+... ......+.| .|+..||+.|..+||++.+|.....|.+......+...   
T Consensus       146 ~i~~syve~~~~lkwCP~~~C~~av~~~-~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~---  220 (444)
T KOG1815|consen  146 YILRSYVEDNVPLKWCPAPGCGLAVKFG-SLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN---  220 (444)
T ss_pred             HHHHHHHhcCCccccCCCCCCCceeecc-CCCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh---
Confidence            99999998755 4599999999988864 233466888 56669999999999999999998887665433322211   


Q ss_pred             HhcCCCccCCCCCcceeccCCCcceEE-e--ccccccccccccccCCCCCcC-CCCCCC
Q 025608          196 AQNQKWNRCPNCKFYVEKKDGCSYIRC-R--CGHAFCYHCGVQLSTVSHGYY-CPSCNK  250 (250)
Q Consensus       196 ~~~~~~~~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~~~h~~~-~~~~~~  250 (250)
                      ....+.++||+|.++|+|++|||||+| .  |+++|||+|+..|.  .|++. .+.|||
T Consensus       221 wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~--~h~~~~~~~c~~  277 (444)
T KOG1815|consen  221 WILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLS--DHGSSTGYSCNR  277 (444)
T ss_pred             hhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccc--cccccceeeeee
Confidence            234556889999999999999999999 5  99999999999996  44333 667764

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=99.92  E-value=1.3e-25  Score=182.52  Aligned_cols=204  Identities=27%  Similarity=0.614  Sum_probs=152.6

Q ss_pred             ccCCCCceecccCcccccCCCceecCCCC--CcchHHHHHHHHHHHhhcCc--------ccccCCCCCCCCCCCHH-HHh
Q 025608           35 RSETSRSFVCEICVETKLRNESFSIKGCS--HMYCVDCTVKYVDSKLQENV--------TSIGCPVTDCGGSLEPE-YCR  103 (250)
Q Consensus        35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~--------~~i~CP~~~C~~~l~~~-~i~  103 (250)
                      ...+.+..+|-.|-+.-.+   ...++|.  |..|.+|++.|....+++..        ..+.||. +|...+-.+ .--
T Consensus       215 i~~N~~ni~C~~Ctdv~~~---vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF  290 (446)
T KOG0006|consen  215 IATNSRNITCITCTDVRSP---VLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHF  290 (446)
T ss_pred             hhcccccceeEEecCCccc---eEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhh
Confidence            4566778899999875443   2234888  99999999999999987743        4678885 777665444 345


Q ss_pred             ccCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCc-ccchhccccCcccCCCCCchhHhh---
Q 025608          104 DILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPN-CHRLFCAQCKVAWHAGIECADFQK---  179 (250)
Q Consensus       104 ~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~---  179 (250)
                      .+|+.+.+.+|++...+..+...+.+.||.|+|+..+...++  ..++.|+. |++.||..|...+|.|. |.+.-.   
T Consensus       291 ~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD--~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~  367 (446)
T KOG0006|consen  291 RILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD--QRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASG  367 (446)
T ss_pred             eecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC--CCcccCCCCchhHhHHHHHhhhcccc-ceeeecccc
Confidence            789999999999999999999999999999999998887763  57899987 99999999999999884 442110   


Q ss_pred             -----hccCCCchHHHH---HHHHHhcCCCccCCCCCcceeccCCCcceEE-e--ccccccccccccccCCCCCcCC
Q 025608          180 -----LHKDEPESEDII---LMKLAQNQKWNRCPNCKFYVEKKDGCSYIRC-R--CGHAFCYHCGVQLSTVSHGYYC  245 (250)
Q Consensus       180 -----~~~~~~~~~~~~---~~~~~~~~~~~~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~~~h~~~~  245 (250)
                           ..-++...+.+.   .....-+..+|+||+|.++.||+|||-||.| .  ||.+|||.|+-+|+-.--+-+|
T Consensus       368 t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~CmgdHW  444 (446)
T KOG0006|consen  368 TTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGDHW  444 (446)
T ss_pred             ccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhccccc
Confidence                 011111111111   1112223567999999999999999999999 4  9999999999999644333333

>smart00647 IBR In Between Ring fingers

Probab=99.21  E-value=1.2e-11  Score=80.65  Aligned_cols=63  Identities=37%  Similarity=0.839  Sum_probs=53.1

Q ss_pred             HHHHHHHHhhccCC-CCeecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCc
Q 025608          112 DKWGKALCESLIPG-AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIEC  174 (250)
Q Consensus       112 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C  174 (250)
                      ++|++++.+.++.. .+..|||+|+|+.++....+.....+.|+.|+..||+.|+.+||.+.+|
T Consensus         1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C   64 (64)
T smart00647        1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC   64 (64)
T ss_pred             ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence            46888888888876 4566999999999888864334578999999999999999999999987

the domains occurs between pairs og RING fingers

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.21  E-value=3.1e-12  Score=83.47  Aligned_cols=63  Identities=30%  Similarity=0.774  Sum_probs=41.4

Q ss_pred             HHHHHHHHhhccCCCCe-ecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCc
Q 025608          112 DKWGKALCESLIPGAQK-FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIEC  174 (250)
Q Consensus       112 ~~~~~~~~~~~~~~~~~-~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C  174 (250)
                      ++|++++.+.++..... .+||+|+|+.++..+++.....+.|+.|+..||+.|+.+||.|.+|
T Consensus         1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C   64 (64)
T PF01485_consen    1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC   64 (64)
T ss_dssp             HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred             ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence            46777777777765544 5999999999999987655445999999999999999999999886

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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>smart00647 IBR In Between Ring fingers

Probab=98.52  E-value=1.5e-07  Score=61.07  Aligned_cols=41  Identities=32%  Similarity=1.010  Sum_probs=36.7

Q ss_pred             cCCCccCC--CCCcceeccC--CCcceEE-eccccccccccccccC
Q 025608          198 NQKWNRCP--NCKFYVEKKD--GCSYIRC-RCGHAFCYHCGVQLST  238 (250)
Q Consensus       198 ~~~~~~CP--~C~~~i~k~~--GCnhm~C-~C~~~FC~~C~~~~~~  238 (250)
                      +..++.||  +|+.+|...+  |..+|+| .|++.|||.|+.+|+.
T Consensus        15 ~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~   60 (64)
T smart00647       15 NPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS   60 (64)
T ss_pred             CCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence            35778999  9999999975  9999999 9999999999999953

the domains occurs between pairs og RING fingers

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

Probab=98.50  E-value=6.5e-08  Score=57.93  Aligned_cols=41  Identities=27%  Similarity=0.652  Sum_probs=32.5

Q ss_pred             ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      +|+||++++..++.+..++|+|.||.+|+..|++..       ..||.
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~   42 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV   42 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence            599999999755555556899999999999999853       28886

...

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

Probab=98.47  E-value=7.2e-08  Score=56.94  Aligned_cols=41  Identities=22%  Similarity=0.577  Sum_probs=28.0

Q ss_pred             cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      |+||++.+..+.   .++|||.||.+|+.++++..-   ...+.||.
T Consensus         1 CpiC~~~~~~Pv---~l~CGH~FC~~Cl~~~~~~~~---~~~~~CP~   41 (42)
T PF15227_consen    1 CPICLDLFKDPV---SLPCGHSFCRSCLERLWKEPS---GSGFSCPE   41 (42)
T ss_dssp             ETTTTSB-SSEE---E-SSSSEEEHHHHHHHHCCSS---SST---SS
T ss_pred             CCccchhhCCcc---ccCCcCHHHHHHHHHHHHccC---CcCCCCcC
Confidence            899999887643   359999999999999997432   22388986

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.46  E-value=6.2e-08  Score=62.89  Aligned_cols=41  Identities=39%  Similarity=1.162  Sum_probs=29.5

Q ss_pred             cCCCccCCC--CCcceeccCCCcc--eEE-eccccccccccccccC
Q 025608          198 NQKWNRCPN--CKFYVEKKDGCSY--IRC-RCGHAFCYHCGVQLST  238 (250)
Q Consensus       198 ~~~~~~CP~--C~~~i~k~~GCnh--m~C-~C~~~FC~~C~~~~~~  238 (250)
                      ...++.||+  |+.++++.+|.++  |+| .|++.|||.|+.+|+.
T Consensus        15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~   60 (64)
T PF01485_consen   15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE   60 (64)
T ss_dssp             ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred             CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence            345589988  9999999999999  999 7999999999999953

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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.46  E-value=1.7e-07  Score=56.08  Aligned_cols=41  Identities=29%  Similarity=0.773  Sum_probs=35.0

Q ss_pred             ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      +|+||++.+.....+.+++|+|.||..|+....       ...+.||.
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~   41 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI   41 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC
Confidence            499999999656667788999999999999988       35688997

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

Probab=98.45  E-value=1.5e-07  Score=55.41  Aligned_cols=40  Identities=33%  Similarity=0.831  Sum_probs=32.7

Q ss_pred             cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      |+||++.+..+.  .+++|+|.||.+|+.+++..     ...+.||.
T Consensus         1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~   40 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLEN-----SGSVKCPL   40 (41)
T ss_dssp             ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHH-----TSSSBTTT
T ss_pred             CCcCCccccCCC--EEecCCCcchHHHHHHHHHh-----cCCccCCc
Confidence            799999876543  35799999999999999997     35567886

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 ....

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.38  E-value=3.6e-07  Score=71.36  Aligned_cols=69  Identities=20%  Similarity=0.507  Sum_probs=50.4

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhh---------cCcccccCCCCCCCCCCCHHHHhccC
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQ---------ENVTSIGCPVTDCGGSLEPEYCRDIL  106 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~i~CP~~~C~~~l~~~~i~~~l  106 (250)
                      ....+.++|+||++.+..+.   ...|+|.||..|+..|+...-.         .......||.  |...++...+..+.
T Consensus        13 ~~~~~~~~CpICld~~~dPV---vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiy   87 (193)
T PLN03208         13 VDSGGDFDCNICLDQVRDPV---VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIY   87 (193)
T ss_pred             ccCCCccCCccCCCcCCCcE---EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEee
Confidence            34456789999999876443   3589999999999999764311         1234679998  99999988877665


Q ss_pred             ChH
Q 025608          107 PEE  109 (250)
Q Consensus       107 ~~~  109 (250)
                      +..
T Consensus        88 grg   90 (193)
T PLN03208         88 GRG   90 (193)
T ss_pred             ccC
Confidence            443

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

Probab=98.37  E-value=3.5e-07  Score=54.05  Aligned_cols=42  Identities=29%  Similarity=0.672  Sum_probs=24.4

Q ss_pred             cccCcccc-cCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCC
Q 025608           44 CEICVETK-LRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCP   89 (250)
Q Consensus        44 C~iC~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   89 (250)
                      |+||.+ + ..+..+.+++|||.||.+|+.+.+....   ...|+||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence            899999 6 4455566779999999999999998443   3568887

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

Probab=98.32  E-value=4.7e-07  Score=52.66  Aligned_cols=38  Identities=32%  Similarity=0.927  Sum_probs=28.9

Q ss_pred             cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      |+||++.+..  .+.+++|||.||.+|+.+|++..       .+||.
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~   38 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKN-------PKCPV   38 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence            7999987765  33457999999999999998852       57775

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

Probab=98.24  E-value=1e-06  Score=67.17  Aligned_cols=57  Identities=18%  Similarity=0.607  Sum_probs=43.5

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR  103 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  103 (250)
                      .....+.|+||++.+.....+ ...|||.||..|++..+.       ...+||.  |+..|+..++-
T Consensus       127 ~~~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk-------~~~~CP~--C~kkIt~k~~~  183 (187)
T KOG0320|consen  127 RKEGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALK-------NTNKCPT--CRKKITHKQFH  183 (187)
T ss_pred             ccccccCCCceecchhhcccc-ccccchhHHHHHHHHHHH-------hCCCCCC--cccccchhhhe
Confidence            445568999999998765544 359999999999999887       3468998  66667666543

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

Probab=98.15  E-value=2.8e-06  Score=50.48  Aligned_cols=44  Identities=32%  Similarity=0.809  Sum_probs=33.2

Q ss_pred             ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC
Q 025608           43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS   96 (250)
Q Consensus        43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   96 (250)
                      +|+||++.+.  ....+.+|+|.||.+|+..|+..      ....||.  |+..
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp~--C~~~   44 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS------GKNTCPL--CRTP   44 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh------CcCCCCC--CCCc
Confidence            4899999873  33445579999999999999885      3457887  6643

>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=97.98  E-value=6.8e-06  Score=50.52  Aligned_cols=45  Identities=27%  Similarity=0.803  Sum_probs=33.9

Q ss_pred             eecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           42 FVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ..|.||++....   ..+.+|+|. ||.+|+.+++.       ....||.  |...++
T Consensus         3 ~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~-------~~~~CP~--Cr~~i~   48 (50)
T PF13920_consen    3 EECPICFENPRD---VVLLPCGHLCFCEECAERLLK-------RKKKCPI--CRQPIE   48 (50)
T ss_dssp             SB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHH-------TTSBBTT--TTBB-S
T ss_pred             CCCccCCccCCc---eEEeCCCChHHHHHHhHHhcc-------cCCCCCc--CChhhc
Confidence            569999997543   345699999 99999999998       3468998  776654

...

>PHA02926 zinc finger-like protein; Provisional

Probab=97.85  E-value=1.6e-05  Score=63.07  Aligned_cols=57  Identities=26%  Similarity=0.708  Sum_probs=40.1

Q ss_pred             CCceecccCcccccC-----CCce-ecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           39 SRSFVCEICVETKLR-----NESF-SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~-----~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ++..+|+||++....     +..| .+.+|+|.||..|+..|..... +....-.||.  |...+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~-~~~~~rsCPi--CR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR-ETGASDNCPI--CRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc-ccCcCCcCCC--Ccceee
Confidence            445689999997521     2222 3669999999999999998653 2234457998  776543

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

Probab=97.80  E-value=1.2e-05  Score=64.22  Aligned_cols=60  Identities=22%  Similarity=0.624  Sum_probs=46.9

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccC
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDIL  106 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l  106 (250)
                      +...|+|.||++....+.   +.-|||.||..||-+|+..+..    .-.||.  |+..++.+.+--+.
T Consensus        44 ~~~~FdCNICLd~akdPV---vTlCGHLFCWpClyqWl~~~~~----~~~cPV--CK~~Vs~~~vvPlY  103 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPV---VTLCGHLFCWPCLYQWLQTRPN----SKECPV--CKAEVSIDTVVPLY  103 (230)
T ss_pred             CCCceeeeeeccccCCCE---EeecccceehHHHHHHHhhcCC----CeeCCc--cccccccceEEeee
Confidence            577899999999776544   3489999999999999996644    236788  88888887766554

>smart00184 RING Ring finger

Probab=97.75  E-value=3.4e-05  Score=44.00  Aligned_cols=38  Identities=29%  Similarity=0.795  Sum_probs=28.2

Q ss_pred             cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      |+||++...   ....++|+|.||..|+..|+.      .....||.
T Consensus         1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~------~~~~~CP~   38 (39)
T smart00184        1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLK------SGNNTCPI   38 (39)
T ss_pred             CCcCccCCC---CcEEecCCChHHHHHHHHHHH------hCcCCCCC
Confidence            789988732   244569999999999999988      12356775

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)

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

Probab=97.74  E-value=4.1e-05  Score=65.11  Aligned_cols=108  Identities=19%  Similarity=0.447  Sum_probs=67.8

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL  118 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~  118 (250)
                      .+.+.|+||++.+..+   .+++|+|.||..|+...+.       ..+.||.  |.. ...    .+.....+.......
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~~~~   73 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCPV--CRP-PSR----NLRPNVLLANLVERL   73 (386)
T ss_pred             cccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCcc--cCC-chh----ccCccHHHHHHHHHH
Confidence            4567899999999876   4569999999999999998       4589998  663 211    222333333333333


Q ss_pred             HhhccCCCC---eecCCCCCCCCceecCccCccCcccCCcccchhccccC-cccCCCCCc
Q 025608          119 CESLIPGAQ---KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCK-VAWHAGIEC  174 (250)
Q Consensus       119 ~~~~~~~~~---~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C  174 (250)
                      ....+....   ...|+.          . .....+.|..|...+|..|. ...|.++.-
T Consensus        74 ~~~~~~~~~~~~~~~c~~----------~-~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~  122 (386)
T KOG2177|consen   74 RQLRLSRPLGSKEELCEK----------H-GEELKLFCEEDEKLLCVLCRESGEHRGHPV  122 (386)
T ss_pred             HhcCCcccccccchhhhh----------c-CCcceEEecccccccCCCCCCcccccCCcc
Confidence            322111111   113331          1 11145778899999999998 566777643

>PHA02929 N1R/p28-like protein; Provisional

Probab=97.69  E-value=4.4e-05  Score=62.27  Aligned_cols=51  Identities=27%  Similarity=0.703  Sum_probs=37.3

Q ss_pred             CCceecccCcccccCCC-----ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           39 SRSFVCEICVETKLRNE-----SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ....+|+||++.+..+.     +..+.+|+|.||.+|+..|+..       .-.||.  |...+.
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCPl--CR~~~~  227 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCPV--CRTPFI  227 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCCC--CCCEee
Confidence            34568999999875432     2345689999999999999863       237998  776543

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

Probab=97.62  E-value=2.7e-05  Score=68.86  Aligned_cols=59  Identities=20%  Similarity=0.589  Sum_probs=46.1

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccC
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDIL  106 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l  106 (250)
                      ...||||++..+...   +..|||.||..||.+|+...  .-..+-.||.  |...+.+.++..+.
T Consensus       186 ~~~CPICL~~~~~p~---~t~CGHiFC~~CiLqy~~~s--~~~~~~~CPi--C~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPV---RTNCGHIFCGPCILQYWNYS--AIKGPCSCPI--CRSTITLKDLLPVF  244 (513)
T ss_pred             CCcCCcccCCCCccc---ccccCceeeHHHHHHHHhhh--cccCCccCCc--hhhhccccceeeee
Confidence            678999998766543   34799999999999999977  2235778998  99888887665543

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

Probab=97.57  E-value=4.2e-05  Score=62.92  Aligned_cols=52  Identities=23%  Similarity=0.758  Sum_probs=40.1

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR  103 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  103 (250)
                      ....|.+|++....+.   ..+|||.||.+|+..|....-       .||.  |...+.+..+-
T Consensus       238 a~~kC~LCLe~~~~pS---aTpCGHiFCWsCI~~w~~ek~-------eCPl--CR~~~~pskvi  289 (293)
T KOG0317|consen  238 ATRKCSLCLENRSNPS---ATPCGHIFCWSCILEWCSEKA-------ECPL--CREKFQPSKVI  289 (293)
T ss_pred             CCCceEEEecCCCCCC---cCcCcchHHHHHHHHHHcccc-------CCCc--ccccCCCccee
Confidence            3457999999875543   459999999999999998542       2998  88887776543

>smart00504 Ubox Modified RING finger domain

Probab=97.48  E-value=0.00015  Score=46.57  Aligned_cols=51  Identities=25%  Similarity=0.258  Sum_probs=39.5

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD  104 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  104 (250)
                      +.|+||.+.+..+   ...+|||.||++|+.+|+..       ...||.  |+..++.+++..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~-------~~~cP~--~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLS-------HGTDPV--TGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHH-------CCCCCC--CcCCCChhhcee
Confidence            4699999987754   23599999999999999985       247897  777777665543

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

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

Probab=97.33  E-value=0.00019  Score=61.45  Aligned_cols=46  Identities=28%  Similarity=0.628  Sum_probs=38.3

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCC
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDC   93 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C   93 (250)
                      .+|.||+|++...+-...++|.|.|...|+..|+...      .-.||.+++
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPvCK~  275 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPVCKR  275 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCCCCC
Confidence            6899999999877777778999999999999999955      125998333

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

Probab=97.33  E-value=0.00011  Score=63.77  Aligned_cols=86  Identities=17%  Similarity=0.393  Sum_probs=54.1

Q ss_pred             CccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCCccCCCCCcceeccCCCcc-eEE-e
Q 025608          146 EAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSY-IRC-R  223 (250)
Q Consensus       146 ~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C~~~i~k~~GCnh-m~C-~  223 (250)
                      +....+.|..|...+|.-|+..-|++..=-....+.....++.    .....-.++.+|-       ..+|=|| |.| .
T Consensus       172 ~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grv----s~~~s~r~~~~ct-------~h~~e~~smyc~~  240 (699)
T KOG4367|consen  172 PKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRV----SRRLSPRKVSTCT-------DHELENHSMYCVQ  240 (699)
T ss_pred             hhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCce----eeccchhhhhhcc-------CCCCCCceEEEEe
Confidence            3456789999999999999998888753222223333222221    1111111223342       1244455 999 9


Q ss_pred             ccccccccccccccCCCCC
Q 025608          224 CGHAFCYHCGVQLSTVSHG  242 (250)
Q Consensus       224 C~~~FC~~C~~~~~~~~h~  242 (250)
                      |+...||.|+.+.+..+|-
T Consensus       241 ck~pvc~~clee~khs~he  259 (699)
T KOG4367|consen  241 CKMPVCYQCLEEGKHSSHE  259 (699)
T ss_pred             cCChHHHHHHHhhcccchh
Confidence            9999999999999877773

>TIGR00599 rad18 DNA repair protein rad18

Probab=97.24  E-value=0.00028  Score=61.77  Aligned_cols=66  Identities=21%  Similarity=0.507  Sum_probs=45.7

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH-hccCChHHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC-RDILPEEAFDKWGK  116 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i-~~~l~~~~~~~~~~  116 (250)
                      ...+.|+||.+.+..+.   +.+|+|.||..|+..++...       ..||.  |...+....+ .+.+-.++++.|..
T Consensus        24 e~~l~C~IC~d~~~~Pv---itpCgH~FCs~CI~~~l~~~-------~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~   90 (397)
T TIGR00599        24 DTSLRCHICKDFFDVPV---LTSCSHTFCSLCIRRCLSNQ-------PKCPL--CRAEDQESKLRSNWLVSEIVESFKN   90 (397)
T ss_pred             ccccCCCcCchhhhCcc---CCCCCCchhHHHHHHHHhCC-------CCCCC--CCCccccccCccchHHHHHHHHHHH
Confidence            44568999999886543   45999999999999998631       37997  8877665433 23333455555543

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

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

Probab=97.21  E-value=0.00024  Score=58.87  Aligned_cols=56  Identities=29%  Similarity=0.719  Sum_probs=43.6

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .+.....+|.||++++.-.+-...++|.|.|.+.|+.+|+...      ..+||.  |...+++
T Consensus       318 ~ea~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y------~~~CPv--Crt~iPP  373 (374)
T COG5540         318 VEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGY------SNKCPV--CRTAIPP  373 (374)
T ss_pred             HhcCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhh------cccCCc--cCCCCCC
Confidence            4556678999999999644445667999999999999999833      458998  8776653

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.10  E-value=0.0012  Score=55.76  Aligned_cols=53  Identities=25%  Similarity=0.478  Sum_probs=36.7

Q ss_pred             eecccCccccc-CCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           42 FVCEICVETKL-RNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        42 ~~C~iC~~~~~-~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ..||+|..+.. .+.+ +....|||.||.+|+...+.    .  .+..||.  |+..+....+
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~--~~~~CP~--C~~~lrk~~f   58 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----R--GSGSCPE--CDTPLRKNNF   58 (309)
T ss_pred             CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----C--CCCCCCC--CCCccchhhc
Confidence            35999998642 2222 22227999999999999974    2  2348996  8887776553

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).

>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=96.75  E-value=0.00097  Score=44.34  Aligned_cols=41  Identities=22%  Similarity=0.600  Sum_probs=29.4

Q ss_pred             ecccCcccccCC----------CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           43 VCEICVETKLRN----------ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        43 ~C~iC~~~~~~~----------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      .|.||++++...          -.+....|+|.|...|+.+|++..       -.||.
T Consensus        21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~   71 (73)
T PF12678_consen   21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPL   71 (73)
T ss_dssp             BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TT
T ss_pred             cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCC
Confidence            399999998221          223355899999999999999733       17886

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 ....

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

Probab=96.72  E-value=0.00073  Score=44.51  Aligned_cols=57  Identities=19%  Similarity=0.412  Sum_probs=26.7

Q ss_pred             ceecccCccccc-CCCcee----cCCCCCcchHHHHHHHHHHHhhcCc--cc--ccCCCCCCCCCCCH
Q 025608           41 SFVCEICVETKL-RNESFS----IKGCSHMYCVDCTVKYVDSKLQENV--TS--IGCPVTDCGGSLEP   99 (250)
Q Consensus        41 ~~~C~iC~~~~~-~~~~~~----~~~C~H~fC~~Cl~~~~~~~i~~~~--~~--i~CP~~~C~~~l~~   99 (250)
                      ..+|+||++... ....+.    ...|+..|...||.+|+...-.+..  .+  =.||.  |...|+.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence            357999998864 322222    3478899999999999987655432  12  26997  8877654

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

Probab=96.56  E-value=0.0015  Score=55.08  Aligned_cols=62  Identities=26%  Similarity=0.516  Sum_probs=46.0

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc-cCChHHHHHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD-ILPEEAFDKWG  115 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~  115 (250)
                      +-|.||++.|..+.+   .+|+|.||.-|++.|+..+       -.||.  |...+....++. .+-.++++.|.
T Consensus        24 LRC~IC~eyf~ip~i---tpCsHtfCSlCIR~~L~~~-------p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~   86 (442)
T KOG0287|consen   24 LRCGICFEYFNIPMI---TPCSHTFCSLCIRKFLSYK-------PQCPT--CCVTVTESDLRNNRILDEIVKSLN   86 (442)
T ss_pred             HHHhHHHHHhcCcee---ccccchHHHHHHHHHhccC-------CCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence            359999999876543   4899999999999999843       35887  888888777753 33445555554

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

Probab=96.45  E-value=0.0022  Score=57.13  Aligned_cols=59  Identities=27%  Similarity=0.667  Sum_probs=44.2

Q ss_pred             ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      ..++....+|.+|-++..  +.+ ...|.|.||+-|++.|+.....+.  .+.||.  |...|+.+
T Consensus       530 ~~enk~~~~C~lc~d~ae--d~i-~s~ChH~FCrlCi~eyv~~f~~~~--nvtCP~--C~i~LsiD  588 (791)
T KOG1002|consen  530 PDENKGEVECGLCHDPAE--DYI-ESSCHHKFCRLCIKEYVESFMENN--NVTCPV--CHIGLSID  588 (791)
T ss_pred             CccccCceeecccCChhh--hhH-hhhhhHHHHHHHHHHHHHhhhccc--CCCCcc--cccccccc
Confidence            345667788999988654  323 349999999999999999775543  399998  77666655

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

Probab=96.43  E-value=0.0027  Score=51.85  Aligned_cols=53  Identities=25%  Similarity=0.612  Sum_probs=38.0

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ..+.|.||++....   +...+|||.||..|+...+..+     ..-.||.  |.....+..+
T Consensus       214 ~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~-----k~~~Cpl--CRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKK-----KYEFCPL--CRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccCC---cccccccchhhHHHHHHHHHhh-----ccccCch--hhhhccchhh
Confidence            35679999986543   4566999999999999954322     2336998  8877666655

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

Probab=96.40  E-value=0.0027  Score=39.97  Aligned_cols=50  Identities=24%  Similarity=0.529  Sum_probs=31.7

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG   94 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   94 (250)
                      ....+.|+|-...+..+  .....|+|.|-++-+..|+     .+...+.||..+|.
T Consensus         8 ~~~~~~CPiT~~~~~~P--V~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~   57 (57)
T PF11789_consen    8 GTISLKCPITLQPFEDP--VKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN   57 (57)
T ss_dssp             SB--SB-TTTSSB-SSE--EEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred             cEeccCCCCcCChhhCC--cCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence            34456899999887644  4456999999999999999     23467899998884

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

Probab=96.23  E-value=0.0011  Score=57.20  Aligned_cols=40  Identities=28%  Similarity=0.724  Sum_probs=37.0

Q ss_pred             CCCccCCC--CCcceeccCCCcceEE-eccccccccccccccC
Q 025608          199 QKWNRCPN--CKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLST  238 (250)
Q Consensus       199 ~~~~~CP~--C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~  238 (250)
                      .+++.||+  |..++....|.+-..| +|+..||..|...|++
T Consensus       271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG  313 (445)
T KOG1814|consen  271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG  313 (445)
T ss_pred             cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC
Confidence            46799998  9999988899999999 9999999999999965

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

Probab=96.10  E-value=0.0026  Score=59.16  Aligned_cols=56  Identities=20%  Similarity=0.596  Sum_probs=42.4

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .....|++|.+...  + ..+..|+|.||-+|++..+...-      =+||.  |+..|...++..+
T Consensus       641 K~~LkCs~Cn~R~K--d-~vI~kC~H~FC~~Cvq~r~etRq------RKCP~--Cn~aFganDv~~I  696 (698)
T KOG0978|consen  641 KELLKCSVCNTRWK--D-AVITKCGHVFCEECVQTRYETRQ------RKCPK--CNAAFGANDVHRI  696 (698)
T ss_pred             HhceeCCCccCchh--h-HHHHhcchHHHHHHHHHHHHHhc------CCCCC--CCCCCCccccccc
Confidence            45678999984322  2 23459999999999999988553      38997  9998988887654

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

Probab=96.05  E-value=0.012  Score=58.55  Aligned_cols=181  Identities=19%  Similarity=0.415  Sum_probs=101.1

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCc---ccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV---TSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL  118 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~---~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~  118 (250)
                      -.|.|||.+.-.......+.|+|.|...|.+.-++..-.+.+   ..|.||.  |...++--.++.+|++ +.+.|+...
T Consensus      3487 DmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP-iKel~edV~ 3563 (3738)
T KOG1428|consen 3487 DMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP-IKELYEDVR 3563 (3738)
T ss_pred             ceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH-HHHHHHHHH
Confidence            359999987643333445699999999999999987766542   4689998  9999999888888864 233333322


Q ss_pred             Hhh-------ccCCCCeecCCCCCCCCceecCc-cCccCcccCCcccchhccccCcccCCCC-CchhHhhhccCCCchHH
Q 025608          119 CES-------LIPGAQKFYCPFKDCSALLIDDA-GEAIRESECPNCHRLFCAQCKVAWHAGI-ECADFQKLHKDEPESED  189 (250)
Q Consensus       119 ~~~-------~~~~~~~~~Cp~~~C~~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~H~~~-~C~~~~~~~~~~~~~~~  189 (250)
                      .++       .+...+.+.=|  +=  -+..++ +...++.     .++.|.+|++.+-+|. .|+....  .+....++
T Consensus      3564 ~KA~MRLEYeGL~ks~AiT~P--~~--~FYNdPa~YAmnRY-----~Y~vC~KCrKAYFGGEaRCdAe~~--~ddydP~E 3632 (3738)
T KOG1428|consen 3564 RKALMRLEYEGLHKSEAITTP--GV--RFYNDPAGYAMNRY-----AYYVCYKCRKAYFGGEARCDAEAG--GDDYDPRE 3632 (3738)
T ss_pred             HHHhhhhhhccccccccccCC--Cc--eeccChhhhhhhhh-----hhhhhhhhhhhhcCchhhcchhcC--CCCCCHHH
Confidence            221       22233333333  11  122221 1111211     3678889999887774 5665332  11122221


Q ss_pred             HHHHHHHhcCCCccCCCCCc-cee-ccCCCcc---eEEeccccccccccccc
Q 025608          190 IILMKLAQNQKWNRCPNCKF-YVE-KKDGCSY---IRCRCGHAFCYHCGVQL  236 (250)
Q Consensus       190 ~~~~~~~~~~~~~~CP~C~~-~i~-k~~GCnh---m~C~C~~~FC~~C~~~~  236 (250)
                      +.-..--.-.+.+.||+=|+ .+| |-.=|-.   ..|-=-+|||-.|-.++
T Consensus      3633 LiCG~CSDvS~aQmCPkHGtdfLEYKCRyCCSvAVfFCFGTTHFCn~CHDDF 3684 (3738)
T KOG1428|consen 3633 LICGACSDVSRAQMCPKHGTDFLEYKCRYCCSVAVFFCFGTTHFCNACHDDF 3684 (3738)
T ss_pred             hhhccccccccceecccccchhhhhhhheeeeEeEEEEcccccccchhhhHH
Confidence            11111111235688998666 332 1111111   33433578898886665

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

Probab=95.70  E-value=0.0012  Score=42.05  Aligned_cols=47  Identities=26%  Similarity=0.721  Sum_probs=21.1

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      .-|++|.+.+..+  +.+..|.|.||..|+...+.         -.||.  |..+--..+
T Consensus         8 LrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---------~~CPv--C~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---------SECPV--CHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--SS---B---SSS--B-TTTGGGGTT---------TB-SS--S--B-S-SS
T ss_pred             cCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---------CCCCC--cCChHHHHH
Confidence            3599999886644  34569999999999966332         24998  765543333

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

Probab=95.36  E-value=0.014  Score=50.33  Aligned_cols=95  Identities=21%  Similarity=0.391  Sum_probs=55.6

Q ss_pred             CCCCceecccCcccccCCC-----ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH---HH--Hh-cc
Q 025608           37 ETSRSFVCEICVETKLRNE-----SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP---EY--CR-DI  105 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~---~~--i~-~~  105 (250)
                      ......+|.||++......     +-.+..|.|.||..|++.|-...-.+....-.||.  |......   ..  +. .-
T Consensus       157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~  234 (344)
T KOG1039|consen  157 QKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPF--CRVPSSFVNPSSFWVETKE  234 (344)
T ss_pred             CccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCc--ccCccccccccceeeeecc
Confidence            3456678999999876443     22356899999999999998544333344558998  6643322   11  11 11


Q ss_pred             CChHHHHHHHHHHHhhcc--CCCCeecCCC
Q 025608          106 LPEEAFDKWGKALCESLI--PGAQKFYCPF  133 (250)
Q Consensus       106 l~~~~~~~~~~~~~~~~~--~~~~~~~Cp~  133 (250)
                      -...+.+.|++.+.....  .......||.
T Consensus       235 ~k~~li~e~~~~~s~~~c~yf~~~~g~cPf  264 (344)
T KOG1039|consen  235 EKQKLIEEYEAEMSAKDCKYFSQGLGSCPF  264 (344)
T ss_pred             cccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence            233456666655543211  1234457885

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

Probab=95.06  E-value=0.073  Score=45.28  Aligned_cols=122  Identities=20%  Similarity=0.407  Sum_probs=65.5

Q ss_pred             ceecccCcccccC---CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC--CCHHHHhccCChH-HHHHH
Q 025608           41 SFVCEICVETKLR---NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS--LEPEYCRDILPEE-AFDKW  114 (250)
Q Consensus        41 ~~~C~iC~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--l~~~~i~~~l~~~-~~~~~  114 (250)
                      ..+|.||-++++.   +..++.+.|+|.+|..|+...+..      ..+.||.  |...  +....++.+-..- .++..
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~------~~i~cpf--cR~~~~~~~~~~~~l~kNf~ll~~~   74 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN------SRILCPF--CRETTEIPDGDVKSLQKNFALLQAI   74 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC------ceeeccC--CCCcccCCchhHhhhhhhHHHHHHH
Confidence            3579999999864   345667899999999999988772      3567776  7766  4445555443222 22222


Q ss_pred             HHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCcccchhccccCc-ccCCCC
Q 025608          115 GKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKV-AWHAGI  172 (250)
Q Consensus       115 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~-~~H~~~  172 (250)
                      ... ...++.......+| +.|+......-......-.|+.-...+|..|.. ..|.++
T Consensus        75 ~~~-~~~~~~~~~~~~~~-~~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~~~~~~  131 (296)
T KOG4185|consen   75 EHM-KKTTVEEKGEADSP-PKCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFGIHKGH  131 (296)
T ss_pred             HHH-hcccccccCcccCC-cccccCcccccceeecCCCcchhhhhhhhhccchhhhhhh
Confidence            222 12222222222344 135433222211111112355666778888876 334443

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

Probab=94.85  E-value=0.0085  Score=48.10  Aligned_cols=26  Identities=42%  Similarity=1.034  Sum_probs=22.5

Q ss_pred             ccccccccccccc-cCCCCCcCCCCCC
Q 025608          224 CGHAFCYHCGVQL-STVSHGYYCPSCN  249 (250)
Q Consensus       224 C~~~FC~~C~~~~-~~~~h~~~~~~~~  249 (250)
                      |||-|||-|+-.| ....+...||.|+
T Consensus        65 CGHLFCWpClyqWl~~~~~~~~cPVCK   91 (230)
T KOG0823|consen   65 CGHLFCWPCLYQWLQTRPNSKECPVCK   91 (230)
T ss_pred             cccceehHHHHHHHhhcCCCeeCCccc
Confidence            9999999999999 4556777799996

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

Probab=94.82  E-value=0.018  Score=38.14  Aligned_cols=52  Identities=17%  Similarity=0.206  Sum_probs=35.7

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ..|.|+|+.+-+..+.   ..++||.|.++++.+|+..      ....||.  ++..++.+++
T Consensus         3 ~~f~CpIt~~lM~dPV---i~~~G~tyer~~I~~~l~~------~~~~~P~--t~~~l~~~~l   54 (73)
T PF04564_consen    3 DEFLCPITGELMRDPV---ILPSGHTYERSAIERWLEQ------NGGTDPF--TRQPLSESDL   54 (73)
T ss_dssp             GGGB-TTTSSB-SSEE---EETTSEEEEHHHHHHHHCT------TSSB-TT--T-SB-SGGGS
T ss_pred             cccCCcCcCcHhhCce---eCCcCCEEcHHHHHHHHHc------CCCCCCC--CCCcCCcccc
Confidence            4578999998877643   3488999999999999995      3457787  6777776544

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 ....

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

Probab=94.73  E-value=0.059  Score=46.29  Aligned_cols=48  Identities=19%  Similarity=0.582  Sum_probs=35.2

Q ss_pred             ecccCcccc-cCC---------CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           43 VCEICVETK-LRN---------ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        43 ~C~iC~~~~-~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .|.||+++. .++         ..++.++|||.+...|++.|++.+       =.||.  |+.++-.
T Consensus       289 ~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCPI--Cr~p~if  346 (491)
T COG5243         289 TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCPI--CRRPVIF  346 (491)
T ss_pred             eEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCCc--ccCcccc
Confidence            599999993 322         123467999999999999999944       36888  7665433

>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=94.61  E-value=0.016  Score=30.12  Aligned_cols=23  Identities=35%  Similarity=0.831  Sum_probs=13.0

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~F  228 (250)
                      |.||.|+..|...    -..| .||+.|
T Consensus         1 K~CP~C~~~V~~~----~~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPECGAEVPES----AKFCPHCGYDF   24 (26)
T ss_pred             CcCCCCcCCchhh----cCcCCCCCCCC
Confidence            4677777766432    2445 466555

Several members are annotated as putative helicases.

>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=94.39  E-value=0.047  Score=40.28  Aligned_cols=37  Identities=19%  Similarity=0.552  Sum_probs=27.5

Q ss_pred             CCceecccCcccccC-CCceecCCCC------CcchHHHHHHHHH
Q 025608           39 SRSFVCEICVETKLR-NESFSIKGCS------HMYCVDCTVKYVD   76 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~-~~~~~~~~C~------H~fC~~Cl~~~~~   76 (250)
                      ...++|.||++.... +-++.+ .++      |.||.+|+++|-.
T Consensus        24 ~~~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   24 RCTVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             ccCeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHHh
Confidence            346799999999876 333333 554      8899999999953

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.

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

Probab=94.26  E-value=0.036  Score=50.01  Aligned_cols=40  Identities=33%  Similarity=0.822  Sum_probs=34.0

Q ss_pred             cCCCccCC--CCCcceec-cCCCcceEEecccccccccccccc
Q 025608          198 NQKWNRCP--NCKFYVEK-KDGCSYIRCRCGHAFCYHCGVQLS  237 (250)
Q Consensus       198 ~~~~~~CP--~C~~~i~k-~~GCnhm~C~C~~~FC~~C~~~~~  237 (250)
                      ...++-||  .|+..+.. .+...-+.|.|++.|||.|+.+++
T Consensus       155 ~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H  197 (444)
T KOG1815|consen  155 NVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESH  197 (444)
T ss_pred             CCccccCCCCCCCceeeccCCCccceeCCCCchhHhhcccccc
Confidence            34467787  59998887 788999999999999999999985

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=93.82  E-value=0.048  Score=32.19  Aligned_cols=41  Identities=32%  Similarity=0.716  Sum_probs=29.3

Q ss_pred             CCCCCcceeccCCCcceEE--eccccccccccccccCCCCCcCCCCCCC
Q 025608          204 CPNCKFYVEKKDGCSYIRC--RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       204 CP~C~~~i~k~~GCnhm~C--~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ||.|.........    .-  .||+.||..|...+.  .....||.|++
T Consensus         2 C~~C~~~~~~~~~----~~l~~CgH~~C~~C~~~~~--~~~~~CP~C~k   44 (44)
T PF14634_consen    2 CNICFEKYSEERR----PRLTSCGHIFCEKCLKKLK--GKSVKCPICRK   44 (44)
T ss_pred             CcCcCccccCCCC----eEEcccCCHHHHHHHHhhc--CCCCCCcCCCC
Confidence            6667665522222    33  799999999999996  45556999986

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

Probab=93.52  E-value=0.042  Score=46.49  Aligned_cols=48  Identities=29%  Similarity=0.750  Sum_probs=35.7

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL   97 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l   97 (250)
                      ....+|.+|-.-+-+.  +....|-|.||++||-+|+..       ...||.  |+..+
T Consensus        13 n~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~-------~~~CP~--C~i~i   60 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEE-------SKYCPT--CDIVI   60 (331)
T ss_pred             ccceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHH-------hccCCc--cceec
Confidence            3445799998877544  334599999999999999995       357997  55433

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

Probab=93.50  E-value=0.06  Score=44.73  Aligned_cols=62  Identities=21%  Similarity=0.368  Sum_probs=41.1

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh-ccCChHHHHHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR-DILPEEAFDKWG  115 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~  115 (250)
                      .-|-||-+.+..+-   ..+|+|.||.-|++.|+..+       --||.  |........++ ..+..++.+.|.
T Consensus        26 lrC~IC~~~i~ip~---~TtCgHtFCslCIR~hL~~q-------p~CP~--Cr~~~~esrlr~~s~~~ei~es~~   88 (391)
T COG5432          26 LRCRICDCRISIPC---ETTCGHTFCSLCIRRHLGTQ-------PFCPV--CREDPCESRLRGSSGSREINESHA   88 (391)
T ss_pred             HHhhhhhheeecce---ecccccchhHHHHHHHhcCC-------CCCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence            35999998776543   35999999999999999844       24777  76554444333 223444455443

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

Probab=93.34  E-value=0.056  Score=47.74  Aligned_cols=84  Identities=18%  Similarity=0.443  Sum_probs=55.1

Q ss_pred             ccccCCCCCCCCCCCHHHHhc----c----------------C---ChHHHHHHHHHHHhh--------ccCCCCeecCC
Q 025608           84 TSIGCPVTDCGGSLEPEYCRD----I----------------L---PEEAFDKWGKALCES--------LIPGAQKFYCP  132 (250)
Q Consensus        84 ~~i~CP~~~C~~~l~~~~i~~----~----------------l---~~~~~~~~~~~~~~~--------~~~~~~~~~Cp  132 (250)
                      ..+.||.++|...+...++..    .                +   +....+.|+++....        ++. .....||
T Consensus       232 ~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la-~~wr~Cp  310 (384)
T KOG1812|consen  232 DRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA-KRWRQCP  310 (384)
T ss_pred             hcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH-HhcCcCc
Confidence            455888888887666554321    0                0   123355555544221        222 4466899


Q ss_pred             CCCCCCceecCccCccCcccCCcccchhccccCcccCCCCC
Q 025608          133 FKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIE  173 (250)
Q Consensus       133 ~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~  173 (250)
                        .|+..+....+  -+.++|. ||..||+.|..+|..+..
T Consensus       311 --kC~~~ie~~~G--Cnhm~Cr-C~~~fcy~C~~~~~~~~~  346 (384)
T KOG1812|consen  311 --KCKFMIELSEG--CNHMTCR-CGHQFCYMCGGDWKTHNG  346 (384)
T ss_pred             --ccceeeeecCC--cceEEee-ccccchhhcCcchhhCCc
Confidence              99998877665  6889998 999999999999865543

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

Probab=93.31  E-value=0.11  Score=42.82  Aligned_cols=55  Identities=29%  Similarity=0.627  Sum_probs=39.0

Q ss_pred             ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ....+-..+|++|.+.-+.+  .....|+|.+|--|+.......     ..+.||.  |+....
T Consensus       233 ss~~t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~-----asf~Cp~--Cg~~~~  287 (298)
T KOG2879|consen  233 SSTGTSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWD-----ASFTCPL--CGENVE  287 (298)
T ss_pred             cccccCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcch-----hhcccCc--cCCCCc
Confidence            34445566899999865544  3345799999999998876633     3478997  776544

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

Probab=93.28  E-value=0.13  Score=31.20  Aligned_cols=41  Identities=15%  Similarity=0.560  Sum_probs=29.2

Q ss_pred             cccCcccccCCCceecCCCC-----CcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           44 CEICVETKLRNESFSIKGCS-----HMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        44 C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      |-||++.....+.+ ..+|.     |.+..+||.+|+.....     .+||.
T Consensus         2 CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~~-----~~C~i   47 (49)
T smart00744        2 CRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESGN-----KTCEI   47 (49)
T ss_pred             ccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcCC-----CcCCC
Confidence            88999844444444 34775     78999999999985532     37776

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

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=93.22  E-value=0.067  Score=33.46  Aligned_cols=47  Identities=26%  Similarity=0.755  Sum_probs=37.6

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      ..|-.|+..|.-.+.--++.| +||..-=|+|-+-.+ .++.|.||+|+
T Consensus         8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk-~~~~Y~CP~CG   55 (59)
T PRK14890          8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRK-QSNPYTCPKCG   55 (59)
T ss_pred             ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHh-cCCceECCCCC
Confidence            578899998887787789999 999886677766553 46778999997

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

Probab=93.14  E-value=0.038  Score=44.80  Aligned_cols=47  Identities=23%  Similarity=0.651  Sum_probs=34.7

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .+.|..|+.--+ .+.|.+.+|.|.||..|.+.-...         .||.  |+..+-.
T Consensus         3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~~---------~C~l--Ckk~ir~   49 (233)
T KOG4739|consen    3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSPD---------VCPL--CKKSIRI   49 (233)
T ss_pred             eEEeccccccCC-CCceeeeechhhhhhhhcccCCcc---------cccc--ccceeee
Confidence            357999987655 566778899999999998754331         7887  8766544

>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=93.01  E-value=0.028  Score=34.27  Aligned_cols=25  Identities=32%  Similarity=0.865  Sum_probs=16.1

Q ss_pred             cCcccCCcccchhccccCcccCCCC
Q 025608          148 IRESECPNCHRLFCAQCKVAWHAGI  172 (250)
Q Consensus       148 ~~~~~C~~C~~~~C~~C~~~~H~~~  172 (250)
                      .....|+.|+..||..|..-.|..+
T Consensus        19 ~~~y~C~~C~~~FC~dCD~fiHE~L   43 (51)
T PF07975_consen   19 SSRYRCPKCKNHFCIDCDVFIHETL   43 (51)
T ss_dssp             -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred             CCeEECCCCCCccccCcChhhhccc
Confidence            3668999999999999999888664

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.

>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=92.86  E-value=0.021  Score=33.06  Aligned_cols=26  Identities=38%  Similarity=0.889  Sum_probs=20.5

Q ss_pred             eccccccccccccccCCCCCcCCCCC
Q 025608          223 RCGHAFCYHCGVQLSTVSHGYYCPSC  248 (250)
Q Consensus       223 ~C~~~FC~~C~~~~~~~~h~~~~~~~  248 (250)
                      .||+.||..|+..|-...-...||.|
T Consensus        16 ~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen   16 PCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             TTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             cCCCcchHHHHHHHHHhcCCccCCcC
Confidence            79999999999998543556669877

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 ....

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=92.67  E-value=0.073  Score=30.21  Aligned_cols=31  Identities=26%  Similarity=0.698  Sum_probs=23.4

Q ss_pred             eecCCCCCCCCceecCcc---CccCcccCCcccchh
Q 025608          128 KFYCPFKDCSALLIDDAG---EAIRESECPNCHRLF  160 (250)
Q Consensus       128 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~  160 (250)
                      .+.||  .|+..+..+++   .....++|+.|+..|
T Consensus         2 ~i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    2 IITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EEECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            35798  99998887743   345689999998765

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

Probab=92.35  E-value=0.075  Score=41.66  Aligned_cols=35  Identities=23%  Similarity=0.636  Sum_probs=28.0

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVD   76 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   76 (250)
                      .-+|.|.||-.++..+.+   ..|||.||..|...-+.
T Consensus       194 ~IPF~C~iCKkdy~spvv---t~CGH~FC~~Cai~~y~  228 (259)
T COG5152         194 KIPFLCGICKKDYESPVV---TECGHSFCSLCAIRKYQ  228 (259)
T ss_pred             CCceeehhchhhccchhh---hhcchhHHHHHHHHHhc
Confidence            446789999999976543   48999999999876655

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

Probab=92.29  E-value=0.041  Score=32.23  Aligned_cols=29  Identities=38%  Similarity=1.017  Sum_probs=18.7

Q ss_pred             eEEeccccccccccccccCCCCC--cCCCCC
Q 025608          220 IRCRCGHAFCYHCGVQLSTVSHG--YYCPSC  248 (250)
Q Consensus       220 m~C~C~~~FC~~C~~~~~~~~h~--~~~~~~  248 (250)
                      ++=.||+.||..|+..+....+.  +.||.|
T Consensus        12 v~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen   12 VSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             EE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             cccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            34469999999999888444443  578876

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

Probab=92.25  E-value=0.25  Score=46.97  Aligned_cols=53  Identities=28%  Similarity=0.653  Sum_probs=41.4

Q ss_pred             CCCceecccCcccccC-CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           38 TSRSFVCEICVETKLR-NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      ....++|.||++.+.. ..++....|-|.|...|+++|..+.-.++...-+||.
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~  241 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA  241 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc
Confidence            3667899999999854 3456666778999999999999985445556678997

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=92.13  E-value=0.073  Score=26.77  Aligned_cols=20  Identities=30%  Similarity=1.050  Sum_probs=9.6

Q ss_pred             ccccccccccCCCCCcCCCCCC
Q 025608          228 FCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       228 FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      ||-.||.++.....+  ||+|+
T Consensus         1 ~Cp~CG~~~~~~~~f--C~~CG   20 (23)
T PF13240_consen    1 YCPNCGAEIEDDAKF--CPNCG   20 (23)
T ss_pred             CCcccCCCCCCcCcc--hhhhC
Confidence            344555555443444  55554

>PF12773 DZR: Double zinc ribbon

Probab=92.01  E-value=0.14  Score=31.01  Aligned_cols=39  Identities=28%  Similarity=0.682  Sum_probs=20.3

Q ss_pred             CccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      .+.||+|++.+..... .       ..+|-.|+........+  |++|+
T Consensus        12 ~~fC~~CG~~l~~~~~-~-------~~~C~~Cg~~~~~~~~f--C~~CG   50 (50)
T PF12773_consen   12 AKFCPHCGTPLPPPDQ-S-------KKICPNCGAENPPNAKF--CPNCG   50 (50)
T ss_pred             ccCChhhcCChhhccC-C-------CCCCcCCcCCCcCCcCc--cCccc
Confidence            4677777776661111 1       13455555555433334  77774

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

Probab=91.91  E-value=0.29  Score=41.90  Aligned_cols=37  Identities=30%  Similarity=0.580  Sum_probs=27.6

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVD   76 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   76 (250)
                      ..++.-.|+||+-. +...+|  .+|+|.-|.+|+.+++-
T Consensus       418 p~sEd~lCpICyA~-pi~Avf--~PC~H~SC~~CI~qHlm  454 (489)
T KOG4692|consen  418 PDSEDNLCPICYAG-PINAVF--APCSHRSCYGCITQHLM  454 (489)
T ss_pred             CCcccccCcceecc-cchhhc--cCCCCchHHHHHHHHHh
Confidence            33555569999953 333334  59999999999999987

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=91.83  E-value=0.13  Score=31.37  Aligned_cols=26  Identities=31%  Similarity=0.708  Sum_probs=20.3

Q ss_pred             cCCCCCcceeccCC--CcceEE-eccccc
Q 025608          203 RCPNCKFYVEKKDG--CSYIRC-RCGHAF  228 (250)
Q Consensus       203 ~CP~C~~~i~k~~G--Cnhm~C-~C~~~F  228 (250)
                      -||.||.++...++  -+++.| .||+++
T Consensus         2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~   30 (52)
T smart00661        2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence            69999997776643  468999 899875

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

Probab=91.73  E-value=0.22  Score=43.32  Aligned_cols=59  Identities=17%  Similarity=0.350  Sum_probs=46.5

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .|.|||=-+.-+.++.+..+.|||.++++=+.+..+    +|...++||.  |+........+++
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCPY--CP~e~~~~~~kql  392 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCPY--CPVEQLASDTKQL  392 (394)
T ss_pred             eeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCCC--CCcccCHHhcccc
Confidence            568999887777777788889999999988777665    5556899998  9887777665543

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=91.67  E-value=0.17  Score=42.59  Aligned_cols=92  Identities=21%  Similarity=0.561  Sum_probs=56.5

Q ss_pred             CCCCcchHHHHHHHHHHHhhcC---cccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHHHhhccCCCCeecCCCCCCC
Q 025608           61 GCSHMYCVDCTVKYVDSKLQEN---VTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCS  137 (250)
Q Consensus        61 ~C~H~fC~~Cl~~~~~~~i~~~---~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~  137 (250)
                      .|+-.||+.|+..|-.-.-...   ...     ..|.-.++...       ....+|..+..+.  .......||  .|.
T Consensus       341 gCgf~FCR~C~e~yh~geC~~~~~as~t-----~tc~y~vde~~-------a~~arwd~as~~T--Ik~tTkpCP--kCh  404 (446)
T KOG0006|consen  341 GCGFAFCRECKEAYHEGECSAVFEASGT-----TTCAYRVDERA-------AEQARWDAASKET--IKKTTKPCP--KCH  404 (446)
T ss_pred             CchhHhHHHHHhhhccccceeeeccccc-----cceeeecChhh-------hhhhhhhhhhhhh--hhhccCCCC--Ccc
Confidence            5889999999999876322211   111     12332333222       3345666654432  233445788  888


Q ss_pred             CceecCccCccCcccCCc--ccchhccccCcccCC
Q 025608          138 ALLIDDAGEAIRESECPN--CHRLFCAQCKVAWHA  170 (250)
Q Consensus       138 ~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~  170 (250)
                      .....+.+  ...+.|+.  ||..||+.|+-.|..
T Consensus       405 vptErnGG--CmHm~Ct~~~Cg~eWCw~C~tEW~r  437 (446)
T KOG0006|consen  405 VPTERNGG--CMHMKCTQPQCGLEWCWNCGTEWNR  437 (446)
T ss_pred             CccccCCc--eEEeecCCCCCCceeEeccCChhhh
Confidence            77777655  35577854  999999999998853

>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=91.50  E-value=0.064  Score=30.71  Aligned_cols=27  Identities=33%  Similarity=0.860  Sum_probs=20.3

Q ss_pred             eEE-eccccccccccccccCCCCCcCCCCC
Q 025608          220 IRC-RCGHAFCYHCGVQLSTVSHGYYCPSC  248 (250)
Q Consensus       220 m~C-~C~~~FC~~C~~~~~~~~h~~~~~~~  248 (250)
                      +.- .||+.||+.|..+|...  ...||.|
T Consensus        12 ~~~~~CGH~fC~~C~~~~~~~--~~~CP~C   39 (39)
T PF13923_consen   12 VVVTPCGHSFCKECIEKYLEK--NPKCPVC   39 (39)
T ss_dssp             EEECTTSEEEEHHHHHHHHHC--TSB-TTT
T ss_pred             CEECCCCCchhHHHHHHHHHC--cCCCcCC
Confidence            355 89999999999999544  2568877

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

Probab=91.47  E-value=0.18  Score=34.24  Aligned_cols=33  Identities=24%  Similarity=0.709  Sum_probs=25.3

Q ss_pred             CCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           60 KGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        60 ~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      -.|+|.|...|+.+|+.++-.    .=.||.  |.+.+.
T Consensus        50 g~C~H~FH~hCI~kWl~~~~~----~~~CPm--CR~~w~   82 (85)
T PF12861_consen   50 GKCSHNFHMHCILKWLSTQSS----KGQCPM--CRQPWK   82 (85)
T ss_pred             ccCccHHHHHHHHHHHccccC----CCCCCC--cCCeee
Confidence            379999999999999997622    227887  776654

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

Probab=91.38  E-value=0.045  Score=45.45  Aligned_cols=29  Identities=34%  Similarity=0.878  Sum_probs=23.2

Q ss_pred             ceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608          219 YIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       219 hm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      |-+| .||+-|||-|...|-  +-.-+||-|-
T Consensus       251 ~pSaTpCGHiFCWsCI~~w~--~ek~eCPlCR  280 (293)
T KOG0317|consen  251 NPSATPCGHIFCWSCILEWC--SEKAECPLCR  280 (293)
T ss_pred             CCCcCcCcchHHHHHHHHHH--ccccCCCccc
Confidence            5678 899999999999994  3344699884

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=91.21  E-value=0.11  Score=26.94  Aligned_cols=11  Identities=36%  Similarity=0.869  Sum_probs=5.7

Q ss_pred             ccCCCCCccee
Q 025608          202 NRCPNCKFYVE  212 (250)
Q Consensus       202 ~~CP~C~~~i~  212 (250)
                      +.||+|+..+.
T Consensus         3 ~~Cp~Cg~~~~   13 (26)
T PF13248_consen    3 MFCPNCGAEID   13 (26)
T ss_pred             CCCcccCCcCC
Confidence            45566555443

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=90.98  E-value=0.16  Score=28.65  Aligned_cols=31  Identities=29%  Similarity=0.640  Sum_probs=22.7

Q ss_pred             eecCCCCCCCCceecCcc---CccCcccCCcccchh
Q 025608          128 KFYCPFKDCSALLIDDAG---EAIRESECPNCHRLF  160 (250)
Q Consensus       128 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~  160 (250)
                      .+.||  .|++.+..++.   .....++|+.|+..|
T Consensus         2 ~i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    2 IITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EEECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            35788  89988887633   345678999998764

>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=90.93  E-value=0.12  Score=29.90  Aligned_cols=41  Identities=29%  Similarity=0.638  Sum_probs=26.8

Q ss_pred             CCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          204 CPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       204 CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ||-|...+     =+-+.- .||+.||+.|+..|... ....||.|++
T Consensus         2 C~iC~~~~-----~~~~~~~~C~H~~c~~C~~~~~~~-~~~~Cp~C~~   43 (45)
T cd00162           2 CPICLEEF-----REPVVLLPCGHVFCRSCIDKWLKS-GKNTCPLCRT   43 (45)
T ss_pred             CCcCchhh-----hCceEecCCCChhcHHHHHHHHHh-CcCCCCCCCC
Confidence            55555544     122334 59999999999988532 3446999974

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

Probab=90.73  E-value=0.15  Score=45.44  Aligned_cols=53  Identities=25%  Similarity=0.657  Sum_probs=37.1

Q ss_pred             CCCceecccCcccccCCCc--------------eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           38 TSRSFVCEICVETKLRNES--------------FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~--------------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ...+..|.||+.+.+....              ..+.+|.|.|.++||.+|+...      .+.||.  |...|+
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y------kl~CPv--CR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY------KLICPV--CRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh------cccCCc--cCCCCC
Confidence            4556689999987642111              1145999999999999999832      378998  554443

>PHA00626 hypothetical protein

Probab=90.60  E-value=0.18  Score=31.06  Aligned_cols=26  Identities=27%  Similarity=0.607  Sum_probs=20.2

Q ss_pred             cCCCCCc-ceeccCCCcc----eEE-eccccc
Q 025608          203 RCPNCKF-YVEKKDGCSY----IRC-RCGHAF  228 (250)
Q Consensus       203 ~CP~C~~-~i~k~~GCnh----m~C-~C~~~F  228 (250)
                      .||+|+. -|.|.+-|+.    ..| .||+.|
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f   33 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND   33 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence            5999999 5778776654    778 888876

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=90.45  E-value=0.18  Score=31.50  Aligned_cols=48  Identities=23%  Similarity=0.612  Sum_probs=39.4

Q ss_pred             CccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      .-.|-.|+..|.-.++=-++.| +||...=|+|-+-. ..++-|.||+|+
T Consensus         9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CR-k~g~~Y~Cp~CG   57 (61)
T COG2888           9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCR-KLGNPYRCPKCG   57 (61)
T ss_pred             CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHH-HcCCceECCCcC
Confidence            4578889999988888888999 99988888887666 357788999996

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

Probab=90.41  E-value=0.28  Score=45.52  Aligned_cols=44  Identities=20%  Similarity=0.509  Sum_probs=33.7

Q ss_pred             ceecccCcccccCC--CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCC
Q 025608           41 SFVCEICVETKLRN--ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVT   91 (250)
Q Consensus        41 ~~~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~   91 (250)
                      .-.|.||.+.....  .....++|+|.|+..|++.|++.+       -.||.+
T Consensus       291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~C  336 (543)
T KOG0802|consen  291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPTC  336 (543)
T ss_pred             CCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCcc
Confidence            45799999998642  113456999999999999999962       368873

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

Probab=89.91  E-value=0.22  Score=31.84  Aligned_cols=37  Identities=35%  Similarity=0.805  Sum_probs=16.7

Q ss_pred             ccCCCCCcceecc---CCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608          202 NRCPNCKFYVEKK---DGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       202 ~~CP~C~~~i~k~---~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      .+|++|...+...   +||.|+       ||+.|-++.-    ++.||.|+
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~-------fCs~Ci~~~~----~~~CPvC~   47 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHI-------FCSSCIRDCI----GSECPVCH   47 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS---------B-TTTGGGGT----TTB-SSS-
T ss_pred             cCCcHHHHHhcCCceeccCccH-------HHHHHhHHhc----CCCCCCcC
Confidence            6899999876543   666665       6666655532    24588886

>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=89.88  E-value=0.13  Score=31.34  Aligned_cols=31  Identities=39%  Similarity=1.061  Sum_probs=19.6

Q ss_pred             CcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608          217 CSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       217 Cnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      =....| +|+.+||+-|-.=++..-|.  ||-|.
T Consensus        19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~--CPGC~   50 (51)
T PF07975_consen   19 SSRYRCPKCKNHFCIDCDVFIHETLHN--CPGCE   50 (51)
T ss_dssp             -EEE--TTTT--B-HHHHHTTTTTS-S--SSTT-
T ss_pred             CCeEECCCCCCccccCcChhhhccccC--CcCCC
Confidence            345778 89999999998888877888  99885

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.

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=89.85  E-value=0.23  Score=49.43  Aligned_cols=43  Identities=35%  Similarity=0.895  Sum_probs=32.4

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccc-----cccccccccCC-CCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAF-----CYHCGVQLSTV-SHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~F-----C~~C~~~~~~~-~h~~~~~~~~~  250 (250)
                      ++||+|+..+...      .| .||.+.     |-.|+....+. +-...||+|+.
T Consensus       668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGt  717 (1337)
T PRK14714        668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDV  717 (1337)
T ss_pred             EECCCCCCccccc------cCcccCCcCCCceeCccCCCccCCCccccccCCCCCC
Confidence            8999999976532      99 899775     99999987322 11567999984

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.80  E-value=0.15  Score=41.36  Aligned_cols=60  Identities=15%  Similarity=0.331  Sum_probs=45.8

Q ss_pred             CCCCceecccCcccccCCC-ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           37 ETSRSFVCEICVETKLRNE-SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      ..++.+.|+||-++++... ...+.+++|.|+.+|..++|.       ..+.+|.  ++..+..++|..|
T Consensus       217 a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-------~D~v~pv--~d~plkdrdiI~L  277 (303)
T KOG3039|consen  217 AASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-------KDMVDPV--TDKPLKDRDIIGL  277 (303)
T ss_pred             hhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-------ccccccC--CCCcCcccceEee
Confidence            3457788999999987543 234779999999999999987       2356787  8888887776544

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=89.75  E-value=0.27  Score=29.31  Aligned_cols=28  Identities=29%  Similarity=0.593  Sum_probs=19.6

Q ss_pred             ccCCCCCcceeccCCCcceEE-ecccccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFC  229 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC  229 (250)
                      -.||+|+..++-.++=..++| .||..+=
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~   32 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYRIL   32 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence            478888887766654447888 7887653

>PRK04023 DNA polymerase II large subunit; Validated

Probab=89.54  E-value=0.28  Score=47.76  Aligned_cols=41  Identities=32%  Similarity=0.873  Sum_probs=32.7

Q ss_pred             CCccCCCCCcceeccCCCcceEE-ecccc-----ccccccccccCCCCCcCCCCCCC
Q 025608          200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..+.||.||...      ....| .||.+     ||-.|+....    .+.||+|+.
T Consensus       625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~----~y~CPKCG~  671 (1121)
T PRK04023        625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE----EDECEKCGR  671 (1121)
T ss_pred             cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC----CCcCCCCCC
Confidence            458999999985      56899 89965     9999977664    367999974

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=89.45  E-value=0.25  Score=30.08  Aligned_cols=26  Identities=23%  Similarity=0.639  Sum_probs=19.5

Q ss_pred             CccCCCCCc-ceeccCCCcceEE-eccccc
Q 025608          201 WNRCPNCKF-YVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       201 ~~~CP~C~~-~i~k~~GCnhm~C-~C~~~F  228 (250)
                      .+.||+|+. .+....  +.++| +||+.+
T Consensus        20 ~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~   47 (50)
T PRK00432         20 NKFCPRCGSGFMAEHL--DRWHCGKCGYTE   47 (50)
T ss_pred             cCcCcCCCcchheccC--CcEECCCcCCEE
Confidence            379999998 433333  79999 999875

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

Probab=89.38  E-value=0.31  Score=41.83  Aligned_cols=50  Identities=24%  Similarity=0.634  Sum_probs=35.0

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ++....+|-||+++..+   +.+++|.|. .|.+|.+...- +  .    =.||.  |.+.+.
T Consensus       286 ~~~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~-q--~----n~CPI--CRqpi~  336 (349)
T KOG4265|consen  286 ESESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRY-Q--T----NNCPI--CRQPIE  336 (349)
T ss_pred             cccCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHH-h--h----cCCCc--cccchH
Confidence            33445689999986543   445699999 89999987762 1  1    25898  876654

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

Probab=89.34  E-value=0.15  Score=30.71  Aligned_cols=45  Identities=24%  Similarity=0.718  Sum_probs=21.0

Q ss_pred             CCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          204 CPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       204 CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ||-|-..+ ...|=+..=|.|+++.|..|...+..... --||.|.+
T Consensus         1 cp~C~e~~-d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~-g~CPgCr~   45 (48)
T PF14570_consen    1 CPLCDEEL-DETDKDFYPCECGFQICRFCYHDILENEG-GRCPGCRE   45 (48)
T ss_dssp             -TTTS-B---CCCTT--SSTTS----HHHHHHHTTSS--SB-TTT--
T ss_pred             CCCccccc-ccCCCccccCcCCCcHHHHHHHHHHhccC-CCCCCCCC
Confidence            45555554 33444566678999999999988864222 24999874

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

Probab=89.06  E-value=0.31  Score=43.25  Aligned_cols=38  Identities=18%  Similarity=0.612  Sum_probs=30.0

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHH
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDS   77 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~   77 (250)
                      ..+...|++|...+..+...  ..|+|.||..|+..+...
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~--~~cgh~fC~~C~~~~~~~   55 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQT--TTCGHRFCAGCLLESLSN   55 (391)
T ss_pred             CcccccCccccccccCCCCC--CCCCCcccccccchhhcc
Confidence            34556799999988755322  499999999999999885

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

Probab=88.79  E-value=0.59  Score=41.36  Aligned_cols=48  Identities=25%  Similarity=0.726  Sum_probs=35.3

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ...|+|.||++.+..+..   .+|||.||..|+.+-+.       ..-.||.  |...+.
T Consensus        82 ~sef~c~vc~~~l~~pv~---tpcghs~c~~Cl~r~ld-------~~~~cp~--Cr~~l~  129 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPPVV---TPCGHSFCLECLDRSLD-------QETECPL--CRDELV  129 (398)
T ss_pred             cchhhhhhhHhhcCCCcc---ccccccccHHHHHHHhc-------cCCCCcc--cccccc
Confidence            667899999988876532   39999999999777222       3346886  876665

>PLN03086 PRLI-interacting factor K; Provisional

Probab=88.65  E-value=0.94  Score=41.88  Aligned_cols=58  Identities=16%  Similarity=0.403  Sum_probs=36.5

Q ss_pred             ccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608           84 TSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLF  160 (250)
Q Consensus        84 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~  160 (250)
                      ..+.||.  |...+....+..++..               =....+.||..+|+..+.....+  +.+.|+.|+..|
T Consensus       406 ~~V~C~N--C~~~i~l~~l~lHe~~---------------C~r~~V~Cp~~~Cg~v~~r~el~--~H~~C~~Cgk~f  463 (567)
T PLN03086        406 DTVECRN--CKHYIPSRSIALHEAY---------------CSRHNVVCPHDGCGIVLRVEEAK--NHVHCEKCGQAF  463 (567)
T ss_pred             CeEECCC--CCCccchhHHHHHHhh---------------CCCcceeCCcccccceeeccccc--cCccCCCCCCcc
Confidence            4668886  8877777665533211               12345678876798888665432  446788887665

>TIGR00622 ssl1 transcription factor ssl1

Probab=88.21  E-value=0.23  Score=35.60  Aligned_cols=41  Identities=22%  Similarity=0.579  Sum_probs=29.6

Q ss_pred             ecCCCCCCCCceecCc------cCccCcccCCcccchhccccCcccCCC
Q 025608          129 FYCPFKDCSALLIDDA------GEAIRESECPNCHRLFCAQCKVAWHAG  171 (250)
Q Consensus       129 ~~Cp~~~C~~~~~~~~------~~~~~~~~C~~C~~~~C~~C~~~~H~~  171 (250)
                      ..|-  +|+..+....      .....+..|+.|+..||..|..-+|+.
T Consensus        56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~  102 (112)
T TIGR00622        56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES  102 (112)
T ss_pred             Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence            3577  8887665431      122356789999999999999988854

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

>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=87.98  E-value=0.11  Score=41.92  Aligned_cols=49  Identities=24%  Similarity=0.597  Sum_probs=35.4

Q ss_pred             ecccCcccc-cCCCce--ecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608           43 VCEICVETK-LRNESF--SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL   97 (250)
Q Consensus        43 ~C~iC~~~~-~~~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l   97 (250)
                      .||||..+. -.+++.  ....|-|.+|-+|+.+.+.      ..+-.||..+|+.+|
T Consensus        12 ~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs------~GpAqCP~~gC~kIL   63 (314)
T COG5220          12 RCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS------RGPAQCPYKGCGKIL   63 (314)
T ss_pred             cCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc------CCCCCCCCccHHHHH
Confidence            599999875 223332  2334999999999988776      246689999998644

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

Probab=87.84  E-value=0.16  Score=47.74  Aligned_cols=47  Identities=28%  Similarity=0.733  Sum_probs=33.8

Q ss_pred             HHhcCCCccCCCCCcceeccCCCcceEE---eccccccccccccccCCCCCcCCCCCCC
Q 025608          195 LAQNQKWNRCPNCKFYVEKKDGCSYIRC---RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       195 ~~~~~~~~~CP~C~~~i~k~~GCnhm~C---~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      +..-....+||-|...        .=-+   +|+|.||+-|-++.....+. -||.||.
T Consensus       637 lk~yK~~LkCs~Cn~R--------~Kd~vI~kC~H~FC~~Cvq~r~etRqR-KCP~Cn~  686 (698)
T KOG0978|consen  637 LKEYKELLKCSVCNTR--------WKDAVITKCGHVFCEECVQTRYETRQR-KCPKCNA  686 (698)
T ss_pred             HHHHHhceeCCCccCc--------hhhHHHHhcchHHHHHHHHHHHHHhcC-CCCCCCC
Confidence            3333556899999852        1112   69999999999998655555 6999995

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

Probab=87.59  E-value=0.21  Score=43.43  Aligned_cols=44  Identities=32%  Similarity=0.879  Sum_probs=32.2

Q ss_pred             ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608           43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG   94 (250)
Q Consensus        43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   94 (250)
                      -|.||.+...+   +...+|||..|..||..|-.+.   +  .-.||.+.|.
T Consensus       371 LCKICaendKd---vkIEPCGHLlCt~CLa~WQ~sd---~--gq~CPFCRcE  414 (563)
T KOG1785|consen  371 LCKICAENDKD---VKIEPCGHLLCTSCLAAWQDSD---E--GQTCPFCRCE  414 (563)
T ss_pred             HHHHhhccCCC---cccccccchHHHHHHHhhcccC---C--CCCCCceeeE
Confidence            49999875433   4567999999999999996532   1  2368886664

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

Probab=87.38  E-value=0.51  Score=39.60  Aligned_cols=44  Identities=20%  Similarity=0.508  Sum_probs=35.9

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHh
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKL   79 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i   79 (250)
                      ..+.....|.||+--|..+.-|...+|.|.|...||.+|+....
T Consensus       110 ~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~  153 (368)
T KOG4445|consen  110 ENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL  153 (368)
T ss_pred             cCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence            45566677999998888777677789999999999999987443

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

Probab=87.37  E-value=0.73  Score=27.72  Aligned_cols=44  Identities=20%  Similarity=0.554  Sum_probs=20.0

Q ss_pred             cccCcccccC--CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC
Q 025608           44 CEICVETKLR--NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS   96 (250)
Q Consensus        44 C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   96 (250)
                      |++|.+++..  .++... +|+..+|+.|+.+-..+      ..=+||.  |+..
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~------~~g~CPg--Cr~~   46 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILEN------EGGRCPG--CREP   46 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTS------S-SB-TT--T--B
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhc------cCCCCCC--CCCC
Confidence            7889988732  233333 78899999999887661      1236886  6643

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=87.34  E-value=0.31  Score=27.61  Aligned_cols=30  Identities=17%  Similarity=0.514  Sum_probs=20.7

Q ss_pred             ecCCCCCCCCceecCcc---CccCcccCCcccchh
Q 025608          129 FYCPFKDCSALLIDDAG---EAIRESECPNCHRLF  160 (250)
Q Consensus       129 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~  160 (250)
                      +.||  .|+..+..+++   .....+.|+.|+..|
T Consensus         3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            5788  89987777632   122368899998764

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=87.25  E-value=1.3  Score=42.41  Aligned_cols=33  Identities=33%  Similarity=0.873  Sum_probs=19.2

Q ss_pred             cCCCCCcceeccCCCcceEE-ecccc-----cccccccc
Q 025608          203 RCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQ  235 (250)
Q Consensus       203 ~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~  235 (250)
                      .||+|..++.-...=+.|.| .||++     .|-.||..
T Consensus       446 ~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~  484 (730)
T COG1198         446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE  484 (730)
T ss_pred             cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence            67777775544433367777 67665     45555444

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

Probab=87.24  E-value=0.12  Score=43.60  Aligned_cols=23  Identities=30%  Similarity=0.868  Sum_probs=19.8

Q ss_pred             CcccCCcccchhccccCcccCCC
Q 025608          149 RESECPNCHRLFCAQCKVAWHAG  171 (250)
Q Consensus       149 ~~~~C~~C~~~~C~~C~~~~H~~  171 (250)
                      ...+|+.|+..||..|..-.|..
T Consensus       344 ~~y~C~~Ck~~FCldCDv~iHes  366 (378)
T KOG2807|consen  344 GRYRCESCKNVFCLDCDVFIHES  366 (378)
T ss_pred             CcEEchhccceeeccchHHHHhh
Confidence            55889999999999999877754

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

Probab=87.12  E-value=0.46  Score=39.89  Aligned_cols=53  Identities=21%  Similarity=0.380  Sum_probs=38.1

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ...-+|.||+.+-..+   ..+.|.|.||--|++.-...-      ...|+.  |...++.+.+
T Consensus         5 ~~~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~nd------k~~Cav--CR~pids~i~   57 (324)
T KOG0824|consen    5 TKKKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKND------KKTCAV--CRFPIDSTID   57 (324)
T ss_pred             ccCCcceeeeccCCcC---ccccccchhhhhhhcchhhcC------CCCCce--ecCCCCcchh
Confidence            4455799999876554   346999999999999876622      224887  8877766543

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

Probab=86.88  E-value=0.13  Score=44.07  Aligned_cols=46  Identities=30%  Similarity=0.734  Sum_probs=32.3

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCC
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG   95 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~   95 (250)
                      ..+.|+||++-+...-  ....|.|.||.+|+-..+...      .=.||.  |..
T Consensus        42 ~~v~c~icl~llk~tm--ttkeClhrfc~~ci~~a~r~g------n~ecpt--cRk   87 (381)
T KOG0311|consen   42 IQVICPICLSLLKKTM--TTKECLHRFCFDCIWKALRSG------NNECPT--CRK   87 (381)
T ss_pred             hhhccHHHHHHHHhhc--ccHHHHHHHHHHHHHHHHHhc------CCCCch--HHh
Confidence            3457999998775432  234999999999998877732      125776  654

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

Probab=86.80  E-value=0.27  Score=40.59  Aligned_cols=57  Identities=16%  Similarity=0.320  Sum_probs=40.5

Q ss_pred             CCceecccCcccccCCC-------ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           39 SRSFVCEICVETKLRNE-------SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      .....|.||-..+..+.       -...++|+|.|...|++.|...-    +. =.||.  |++.++...+
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG----Kk-qtCPY--CKekVdl~rm  285 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG----KK-QTCPY--CKEKVDLKRM  285 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec----CC-CCCch--HHHHhhHhhh
Confidence            34446999998775433       22345999999999999998732    22 26997  8888777654

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

Probab=86.78  E-value=0.57  Score=41.00  Aligned_cols=52  Identities=25%  Similarity=0.698  Sum_probs=38.3

Q ss_pred             eecccCcccccC--CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           42 FVCEICVETKLR--NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        42 ~~C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      .+|+||++.+..  +.-...+.|+|.|=.+|+++|+.     ......||.  |...-...
T Consensus         5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-----k~~~~~cp~--c~~katkr   58 (463)
T KOG1645|consen    5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-----KKTKMQCPL--CSGKATKR   58 (463)
T ss_pred             ccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-----hhhhhhCcc--cCChhHHH
Confidence            479999999753  33344669999999999999993     345678998  66544433

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=86.77  E-value=0.42  Score=29.05  Aligned_cols=28  Identities=32%  Similarity=0.832  Sum_probs=19.9

Q ss_pred             cCCCCCCCCceecCccCccCcccCCcccch
Q 025608          130 YCPFKDCSALLIDDAGEAIRESECPNCHRL  159 (250)
Q Consensus       130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~  159 (250)
                      +||  .|+..+..........+.|+.||+.
T Consensus         2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~   29 (52)
T smart00661        2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE   29 (52)
T ss_pred             CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence            688  8999887765433346788888854

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=86.60  E-value=0.84  Score=24.80  Aligned_cols=26  Identities=31%  Similarity=0.623  Sum_probs=16.1

Q ss_pred             ccCCCCCcceeccCCCcceEE-ecccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHA  227 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~  227 (250)
                      +-||.||.+.....+=-.+.| .|+..
T Consensus         4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    4 RFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             cccCcCCccccCCCCcCEeECCCCcCE
Confidence            678999998888877677888 88764

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

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

Probab=86.46  E-value=0.17  Score=29.68  Aligned_cols=41  Identities=32%  Similarity=0.705  Sum_probs=25.2

Q ss_pred             CCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCC
Q 025608          204 CPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSC  248 (250)
Q Consensus       204 CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~  248 (250)
                      ||=|...+..  +=.-+.-.||+.|++.|+..|-...  ..||.|
T Consensus         3 C~IC~~~~~~--~~~~~~l~C~H~fh~~Ci~~~~~~~--~~CP~C   43 (44)
T PF13639_consen    3 CPICLEEFED--GEKVVKLPCGHVFHRSCIKEWLKRN--NSCPVC   43 (44)
T ss_dssp             ETTTTCBHHT--TSCEEEETTSEEEEHHHHHHHHHHS--SB-TTT
T ss_pred             CcCCChhhcC--CCeEEEccCCCeeCHHHHHHHHHhC--CcCCcc
Confidence            4445554433  2222333799999999999995322  379988

...

>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding

Probab=86.20  E-value=0.42  Score=27.87  Aligned_cols=26  Identities=31%  Similarity=0.888  Sum_probs=18.3

Q ss_pred             CCCccCCCCCcceeccCCCcceEE---eccccc
Q 025608          199 QKWNRCPNCKFYVEKKDGCSYIRC---RCGHAF  228 (250)
Q Consensus       199 ~~~~~CP~C~~~i~k~~GCnhm~C---~C~~~F  228 (250)
                      ..+++||+||++-    |+--+.|   .|++.|
T Consensus         9 RGirkCp~CGt~N----G~R~~~CKN~~C~~~~   37 (44)
T PF14952_consen    9 RGIRKCPKCGTYN----GTRGLSCKNKSCPQVF   37 (44)
T ss_pred             hccccCCcCcCcc----CcccccccCCccchhh
Confidence            3569999999974    6666666   465544

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

Probab=85.91  E-value=0.36  Score=39.94  Aligned_cols=43  Identities=30%  Similarity=0.797  Sum_probs=29.0

Q ss_pred             CccCCCCCc--ceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608          201 WNRCPNCKF--YVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       201 ~~~CP~C~~--~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      ...||-|+.  .|....|      .|++-+||.|.+.--..+-++-||.||
T Consensus       239 ~~~C~~Cg~~PtiP~~~~------~C~HiyCY~Ci~ts~~~~asf~Cp~Cg  283 (298)
T KOG2879|consen  239 DTECPVCGEPPTIPHVIG------KCGHIYCYYCIATSRLWDASFTCPLCG  283 (298)
T ss_pred             CceeeccCCCCCCCeeec------cccceeehhhhhhhhcchhhcccCccC
Confidence            389999999  4555555      366677788866554334455688887

>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Probab=85.88  E-value=0.47  Score=38.88  Aligned_cols=19  Identities=21%  Similarity=0.581  Sum_probs=15.0

Q ss_pred             CCCeecCCCCCCCCceecC
Q 025608          125 GAQKFYCPFKDCSALLIDD  143 (250)
Q Consensus       125 ~~~~~~Cp~~~C~~~~~~~  143 (250)
                      +..++-||.|+|+.++.-.
T Consensus       120 sS~rIaCPRp~CkRiI~L~  138 (256)
T PF09788_consen  120 SSQRIACPRPNCKRIINLG  138 (256)
T ss_pred             ccccccCCCCCCcceEEeC
Confidence            4667899999999877654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=85.85  E-value=0.87  Score=38.87  Aligned_cols=62  Identities=24%  Similarity=0.547  Sum_probs=40.4

Q ss_pred             CCceecccCccccc--CCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc-CChHH
Q 025608           39 SRSFVCEICVETKL--RNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI-LPEEA  110 (250)
Q Consensus        39 ~~~~~C~iC~~~~~--~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~-l~~~~  110 (250)
                      .+.+ |++|+++..  +..++.. +||-.+|+-||...-+ .++     =+||.  |....+.+-++-. |++++
T Consensus        13 eed~-cplcie~mditdknf~pc-~cgy~ic~fc~~~irq-~ln-----grcpa--crr~y~denv~~~~~s~ee   77 (480)
T COG5175          13 EEDY-CPLCIEPMDITDKNFFPC-PCGYQICQFCYNNIRQ-NLN-----GRCPA--CRRKYDDENVRYVTLSPEE   77 (480)
T ss_pred             cccc-CcccccccccccCCcccC-CcccHHHHHHHHHHHh-hcc-----CCChH--hhhhccccceeEEecCHHH
Confidence            3444 999999874  4454444 8888999999975433 222     27997  8877776665432 44443

>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues

Probab=85.66  E-value=0.13  Score=34.02  Aligned_cols=47  Identities=28%  Similarity=0.528  Sum_probs=28.2

Q ss_pred             ccCCCCCccee----c-cCCCcceEE-ecccccccc------ccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVE----K-KDGCSYIRC-RCGHAFCYH------CGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~----k-~~GCnhm~C-~C~~~FC~~------C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||.|+..++    + .+.-.++.+ ..---+||.      |....+...|+  ||+||+
T Consensus         8 ~~CP~C~~~~~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~--Cp~C~~   66 (73)
T PF10601_consen    8 IYCPYCQQQVQTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHY--CPNCGA   66 (73)
T ss_pred             eECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEE--CCCCCC
Confidence            68999998554    2 355556555 222222243      34444666888  999985

Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=85.65  E-value=0.51  Score=32.69  Aligned_cols=28  Identities=32%  Similarity=0.762  Sum_probs=21.7

Q ss_pred             ccCCCCCcc--eeccCCCcceEE-ecccccc
Q 025608          202 NRCPNCKFY--VEKKDGCSYIRC-RCGHAFC  229 (250)
Q Consensus       202 ~~CP~C~~~--i~k~~GCnhm~C-~C~~~FC  229 (250)
                      .-||.|+.+  |+..+.||.+.| .|.+.|=
T Consensus         2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~   32 (105)
T KOG2906|consen    2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFP   32 (105)
T ss_pred             cccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence            369999994  445556999999 9999874

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=85.33  E-value=0.69  Score=26.85  Aligned_cols=22  Identities=45%  Similarity=1.126  Sum_probs=17.3

Q ss_pred             ccCCCCCcceec-cCCCcceEE-ecc
Q 025608          202 NRCPNCKFYVEK-KDGCSYIRC-RCG  225 (250)
Q Consensus       202 ~~CP~C~~~i~k-~~GCnhm~C-~C~  225 (250)
                      ..||.|++++.+ .+|  .+.| .|+
T Consensus        18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~   41 (41)
T PF06677_consen   18 EHCPDCGTPLMRDKDG--KIYCVSCG   41 (41)
T ss_pred             CccCCCCCeeEEecCC--CEECCCCC
Confidence            699999999888 455  5777 664

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

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

Probab=85.33  E-value=0.4  Score=42.38  Aligned_cols=39  Identities=21%  Similarity=0.474  Sum_probs=29.5

Q ss_pred             CCCceecccCcccccCCC-ceecCCCCCcchHHHHHHHHH
Q 025608           38 TSRSFVCEICVETKLRNE-SFSIKGCSHMYCVDCTVKYVD   76 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~   76 (250)
                      -.+..+|+||++....+. .+....|+|.|...|+..|..
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~  211 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD  211 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhccc
Confidence            355668999999875442 233458999999999998865

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=85.26  E-value=0.56  Score=33.56  Aligned_cols=27  Identities=30%  Similarity=0.715  Sum_probs=20.5

Q ss_pred             CccCCCCCcceeccCCCcceEE-eccccc
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~F  228 (250)
                      -+.||+||...--..- +-++| +||+.|
T Consensus         9 KR~Cp~CG~kFYDLnk-~PivCP~CG~~~   36 (108)
T PF09538_consen    9 KRTCPSCGAKFYDLNK-DPIVCPKCGTEF   36 (108)
T ss_pred             cccCCCCcchhccCCC-CCccCCCCCCcc
Confidence            3789999986655544 77888 888876

The function of members of this family is unknown.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=85.23  E-value=0.72  Score=27.40  Aligned_cols=29  Identities=21%  Similarity=0.497  Sum_probs=21.6

Q ss_pred             eecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608          128 KFYCPFKDCSALLIDDAGEAIRESECPNCHRLF  160 (250)
Q Consensus       128 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~  160 (250)
                      .+.||  +|++.+..++...  .+.||.||..+
T Consensus         3 ~y~C~--~CG~~~~~~~~~~--~~~Cp~CG~~~   31 (46)
T PRK00398          3 EYKCA--RCGREVELDEYGT--GVRCPYCGYRI   31 (46)
T ss_pred             EEECC--CCCCEEEECCCCC--ceECCCCCCeE
Confidence            45788  9999888775432  58899998764

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=85.04  E-value=0.72  Score=43.55  Aligned_cols=10  Identities=40%  Similarity=1.016  Sum_probs=5.7

Q ss_pred             cccccccccc
Q 025608          227 AFCYHCGVQL  236 (250)
Q Consensus       227 ~FC~~C~~~~  236 (250)
                      .||-.||.+.
T Consensus        42 ~fC~~CG~~~   51 (645)
T PRK14559         42 AHCPNCGAET   51 (645)
T ss_pred             ccccccCCcc
Confidence            3666665554

>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus

Probab=84.97  E-value=0.28  Score=46.90  Aligned_cols=41  Identities=37%  Similarity=1.002  Sum_probs=0.0

Q ss_pred             CCccCCCCCcceeccCCCcceEE-ecccc-----ccccccccccCCCCCcCCCCCCC
Q 025608          200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..++||+|+....      ..+| .||.+     +|..|+....+.    .||+|++
T Consensus       654 ~~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~~----~C~~C~~  700 (900)
T PF03833_consen  654 GRRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEED----ECPKCGR  700 (900)
T ss_dssp             ---------------------------------------------------------
T ss_pred             ecccCcccCCcch------hhcCcccCCccccceeccccccccCcc----ccccccc
Confidence            3489999999754      5689 89988     999999998543    6999974

The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=84.60  E-value=0.51  Score=37.29  Aligned_cols=33  Identities=27%  Similarity=0.532  Sum_probs=24.4

Q ss_pred             CCCccCCCCCcceeccCCCcceEEeccccccccccccc
Q 025608          199 QKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQL  236 (250)
Q Consensus       199 ~~~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~  236 (250)
                      ...-.||=|.-.+...     +.=.||+.|||.|...|
T Consensus        16 ~~~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~w   48 (193)
T PLN03208         16 GGDFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKW   48 (193)
T ss_pred             CCccCCccCCCcCCCc-----EEcCCCchhHHHHHHHH
Confidence            3446899998865321     22289999999999988

>PRK14873 primosome assembly protein PriA; Provisional

Probab=84.55  E-value=2  Score=40.89  Aligned_cols=25  Identities=28%  Similarity=0.614  Sum_probs=13.8

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGH  226 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~  226 (250)
                      -.||+|..++.-..+=+.+.| .||+
T Consensus       393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~  418 (665)
T PRK14873        393 ARCRHCTGPLGLPSAGGTPRCRWCGR  418 (665)
T ss_pred             eECCCCCCceeEecCCCeeECCCCcC
Confidence            367777765554333345666 5654

>PF04641 Rtf2: Rtf2 RING-finger

Probab=84.53  E-value=2.1  Score=35.77  Aligned_cols=71  Identities=20%  Similarity=0.431  Sum_probs=51.5

Q ss_pred             CCCceecccCcccccCC-CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCC-hHHHHHHH
Q 025608           38 TSRSFVCEICVETKLRN-ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILP-EEAFDKWG  115 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~-~~~~~~~~  115 (250)
                      ....|.|||-..++... .+..+.+|||.|....++..-    .    .-.||.  |+..+...+|-.|-+ .+.++.+.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~----~~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l~  179 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K----SKKCPV--CGKPFTEEDIIPLNPPEEELEKLR  179 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c----cccccc--cCCccccCCEEEecCCccHHHHHH
Confidence            56778899999998653 455678999999999999882    1    224998  999999888776654 23455554


Q ss_pred             HHH
Q 025608          116 KAL  118 (250)
Q Consensus       116 ~~~  118 (250)
                      ..+
T Consensus       180 ~~~  182 (260)
T PF04641_consen  180 ERM  182 (260)
T ss_pred             HHH
Confidence            444

>PF15616 TerY-C: TerY-C metal binding domain

Probab=84.44  E-value=0.9  Score=33.61  Aligned_cols=24  Identities=33%  Similarity=0.935  Sum_probs=14.7

Q ss_pred             CccCCCCCcceeccCCCcceEEeccccccc
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCY  230 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~  230 (250)
                      .--||.|+...-      ...|.||.-|||
T Consensus        77 ~PgCP~CGn~~~------fa~C~CGkl~Ci  100 (131)
T PF15616_consen   77 APGCPHCGNQYA------FAVCGCGKLFCI  100 (131)
T ss_pred             CCCCCCCcChhc------EEEecCCCEEEe
Confidence            378999998522      334455555554

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

Probab=83.88  E-value=0.37  Score=37.28  Aligned_cols=45  Identities=33%  Similarity=0.783  Sum_probs=32.9

Q ss_pred             CccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      .-.||.|...+.+..-   +.=+||+-||-.|.+..-...|.  ||-|+|
T Consensus       131 ~~~CPiCl~~~sek~~---vsTkCGHvFC~~Cik~alk~~~~--CP~C~k  175 (187)
T KOG0320|consen  131 TYKCPICLDSVSEKVP---VSTKCGHVFCSQCIKDALKNTNK--CPTCRK  175 (187)
T ss_pred             ccCCCceecchhhccc---cccccchhHHHHHHHHHHHhCCC--CCCccc
Confidence            4689999987766542   21278889999998888555666  998874

>PHA03096 p28-like protein; Provisional

Probab=82.37  E-value=1.8  Score=36.55  Aligned_cols=39  Identities=18%  Similarity=0.453  Sum_probs=30.0

Q ss_pred             eecccCcccccCC----Cce-ecCCCCCcchHHHHHHHHHHHhh
Q 025608           42 FVCEICVETKLRN----ESF-SIKGCSHMYCVDCTVKYVDSKLQ   80 (250)
Q Consensus        42 ~~C~iC~~~~~~~----~~~-~~~~C~H~fC~~Cl~~~~~~~i~   80 (250)
                      .+|+||++.....    ..| .+..|.|.||..|++.|......
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~  222 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY  222 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence            5699999887432    223 26699999999999999997653

>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=81.89  E-value=1.2  Score=31.50  Aligned_cols=31  Identities=23%  Similarity=0.498  Sum_probs=24.9

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHH
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTV   72 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~   72 (250)
                      ...|++|...+..+ .|...+|+|.|...|++
T Consensus        78 ~~~C~vC~k~l~~~-~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGNS-VFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCCc-eEEEeCCCeEEeccccc
Confidence            34599999998764 46667999999999975

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 [].

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

Probab=81.43  E-value=1.2  Score=30.29  Aligned_cols=45  Identities=38%  Similarity=0.875  Sum_probs=35.1

Q ss_pred             ccCCCCCcceeccCCCcceEEecccccccccccccc-CCCCCcCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS-TVSHGYYCPSCN  249 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~-~~~h~~~~~~~~  249 (250)
                      ..||.|+.+   .+.|--+...|++.|=..|..+|- +.+..-.||-|-
T Consensus        33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR   78 (85)
T PF12861_consen   33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCR   78 (85)
T ss_pred             cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcC
Confidence            478999997   567888888999999999999993 323344698874

>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=80.26  E-value=2.4  Score=35.57  Aligned_cols=50  Identities=24%  Similarity=0.616  Sum_probs=34.1

Q ss_pred             ecccCcccc-cCCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           43 VCEICVETK-LRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        43 ~C~iC~~~~-~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      .|++|-.+. ..+++ +...+|+|..|-+|+-..+..      .+-.||  .|..++-..
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~------g~~~Cp--eC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL------GPAQCP--ECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhc------CCCCCC--cccchhhhc
Confidence            388888764 23333 334599999999999988772      244688  488766443

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=80.05  E-value=0.67  Score=25.87  Aligned_cols=28  Identities=29%  Similarity=0.726  Sum_probs=19.0

Q ss_pred             ecCCCCCCCCceecCccCccCcccCCcccch
Q 025608          129 FYCPFKDCSALLIDDAGEAIRESECPNCHRL  159 (250)
Q Consensus       129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~  159 (250)
                      .+||  .|++.+.+..+..... .|+.|++.
T Consensus         2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE   29 (35)
T ss_dssp             -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred             eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence            3688  9999998876544443 68777764

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	250
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	3e-13
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	3e-08
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	2e-06

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 94

 Score = 63.0 bits (153), Expect = 3e-13
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 39  SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQE-NVTSIGCPVTDCG--G 95
           S S  C++C+      +  +I  C  ++C  C  +YV+  ++E   T+I CP   C   G
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQG 62

Query: 96  SLEPEYCRDILPEEAFDKWGKALCESLIPGA 126
            L+      ++  E   ++ K   E   P +
Sbjct: 63  HLQENEIECMVAAEIMQRYKKLQFERSGPSS 93

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 60

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 201 WNRCPNCKFYVEKKDGCSYIRCR---CGHAFCYHCGVQLSTVSHGYYCPSCNK 250
              CP C   +EK  GC+++ CR   C   FC+ C          +Y  +CN+
Sbjct: 6   TKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWY--NCNR 56

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4 Length = 86

 Score = 44.2 bits (104), Expect = 2e-06
 Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 109 EAFDKWGKALCESLIPGAQKF-YCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVA 167
            +   + K L E ++    KF +C    CS   I +  +   E+ CP CH+ FC +CK  
Sbjct: 5   SSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYEREQ--LEATCPQCHQTFCVRCKRQ 60

Query: 168 W---HAGIECADFQKLHKD-EPESE 188
           W   H G  C DFQ   +     S 
Sbjct: 61  WEEQHRGRSCEDFQNWKRMNSGPSS 85

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	250
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.78
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.72
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	99.27
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	99.25
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.01
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.85
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	98.75
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	98.57
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.57
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	98.55
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.55
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.55
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	98.55
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	98.55
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.52
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	98.51
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	98.5
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.5
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	98.49
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.47
2ect_A	78	Ring finger protein 126; metal binding protein, st	98.47
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.47
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.44
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.42
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.41
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.41
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.4
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.4
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	98.39
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	98.39
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.35
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	98.34
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.31
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.3
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	98.29
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.27
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.24
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.24
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.21
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.17
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.09
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.08
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.07
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.07
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.03
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.01
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.0
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	97.94
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	97.91
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	97.89
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	97.89
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	97.87
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	97.86
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	97.82
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	97.78
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	97.76
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	97.72
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.68
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	97.65
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	97.59
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	97.58
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	97.55
2ea5_A	68	Cell growth regulator with ring finger domain prot	97.37
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	97.34
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	97.32
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	97.31
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	97.25
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	97.21
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	97.06
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	96.74
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	96.72
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.68
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.54
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	95.93
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	95.71
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	95.51
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	95.2
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	94.81
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	94.68
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	94.57
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	93.99
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	93.9
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	93.63
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	93.53
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	93.48
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	93.2
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	93.11
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	92.96
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	92.88
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	92.58
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	92.53
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	92.52
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	92.44
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	92.1
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	91.94
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	91.73
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	91.69
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	91.56
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	91.42
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	91.34
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	91.23
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	91.12
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	91.11
2ect_A	78	Ring finger protein 126; metal binding protein, st	91.09
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	90.91
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	90.86
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	90.79
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	90.6
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	90.27
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	90.2
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	90.2
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	90.07
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	90.04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	89.69
1z60_A	59	TFIIH basal transcription factor complex P44 subun	89.68
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	89.64
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	89.03
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	88.65
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	88.21
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	88.09
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	87.92
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	87.81
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	87.0
1z60_A	59	TFIIH basal transcription factor complex P44 subun	86.75
3nw0_A	238	Non-structural maintenance of chromosomes element	85.99
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	85.92
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	85.42
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	84.83
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	84.63
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	83.71
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	81.98
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	81.55
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	81.51
1z6u_A	150	NP95-like ring finger protein isoform B; structura	80.38

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.78  E-value=6.1e-20  Score=116.26  Aligned_cols=50  Identities=32%  Similarity=0.834  Sum_probs=44.6

Q ss_pred             CCCccCCCCCcceeccCCCcceEE-e--ccccccccccccccCCCCCcCCCCCCC
Q 025608          199 QKWNRCPNCKFYVEKKDGCSYIRC-R--CGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       199 ~~~~~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      .++|+||+|+++|||++|||||+| +  |+++|||+|+++|+  .|+.+++.|||
T Consensus         4 ~~~k~CP~C~~~Iek~~GCnhmtC~~~~C~~~FCw~C~~~~~--~~~~~~y~C~~   56 (60)
T 1wd2_A            4 ANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWE--PHGSAWYNCNR   56 (60)
T ss_dssp             CCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSG--GGGTSSSSSCS
T ss_pred             ccceECcCCCCeeEeCCCCCcEEECCCCcCCEEeeCcCCCcc--cCCCccccCCC
Confidence            457999999999999999999999 6  99999999999997  45556888886

>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=99.72  E-value=1.2e-17  Score=116.86  Aligned_cols=87  Identities=24%  Similarity=0.500  Sum_probs=77.9

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCc-ccccCCCCCCCCC--CCHHHHhccCChHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV-TSIGCPVTDCGGS--LEPEYCRDILPEEAFDKWG  115 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~i~CP~~~C~~~--l~~~~i~~~l~~~~~~~~~  115 (250)
                      .+.++|+||+++++.++++.+.+|+|.||.+||+.|+...+.++. .++.||..+|...  ++.+.++.+|+++.+++|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky~   82 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQRYK   82 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHHSCHHHHHHHH
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHHHHCCHHHHHHHH
Confidence            456789999999988887777789999999999999999998764 6899999999999  9999999999999999999


Q ss_pred             HHHHhhccCC
Q 025608          116 KALCESLIPG  125 (250)
Q Consensus       116 ~~~~~~~~~~  125 (250)
                      +++.+.++.+
T Consensus        83 ~~~~~~~v~~   92 (94)
T 1wim_A           83 KLQFERSGPS   92 (94)
T ss_dssp             HHHHHSSCSS
T ss_pred             HHHHHhhhcc
Confidence            9988877654

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=99.27  E-value=8.5e-14  Score=95.20  Aligned_cols=73  Identities=32%  Similarity=0.705  Sum_probs=60.7

Q ss_pred             ChHHHHHHHHHHHhhccCCCC-eecCCCCCCCCceecCccCccCcccCCcccchhccccCccc---CCCCCchhHhhhcc
Q 025608          107 PEEAFDKWGKALCESLIPGAQ-KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAW---HAGIECADFQKLHK  182 (250)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~-~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~~~  182 (250)
                      +++++++|.+++.+.++...+ .+|||  +|+++++.+.+  ...+.|+.|+..||+.|+.+|   |.|++|+++++|.+
T Consensus         3 s~~~~e~y~~~l~e~~v~~~~~~~wCP--~C~~~~~~~~~--~~~v~C~~C~~~FC~~C~~~w~~~H~~~sC~~~~~w~~   78 (86)
T 2ct7_A            3 SGSSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE--QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKR   78 (86)
T ss_dssp             CCCCCCSSSSCCCCSCCCSCCCEECCS--SSCCCEECCCS--CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEeECc--CCCchheecCC--CCceEeCCCCCccccccCCchhhcCCCCChHHHHHHHH
Confidence            345677888888888887655 45999  99998887653  466899999999999999999   99999999998764


Q ss_pred             C
Q 025608          183 D  183 (250)
Q Consensus       183 ~  183 (250)
                      +
T Consensus        79 ~   79 (86)
T 2ct7_A           79 M   79 (86)
T ss_dssp             H
T ss_pred             h
Confidence            3

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; NMR {Homo sapiens}

Probab=99.25  E-value=1.8e-13  Score=92.12  Aligned_cols=69  Identities=28%  Similarity=0.601  Sum_probs=60.9

Q ss_pred             cCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCC-----cccchhccccCcccCCCCCchh
Q 025608          105 ILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECP-----NCHRLFCAQCKVAWHAGIECAD  176 (250)
Q Consensus       105 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~-----~C~~~~C~~C~~~~H~~~~C~~  176 (250)
                      +|+++++++|++++.+.++...+.+|||.|+|++++..++  ....+.|+     .|+..||..|+.+||. .+|+.
T Consensus         2 ~l~~~~~~rY~~~~~e~~v~~~~~~~CP~p~C~~~v~~~~--~~~~v~C~~~~~~~C~~~FC~~C~~~wH~-~~C~~   75 (80)
T 2jmo_A            2 HMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEP--DQRKVTCEGGNGLGCGFAFCRECKEAYHE-GECSA   75 (80)
T ss_dssp             CCCCCCCCSCCCSSSCCSSCCCSSCCCCSSSCCCCCCCCS--CTTSBCTTSSSTTCCSCCEETTTTEECCS-SCSSS
T ss_pred             CCCHHHHHHHHHHHHHHHhhhCCcEECCCCCCCcccEECC--CCCcCCCCCCCCCCCCCeeccccCccccC-Ccccc
Confidence            5788889999999999999877778999999999988765  34668998     9999999999999999 99986

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.01  E-value=1.8e-11  Score=90.49  Aligned_cols=118  Identities=23%  Similarity=0.521  Sum_probs=80.0

Q ss_pred             CCceecccCcccccCC----CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHH
Q 025608           39 SRSFVCEICVETKLRN----ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKW  114 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~  114 (250)
                      ...++|+||++.+..+    .....++|||.||.+|+.+|+...       ..||.  |+..+....+..+.        
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~~~~l~~l~--------   67 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCPT--CRKKINHKRYHPIY--------   67 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTC-------SBCTT--TCCBCTTTCEEECB--------
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhC-------CCCCC--CCCcCccccccccc--------
Confidence            3457899999988543    333456999999999999998732       38998  99888876655431        


Q ss_pred             HHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHH
Q 025608          115 GKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMK  194 (250)
Q Consensus       115 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~  194 (250)
                               ...+...|+  -|...+...... ........||..||..|...|...                       
T Consensus        68 ---------i~~~~~~C~--iC~~~~~~~~~~-~~~~~~~~CgH~fc~~Ci~~~~~~-----------------------  112 (133)
T 4ap4_A           68 ---------IGSGTVSCP--ICMDGYSEIVQN-GRLIVSTECGHVFCSQCLRDSLKN-----------------------  112 (133)
T ss_dssp             ---------CSSSSCBCT--TTCCBHHHHHHT-TCCEEEETTSBEEEHHHHHHHHHH-----------------------
T ss_pred             ---------cCCCCCCCC--CCCCcccccccc-CcceEeCCCCChhhHHHHHHHHHc-----------------------
Confidence                     234456788  676655432111 112234478999999998654311                       


Q ss_pred             HHhcCCCccCCCCCcceecc
Q 025608          195 LAQNQKWNRCPNCKFYVEKK  214 (250)
Q Consensus       195 ~~~~~~~~~CP~C~~~i~k~  214 (250)
                            .+.||.|+..+.++
T Consensus       113 ------~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A          113 ------ANTCPTCRKKINHK  126 (133)
T ss_dssp             ------CSBCTTTCCBCCGG
T ss_pred             ------CCCCCCCCCcCChh
Confidence                  16999999988765

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.85  E-value=2.3e-09  Score=82.77  Aligned_cols=101  Identities=22%  Similarity=0.471  Sum_probs=65.4

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGK  116 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~  116 (250)
                      .-...+.|+||++.+..+  . ..+|||.||.+|+..++...      ...||.  |+..+..+.+.   ....++   +
T Consensus        14 ~~~~~~~C~IC~~~~~~p--v-~~~CgH~fC~~Ci~~~~~~~------~~~CP~--Cr~~~~~~~~~---~~~~~~---~   76 (170)
T 3hcs_A           14 PLESKYECPICLMALREA--V-QTPCGHRFCKACIIKSIRDA------GHKCPV--DNEILLENQLF---PDNFAK---R   76 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSE--E-ECTTSCEEEHHHHHHHHHHH------CSBCTT--TCCBCCGGGCE---ECHHHH---H
T ss_pred             CCCCCCCCCCCChhhcCc--E-ECCCCCHHHHHHHHHHHHhC------CCCCCC--CccCcchhhhh---hhHHHH---H
Confidence            345567899999988654  2 25999999999999999854      138997  88888776432   111111   1


Q ss_pred             HHHhhccCCCCeecCCCCCCCCceecCccC------ccCcccCCcccchh
Q 025608          117 ALCESLIPGAQKFYCPFKDCSALLIDDAGE------AIRESECPNCHRLF  160 (250)
Q Consensus       117 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~------~~~~~~C~~C~~~~  160 (250)
                      .+      ..-.++||+.+|+..+....-.      ....+.|+.|+..+
T Consensus        77 ~i------~~l~v~C~n~GC~~~~~~~~l~~H~~~C~~~~v~C~~C~~~~  120 (170)
T 3hcs_A           77 EI------LSLMVKCPNEGCLHKMELRHLEDHQAHCEFALMDCPQCQRPF  120 (170)
T ss_dssp             HH------HTSEEECCSTTCCCEEEGGGHHHHHTTCTTSEEECTTTCCEE
T ss_pred             HH------hhcccCCCCCCCCceecHhHHHHHHhcCCceeeECCCCChHH
Confidence            11      1245799988999887765321      12345565555443

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

Probab=98.75  E-value=9.4e-09  Score=70.22  Aligned_cols=64  Identities=20%  Similarity=0.504  Sum_probs=48.1

Q ss_pred             cCCCCceecccCcccccCCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           36 SETSRSFVCEICVETKLRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      ....+.++|+||++.+...+. +..++|+|.||.+|+..|+...    ...+.||.  |+..+....+..+
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~----~~~~~CP~--Cr~~~~~~~i~~l   74 (88)
T 2ct2_A           10 DALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASS----INGVRCPF--CSKITRITSLTQL   74 (88)
T ss_dssp             CCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHC----SSCBCCTT--TCCCBCCSSTTTS
T ss_pred             hhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcC----CCCcCCCC--CCCcccchhHHHH
Confidence            344556789999999876432 4456999999999999999854    24679998  8888777665544

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.57  E-value=4.6e-08  Score=66.16  Aligned_cols=62  Identities=24%  Similarity=0.547  Sum_probs=46.9

Q ss_pred             ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      .....+.++|+||++.+..+.   .++|+|.||.+|+..|+......+ ....||.  |+..+..+.+
T Consensus        13 ~~~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~~~~~-~~~~CP~--Cr~~~~~~~~   74 (85)
T 2ecv_A           13 LVNVKEEVTCPICLELLTQPL---SLDCGHSFCQACLTANHKKSMLDK-GESSCPV--CRISYQPENI   74 (85)
T ss_dssp             CCCCCCCCCCTTTCSCCSSCB---CCSSSCCBCTTHHHHHHHHHHHTT-SCCCCTT--TCCSSCSSSC
T ss_pred             HHHccCCCCCCCCCcccCCce---eCCCCCHHHHHHHHHHHHHhhcCC-CCCcCCC--CCCccCHHhc
Confidence            344455678999999886543   349999999999999999765443 3679998  8888776544

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=98.57  E-value=9.9e-09  Score=68.65  Aligned_cols=60  Identities=25%  Similarity=0.458  Sum_probs=45.7

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR  103 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  103 (250)
                      .+.++|+||++.+..+.   .++|+|.||.+|+..|+............||.  |+..+..+.+.
T Consensus        10 ~~~~~C~IC~~~~~~p~---~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~--Cr~~~~~~~l~   69 (79)
T 2egp_A           10 QEEVTCPICLELLTEPL---SLDCGHSLCRACITVSNKEAVTSMGGKSSCPV--CGISYSFEHLQ   69 (79)
T ss_dssp             CCCCEETTTTEECSSCC---CCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSS--SCCCCCSSGGG
T ss_pred             ccCCCCcCCCcccCCee---ECCCCCHHHHHHHHHHHHhcccCCCCCCcCCC--CCCcCCHhhCC
Confidence            45678999999886543   24999999999999998864433345789998  88888765543

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

Probab=98.55  E-value=7.1e-08  Score=62.13  Aligned_cols=54  Identities=20%  Similarity=0.536  Sum_probs=41.6

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      .....+.|+||++.+..+..   ++|+|.||..|+..|+.      .....||.  |+..+..++
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~---~~CgH~fC~~Ci~~~~~------~~~~~CP~--Cr~~~~~~~   64 (66)
T 2ecy_A           11 TVEDKYKCEKCHLVLCSPKQ---TECGHRFCESCMAALLS------SSSPKCTA--CQESIVKDK   64 (66)
T ss_dssp             SCCCCEECTTTCCEESSCCC---CSSSCCCCHHHHHHHHT------TSSCCCTT--TCCCCCTTT
T ss_pred             cCCcCCCCCCCChHhcCeeE---CCCCCHHHHHHHHHHHH------hCcCCCCC--CCcCCChhh
Confidence            33556889999998865432   49999999999999986      13467998  888877654

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.55  E-value=1.2e-07  Score=67.62  Aligned_cols=69  Identities=22%  Similarity=0.553  Sum_probs=49.1

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc-CChHHHHHHHHHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI-LPEEAFDKWGKALC  119 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~-l~~~~~~~~~~~~~  119 (250)
                      +.|+||++.+..+.   .++|+|.||..|+..|+...    ...+.||.  |+..+....+... .-...++.+.+.+.
T Consensus        22 ~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~----~~~~~CP~--Cr~~~~~~~~~~~~~l~~~~~~~~~~~~   91 (112)
T 1jm7_A           22 LECPICLELIKEPV---STKCDHIFCKFCMLKLLNQK----KGPSQCPL--CKNDITKRSLQESTRFSQLVEELLKIIC   91 (112)
T ss_dssp             TSCSSSCCCCSSCC---BCTTSCCCCSHHHHHHHHSS----SSSCCCTT--TSCCCCTTTCBCCCSSSHHHHHHHHHHH
T ss_pred             CCCcccChhhcCeE---ECCCCCHHHHHHHHHHHHhC----CCCCCCcC--CCCcCCHhhcCccHHHHHHHHHHHHHHH
Confidence            47999999886543   24999999999999998843    23578998  9988887766432 23445555554443

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=98.55  E-value=5e-08  Score=70.28  Aligned_cols=82  Identities=21%  Similarity=0.469  Sum_probs=57.0

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHHH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALC  119 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~  119 (250)
                      +.+.|+||++.+..+.   .++|||.||..|+..|+...      ...||.  |+..+....+... ..    .+.+.+ 
T Consensus        22 ~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~------~~~CP~--Cr~~~~~~~~~~~-~~----~l~~~i-   84 (116)
T 1rmd_A           22 KSISCQICEHILADPV---ETSCKHLFCRICILRCLKVM------GSYCPS--CRYPCFPTDLESP-VK----SFLNIL-   84 (116)
T ss_dssp             HHTBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHT------CSBCTT--TCCBCCGGGCBCC-CH----HHHHHH-
T ss_pred             CCCCCCCCCcHhcCcE---EcCCCCcccHHHHHHHHhHC------cCcCCC--CCCCCCHhhcccc-HH----HHHHHH-
Confidence            4568999999876432   25999999999999999852      347997  9999888765433 11    122222 


Q ss_pred             hhccCCCCeecCCCCCCCCceecC
Q 025608          120 ESLIPGAQKFYCPFKDCSALLIDD  143 (250)
Q Consensus       120 ~~~~~~~~~~~Cp~~~C~~~~~~~  143 (250)
                           ..-.++||+.+|+..+...
T Consensus        85 -----~~l~v~C~~~gC~~~~~~~  103 (116)
T 1rmd_A           85 -----NSLMVKCPAQDCNEEVSLE  103 (116)
T ss_dssp             -----HHCEEECCSTTCCCEEEHH
T ss_pred             -----HHhcCCCCCCCCcchhhHh
Confidence                 1234589988898776654

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.55  E-value=5.5e-08  Score=65.77  Aligned_cols=62  Identities=21%  Similarity=0.402  Sum_probs=46.3

Q ss_pred             ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ...-.+.+.|+||++.+..+.   .++|+|.||..|+..|+..... ......||.  |+..+..+.+
T Consensus        13 ~~~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~~~-~~~~~~CP~--Cr~~~~~~~~   74 (85)
T 2ecw_A           13 LEMIKEEVTCPICLELLKEPV---SADCNHSFCRACITLNYESNRN-TDGKGNCPV--CRVPYPFGNL   74 (85)
T ss_dssp             CCCCCTTTSCTTTCSCCSSCE---ECTTSCCBCHHHHHHHHHHSBC-TTSCBCCTT--TCCCCCTTCC
T ss_pred             HHhCccCCCCcCCChhhCcce---eCCCCCHHHHHHHHHHHHhccC-CCCCCCCCC--CCCcCCHHhC
Confidence            333455678999999886543   3589999999999999986542 234679997  8888876644

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

Probab=98.55  E-value=7e-08  Score=63.31  Aligned_cols=58  Identities=24%  Similarity=0.477  Sum_probs=44.0

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .....+.|+||++.+..+  ..+.+|+|.||..|+..|+..       ...||.  |+..+...++...
T Consensus        11 ~~~~~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~-------~~~CP~--Cr~~~~~~~~~~~   68 (72)
T 2djb_A           11 ELTPYILCSICKGYLIDA--TTITECLHTFCKSCIVRHFYY-------SNRCPK--CNIVVHQTQPLSG   68 (72)
T ss_dssp             CCCGGGSCTTTSSCCSSC--EECSSSCCEECHHHHHHHHHH-------CSSCTT--TCCCCCSSCSCCC
T ss_pred             hcCCCCCCCCCChHHHCc--CEECCCCCHHHHHHHHHHHHc-------CCcCCC--cCcccCccccccc
Confidence            334567899999987653  334599999999999999974       358997  9888877655443

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=98.52  E-value=1.5e-07  Score=61.09  Aligned_cols=54  Identities=22%  Similarity=0.536  Sum_probs=40.8

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ......+|+||++.+........++|+|.||..|+..|+...       ..||.  |...+..
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~~   63 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITN-------KKCPI--CRVDIEA   63 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHC-------SBCTT--TCSBSCS
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcC-------CCCcC--cCccccC
Confidence            334556799999988655445566999999999999999742       25998  8766543

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=98.51  E-value=3.2e-08  Score=64.69  Aligned_cols=57  Identities=19%  Similarity=0.541  Sum_probs=43.5

Q ss_pred             CCceecccCcccccCC----CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc
Q 025608           39 SRSFVCEICVETKLRN----ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD  104 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  104 (250)
                      ....+|+||++.+..+    .....++|+|.||.+|+..|+...       ..||.  |...+....+..
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~~~~~~~   68 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCPT--CRKKINHKRYHP   68 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC-------SBCTT--TCCBCCCCSCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC-------CCCCC--CCCccChhheee
Confidence            4556899999987542    334567999999999999999743       48998  888887665543

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

Probab=98.50  E-value=3.1e-08  Score=63.25  Aligned_cols=56  Identities=20%  Similarity=0.559  Sum_probs=42.9

Q ss_pred             ceecccCcccccCC----CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           41 SFVCEICVETKLRN----ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        41 ~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .++|+||++.+..+    +.+..++|+|.||.+|+..|+..       ...||.  |+..+..+++..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP~--Cr~~~~~~~~~~~   62 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCPT--CRKKINHKRYHPI   62 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH-------CSBCTT--TCCBCTTTCEEEC
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc-------CCCCCC--CCccCCccceeee
Confidence            46799999987532    33345699999999999999984       248997  9988887665543

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=98.50  E-value=1e-07  Score=58.93  Aligned_cols=50  Identities=24%  Similarity=0.539  Sum_probs=38.7

Q ss_pred             CceecccCcccccC-CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           40 RSFVCEICVETKLR-NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        40 ~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ...+|+||++.+.. ......++|+|.||.+|+..|+...       ..||.  |...++
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG-------YRCPL--CSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT-------CCCTT--SCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC-------CcCCC--CCCcCC
Confidence            34579999999853 3345567999999999999999854       67997  776653

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.49  E-value=3.7e-08  Score=64.75  Aligned_cols=56  Identities=20%  Similarity=0.626  Sum_probs=42.1

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      .....+.|+||++.+..+  . .++|+|.||.+|+..|+.    .......||.  |+..+..++
T Consensus        16 ~~~~~~~C~IC~~~~~~~--~-~~~CgH~fC~~Ci~~~~~----~~~~~~~CP~--Cr~~~~~~~   71 (73)
T 2ysl_A           16 KLQEEVICPICLDILQKP--V-TIDCGHNFCLKCITQIGE----TSCGFFKCPL--CKTSVRKNA   71 (73)
T ss_dssp             CCCCCCBCTTTCSBCSSE--E-ECTTCCEEEHHHHHHHCS----SSCSCCCCSS--SCCCCCCCC
T ss_pred             hCccCCEeccCCcccCCe--E-EcCCCChhhHHHHHHHHH----cCCCCCCCCC--CCCcCCccc
Confidence            345567899999987643  2 349999999999999986    2234678998  888776654

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.47  E-value=4.7e-08  Score=62.78  Aligned_cols=57  Identities=21%  Similarity=0.413  Sum_probs=42.4

Q ss_pred             ceecccCcc-cccCCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           41 SFVCEICVE-TKLRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        41 ~~~C~iC~~-~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .+.|+||++ .+..+.. +..++|||.||.+|+.+++..      ....||.  |+..+..+.++..
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~------~~~~CP~--Cr~~~~~~~~~~~   61 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR------GAGNCPE--CGTPLRKSNFRVQ   61 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT------TSSSCTT--TCCCCSSCCCEEE
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHc------CCCcCCC--CCCccccccceee
Confidence            457999999 5654432 234699999999999999863      2468997  9988887766544

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.47  E-value=4.7e-08  Score=65.15  Aligned_cols=57  Identities=26%  Similarity=0.592  Sum_probs=44.1

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR  103 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  103 (250)
                      .....+|+||++.+........++|+|.||..|+..|+...       ..||.  |...+....+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~~~~~~   68 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH-------DSCPV--CRKSLTGQNTA   68 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTT-------CSCTT--TCCCCCCSCSC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcC-------CcCcC--cCCccCCcccC
Confidence            34556899999998766555566999999999999998632       47998  88877765443

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

Probab=98.47  E-value=1.6e-07  Score=61.86  Aligned_cols=52  Identities=21%  Similarity=0.608  Sum_probs=40.6

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      .....+|+||++.+........++|+|.||..|+..|+...       ..||.  |...+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-------~~CP~--Cr~~~~   63 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR-------KVCPL--CNMPVL   63 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC-------SBCTT--TCCBCS
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC-------CcCCC--cCcccc
Confidence            34456799999998766655556999999999999999742       27998  876654

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

Probab=98.44  E-value=9.1e-08  Score=63.75  Aligned_cols=56  Identities=18%  Similarity=0.371  Sum_probs=40.3

Q ss_pred             CCceecccCcccccCCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           39 SRSFVCEICVETKLRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      .+.++|+||++.+..++. +...+|||.||..|+.+++..      ....||.  |...+....+
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~------~~~~CP~--CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTD------ENGLCPA--CRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTS------SCSBCTT--TCCBCSSCSS
T ss_pred             ccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhc------CCCCCCC--CCCccCCCch
Confidence            455789999998864332 222259999999999988752      3468998  8887776543

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=98.42  E-value=5.1e-07  Score=65.12  Aligned_cols=85  Identities=19%  Similarity=0.403  Sum_probs=58.3

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGK  116 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~  116 (250)
                      .-...+.|+||++.+..+  . .++|+|.||.+|+..|+...      ...||.  |+..+....+.   ....+++   
T Consensus        14 ~~~~~~~C~IC~~~~~~p--~-~~~CgH~fC~~Ci~~~~~~~------~~~CP~--Cr~~~~~~~~~---~~~~l~~---   76 (118)
T 3hct_A           14 PLESKYECPICLMALREA--V-QTPCGHRFCKACIIKSIRDA------GHKCPV--DNEILLENQLF---PDNFAKR---   76 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSE--E-ECTTSCEEEHHHHHHHHHHH------CSBCTT--TCCBCCGGGCE---ECHHHHH---
T ss_pred             CCCCCCCCCcCChhhcCe--E-ECCcCChhhHHHHHHHHhhC------CCCCCC--CCCCcCHHhcc---cCHHHHH---
Confidence            335567899999987654  2 34899999999999999854      128998  88888775432   2221111   


Q ss_pred             HHHhhccCCCCeecCCCCCCCCceecCc
Q 025608          117 ALCESLIPGAQKFYCPFKDCSALLIDDA  144 (250)
Q Consensus       117 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~  144 (250)
                      .+      ..-.++||+.+|...+....
T Consensus        77 ~i------~~l~v~C~n~gC~~~~~~~~   98 (118)
T 3hct_A           77 EI------LSLMVKCPNEGCLHKMELRH   98 (118)
T ss_dssp             HH------HTSEEECSSTTCCCEEEGGG
T ss_pred             HH------ccceeECCCCCCCCEEeeHH
Confidence            11      13457999889998877653

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.41  E-value=3.2e-07  Score=58.39  Aligned_cols=47  Identities=19%  Similarity=0.659  Sum_probs=35.6

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      .....+.|+||++.+..+.   .++|+|.||..|+.+|+..    ......||.
T Consensus        16 ~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~----~~~~~~CP~   62 (63)
T 2ysj_A           16 KLQEEVICPICLDILQKPV---TIDCGHNFCLKCITQIGET----SCGFFKCPL   62 (63)
T ss_dssp             CCCCCCBCTTTCSBCSSCE---ECTTSSEECHHHHHHHHHH----CSSCCCCSC
T ss_pred             hCccCCCCCcCCchhCCeE---EeCCCCcchHHHHHHHHHc----CCCCCcCcC
Confidence            3355678999999887542   3499999999999999984    223567886

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

Probab=98.41  E-value=1.8e-07  Score=60.55  Aligned_cols=53  Identities=21%  Similarity=0.609  Sum_probs=40.0

Q ss_pred             CCCCceecccCcccccCC----CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           37 ETSRSFVCEICVETKLRN----ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      .....++|+||++.+...    ..+..++|+|.||.+|+..|+..       ...||.  |+..+.
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP~--Cr~~~~   67 (69)
T 2ea6_A           11 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCPT--CRKKIN   67 (69)
T ss_dssp             CTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH-------CSSCTT--TCCCCC
T ss_pred             CCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc-------CCCCCC--CCCccC
Confidence            335567899999987532    33356799999999999999974       247997  877664

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=98.40  E-value=3.6e-07  Score=63.91  Aligned_cols=55  Identities=24%  Similarity=0.559  Sum_probs=43.3

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .+.|+||++.+..+  ...++|+|.||..|+..|+...      ...||.  |...+..+.+...
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~CgH~FC~~Ci~~~~~~~------~~~CP~--Cr~~~~~~~l~~~   76 (100)
T 3lrq_A           22 VFRCFICMEKLRDA--RLCPHCSKLCCFSCIRRWLTEQ------RAQCPH--CRAPLQLRELVNC   76 (100)
T ss_dssp             HTBCTTTCSBCSSE--EECTTTCCEEEHHHHHHHHHHT------CSBCTT--TCCBCCGGGCEEC
T ss_pred             CCCCccCCccccCc--cccCCCCChhhHHHHHHHHHHC------cCCCCC--CCCcCCHHHhHhh
Confidence            45799999988643  3336999999999999999854      168998  9999988776544

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=98.40  E-value=1.8e-07  Score=64.38  Aligned_cols=50  Identities=20%  Similarity=0.534  Sum_probs=38.7

Q ss_pred             CCCceecccCcccccCCCceecCC-CCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608           38 TSRSFVCEICVETKLRNESFSIKG-CSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL   97 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l   97 (250)
                      -...+.|+||++.+..+.   .++ |||.||..|+..|+...     ....||.  |...+
T Consensus        10 ~~~~~~C~IC~~~~~~p~---~~~~CgH~fC~~Ci~~~~~~~-----~~~~CP~--Cr~~~   60 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDAV---VIPCCGNSYCDECIRTALLES-----DEHTCPT--CHQND   60 (92)
T ss_dssp             CCTTTEETTTTEECSSCE---ECTTTCCEECHHHHHHHHHHC-----TTCCCTT--TCCSS
T ss_pred             CCcCCCCCCCChhhcCce---ECCCCCCHHHHHHHHHHHHhc-----CCCcCcC--CCCcC
Confidence            345678999999887543   347 99999999999999732     2368998  88776

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

Probab=98.39  E-value=1.1e-07  Score=62.12  Aligned_cols=58  Identities=17%  Similarity=0.410  Sum_probs=44.3

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      ......++|+||++.+...  . .++|+|.||..|+..|+...       ..||.  |...+..+.+...
T Consensus        10 ~~~~~~~~C~IC~~~~~~~--~-~~~CgH~fC~~Ci~~~~~~~-------~~CP~--Cr~~~~~~~~~~p   67 (71)
T 2d8t_A           10 APSLTVPECAICLQTCVHP--V-SLPCKHVFCYLCVKGASWLG-------KRCAL--CRQEIPEDFLDSG   67 (71)
T ss_dssp             CSSSSCCBCSSSSSBCSSE--E-EETTTEEEEHHHHHHCTTCS-------SBCSS--SCCBCCHHHHSCS
T ss_pred             ccCCCCCCCccCCcccCCC--E-EccCCCHHHHHHHHHHHHCC-------CcCcC--cCchhCHhhccCC
Confidence            3345567899999987543  2 34899999999999988632       58998  9999988877643

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=98.39  E-value=2e-07  Score=62.04  Aligned_cols=67  Identities=18%  Similarity=0.281  Sum_probs=47.8

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh-ccCChHHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR-DILPEEAFDKWGK  116 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~~  116 (250)
                      ...+.|+||++.+..+.   .++|||.||..|+..|+..      ....||.  |+..+....+. +..-...++.|.+
T Consensus         6 ~~~~~C~IC~~~~~~Pv---~~~CgH~fc~~Ci~~~~~~------~~~~CP~--C~~~~~~~~l~~n~~l~~~i~~~~~   73 (78)
T 1t1h_A            6 PEYFRCPISLELMKDPV---IVSTGQTYERSSIQKWLDA------GHKTCPK--SQETLLHAGLTPNYVLKSLIALWCE   73 (78)
T ss_dssp             SSSSSCTTTSCCCSSEE---EETTTEEEEHHHHHHHHTT------TCCBCTT--TCCBCSSCCCEECTTTHHHHHHHHH
T ss_pred             cccCCCCCccccccCCE---EcCCCCeecHHHHHHHHHH------CcCCCCC--CcCCCChhhCccCHHHHHHHHHHHH
Confidence            45678999999886542   2489999999999999962      2467998  88888765443 3334555666553

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

Probab=98.35  E-value=2.7e-07  Score=60.94  Aligned_cols=52  Identities=21%  Similarity=0.614  Sum_probs=40.8

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .+..+|+||++.+...+....++|+|.||.+|+..|+...       ..||.  |...+..
T Consensus        21 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~-------~~CP~--Cr~~~~~   72 (75)
T 1x4j_A           21 SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN-------RTCPI--CRADSGP   72 (75)
T ss_dssp             SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHC-------SSCTT--TCCCCCC
T ss_pred             CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcC-------CcCcC--cCCcCCC
Confidence            4556899999998766655666999999999999998742       37998  8766643

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

Probab=98.34  E-value=6.9e-07  Score=59.87  Aligned_cols=50  Identities=22%  Similarity=0.601  Sum_probs=39.3

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      .....+.|+||++.+..+   ..++|+|.||..|+..|+..       ...||.  |+..+.
T Consensus        11 ~~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~-------~~~CP~--Cr~~~~   60 (81)
T 2csy_A           11 EEEIPFRCFICRQAFQNP---VVTKCRHYFCESCALEHFRA-------TPRCYI--CDQPTG   60 (81)
T ss_dssp             CCCCCSBCSSSCSBCCSE---EECTTSCEEEHHHHHHHHHH-------CSBCSS--SCCBCC
T ss_pred             cCCCCCCCcCCCchhcCe---eEccCCCHhHHHHHHHHHHC-------CCcCCC--cCcccc
Confidence            334567899999988653   24699999999999999973       357998  888776

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

Probab=98.31  E-value=2.6e-07  Score=57.05  Aligned_cols=50  Identities=20%  Similarity=0.545  Sum_probs=37.1

Q ss_pred             CceecccCcccccCCCceecCC-CCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           40 RSFVCEICVETKLRNESFSIKG-CSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      +..+|+||++.+...+....++ |+|.||.+|+..|+..       ...||.  |...+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~-------~~~CP~--Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-------HSTCPL--CRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-------CCSCSS--SCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc-------CCcCcC--CCCEeE
Confidence            3457999999987654444444 9999999999999853       247998  776553

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

Probab=98.30  E-value=4.6e-07  Score=62.25  Aligned_cols=52  Identities=21%  Similarity=0.607  Sum_probs=40.4

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ....+|+||++.+........++|+|.||..|+..|+...       -.||.  |...+..
T Consensus        38 ~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~-------~~CP~--Cr~~~~~   89 (91)
T 2l0b_A           38 GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS-------GTCPV--CRCMFPP   89 (91)
T ss_dssp             SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTT-------CBCTT--TCCBSSC
T ss_pred             CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcC-------CcCcC--cCccCCC
Confidence            4556799999998766555556899999999999998632       37998  8776643

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=98.29  E-value=5.1e-07  Score=59.47  Aligned_cols=52  Identities=19%  Similarity=0.487  Sum_probs=39.2

Q ss_pred             cCCCCceecccCcccccCCCceecCC-CCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKG-CSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL   97 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l   97 (250)
                      ......+.|+||++.+..+.  . ++ |+|.||..|+..|+...     ....||.  |+..+
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~--~-~~~CgH~fC~~Ci~~~~~~~-----~~~~CP~--Cr~~~   62 (74)
T 2yur_A           10 DPIPDELLCLICKDIMTDAV--V-IPCCGNSYCDECIRTALLES-----DEHTCPT--CHQND   62 (74)
T ss_dssp             CCSCGGGSCSSSCCCCTTCE--E-CSSSCCEECTTHHHHHHHHS-----SSSCCSS--SCCSS
T ss_pred             ccCCCCCCCcCCChHHhCCe--E-cCCCCCHHHHHHHHHHHHhc-----CCCcCCC--CCCcC
Confidence            33455678999999887543  2 46 99999999999999843     2468998  87653

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.27  E-value=5.4e-07  Score=62.29  Aligned_cols=61  Identities=25%  Similarity=0.450  Sum_probs=45.6

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC-CCHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS-LEPEYC  102 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~-l~~~~i  102 (250)
                      ...+.|+||++.+..+.  .+..|||.||+.|+..|+...-. +.....||..+|... +....+
T Consensus         5 ~~~~~CPI~~~~~~dPV--~~~~cGh~f~r~cI~~~l~~~~~-~~~~~~CP~tgc~~~~l~~~~L   66 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKPV--KNKVCGHTYEEDAIVRMIESRQK-RKKKAYCPQIGCSHTDIRKSDL   66 (94)
T ss_dssp             SSCCBCTTTCSBCSSEE--EESSSCCEEEHHHHHHHHHHHHT-TTCCBCCCSTTCCCCCBCGGGE
T ss_pred             CcEeECcCcCchhcCCE--EcCCCCCeecHHHHHHHHHHccC-cCCCCCCCcCcCcccccCHhhC
Confidence            45678999999887543  23259999999999999986421 224678999999977 776554

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.24  E-value=9.9e-07  Score=54.94  Aligned_cols=45  Identities=24%  Similarity=0.639  Sum_probs=34.1

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      ...+.|+||++.+..+.   .++|+|.||.+|+..|+...    .....||.
T Consensus        13 ~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~----~~~~~CP~   57 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEPV---IIECGHNFCKACITRWWEDL----ERDFPCPV   57 (58)
T ss_dssp             CCCCBCSSSCCBCSSCC---CCSSCCCCCHHHHHHHTTSS----CCSCCCSC
T ss_pred             ccCCCCccCCcccCccE---eCCCCCccCHHHHHHHHHhc----CCCCCCCC
Confidence            45568999999887543   35899999999999997631    23567885

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=98.24  E-value=6.9e-07  Score=62.30  Aligned_cols=68  Identities=25%  Similarity=0.468  Sum_probs=47.3

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh-ccCChHHHHHHHHHH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR-DILPEEAFDKWGKAL  118 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~~~~  118 (250)
                      +.+.|+||++.+..+  ..+.+|||.||..|+..|+..       ...||.  |+..+....+. +.+-.+.++.|.+..
T Consensus        21 ~~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~-------~~~CP~--Cr~~~~~~~l~~n~~l~~~i~~~~~~~   89 (99)
T 2y43_A           21 DLLRCGICFEYFNIA--MIIPQCSHNYCSLCIRKFLSY-------KTQCPT--CCVTVTEPDLKNNRILDELVKSLNFAR   89 (99)
T ss_dssp             HHTBCTTTCSBCSSE--EECTTTCCEEEHHHHHHHHTT-------CCBCTT--TCCBCCGGGCEECHHHHHHHHHHHHHH
T ss_pred             CCCCcccCChhhCCc--CEECCCCCHhhHHHHHHHHHC-------CCCCCC--CCCcCChhhCCcCHHHHHHHHHHHHHH
Confidence            346799999988653  233489999999999999873       258997  99888875543 222334555555443

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=98.21  E-value=3.2e-07  Score=68.12  Aligned_cols=46  Identities=26%  Similarity=0.777  Sum_probs=35.6

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      .+.|+||++.+..+   ..++|||.||.+|+..|+..       ...||.  |...+.
T Consensus        53 ~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~-------~~~CP~--Cr~~~~   98 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLNCAHSFCSYCINEWMKR-------KIECPI--CRKDIK   98 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEETTSCEEEHHHHHHHTTT-------CSBCTT--TCCBCC
T ss_pred             cCCCcccCcccCCc---eECCCCCCccHHHHHHHHHc-------CCcCCC--CCCcCC
Confidence            35799999988643   23599999999999999762       246998  887664

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=98.17  E-value=2.4e-06  Score=61.04  Aligned_cols=54  Identities=22%  Similarity=0.386  Sum_probs=39.6

Q ss_pred             eecccCcccccCCC---------------ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRNE---------------SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .+|+||++.+....               +..+++|+|.||..||..|+....  ......||.  |...+..
T Consensus        26 ~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~--~~~~~~CP~--CR~~~~~   94 (114)
T 1v87_A           26 EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN--KDGSLQCPS--CKTIYGE   94 (114)
T ss_dssp             CEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC--CSSCCBCTT--TCCBSSS
T ss_pred             CcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHccc--CCCCCcCCC--CCCccCC
Confidence            47999999985432               233679999999999999996332  134568998  8876653

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=98.09  E-value=3.3e-06  Score=61.31  Aligned_cols=49  Identities=29%  Similarity=0.625  Sum_probs=38.5

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ..+.|+||++.+..+.   .++|||.||..|+..|+..      ....||.  |+..+..
T Consensus        51 ~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~------~~~~CP~--Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRPI---TTVCQHNVCKDCLDRSFRA------QVFSCPA--CRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSEE---ECTTSCEEEHHHHHHHHHT------TCCBCTT--TCCBCCT
T ss_pred             cCCCCCcCChHHcCcE---EeeCCCcccHHHHHHHHhH------CcCCCCC--CCccCCC
Confidence            3467999999887432   3499999999999999981      3458998  8887765

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=98.08  E-value=3.8e-06  Score=56.80  Aligned_cols=68  Identities=9%  Similarity=-0.018  Sum_probs=47.4

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh-ccCChHHHHHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR-DILPEEAFDKWG  115 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~  115 (250)
                      .....+.|+||++.+..+.   .++|||.||+.|+..|+..       ...||.  |+..+..+.+. +..-...++.|.
T Consensus        10 ~~p~~~~CpI~~~~m~dPV---~~~cGhtf~r~~I~~~l~~-------~~~cP~--~~~~l~~~~l~pn~~L~~~i~~~~   77 (85)
T 2kr4_A           10 DAPDEFRDPLMDTLMTDPV---RLPSGTVMDRSIILRHLLN-------SPTDPF--NRQMLTESMLEPVPELKEQIQAWM   77 (85)
T ss_dssp             TCCTTTBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHH-------CSBCTT--TCCBCCGGGCEECHHHHHHHHHHH
T ss_pred             cCchheECcccCchhcCCe---ECCCCCEECHHHHHHHHhc-------CCCCCC--CcCCCChHhcchHHHHHHHHHHHH
Confidence            3456788999999887543   3489999999999999983       247998  88888876432 111234445554


Q ss_pred             H
Q 025608          116 K  116 (250)
Q Consensus       116 ~  116 (250)
                      .
T Consensus        78 ~   78 (85)
T 2kr4_A           78 R   78 (85)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=98.07  E-value=7.9e-07  Score=55.20  Aligned_cols=46  Identities=20%  Similarity=0.562  Sum_probs=35.4

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .+.+.|+||++.+..+   ..++|+|.||..|+..          ..+.||.  |+..+..
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~----------~~~~CP~--Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEA----------SGMQCPI--CQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSS----------SSSSCSS--CCSSSSC
T ss_pred             ccCCCceEeCCccCCe---EEcCCCCcccHHHHcc----------CCCCCCc--CCcEeec
Confidence            4556799999988754   3458999999999876          3578998  7766553

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=98.07  E-value=1.4e-07  Score=70.26  Aligned_cols=86  Identities=21%  Similarity=0.407  Sum_probs=54.1

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh------ccCChHHH
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR------DILPEEAF  111 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~------~~l~~~~~  111 (250)
                      -...+.|+||++.+..+  + .++|||.||..|+..|+..      ....||.  |...+..+...      .++....+
T Consensus        28 l~~~~~C~IC~~~~~~p--v-~~~CgH~FC~~Ci~~~~~~------~~~~CP~--Cr~~~~~~~~~~~l~~~~~~~d~~~   96 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP--F-QAQCGHRYCSFCLASILSS------GPQNCAA--CVHEGIYEEGISILESSSAFPDNAA   96 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE--E-ECTTSCEEEHHHHHHHGGG------SCEECHH--HHHTTCCCTTTTEECGGGCEECHHH
T ss_pred             CCcCcCCCCCChhhcCc--E-ECCCCCccCHHHHHHHHhc------CCCCCCC--CCCcccccccccccchhhhcccHHH
Confidence            35567899999988654  2 2599999999999999852      2357997  76554333221      12222222


Q ss_pred             HHHHHHHHhhccCCCCeecCCCCCCCCceecC
Q 025608          112 DKWGKALCESLIPGAQKFYCPFKDCSALLIDD  143 (250)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~  143 (250)
                      +   +.+      ..-.++||+.+|...+...
T Consensus        97 ~---~~i------~~L~v~Cpn~GC~~~~~l~  119 (141)
T 3knv_A           97 R---REV------ESLPAVCPSDGCTWKGTLK  119 (141)
T ss_dssp             H---HHH------HTSEEECCSTTCCCEEEHH
T ss_pred             H---HHH------cccccccCCCCCCCEeEHH
Confidence            1   111      1345699988888776654

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

Probab=98.03  E-value=3.9e-06  Score=54.03  Aligned_cols=47  Identities=26%  Similarity=0.663  Sum_probs=36.5

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ..+|+||++.+..+  ...++|+|.||.+|+..|+...       ..||.  |+..+.
T Consensus         5 ~~~C~IC~~~~~~~--~~~~~C~H~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~   51 (68)
T 1chc_A            5 AERCPICLEDPSNY--SMALPCLHAFCYVCITRWIRQN-------PTCPL--CKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCSC--EEETTTTEEESTTHHHHHHHHS-------CSTTT--TCCCCC
T ss_pred             CCCCeeCCccccCC--cEecCCCCeeHHHHHHHHHhCc-------CcCcC--CChhhH
Confidence            35799999987643  2356999999999999998632       37998  887665

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=98.01  E-value=2.6e-06  Score=60.33  Aligned_cols=49  Identities=27%  Similarity=0.733  Sum_probs=38.1

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ..+.|+||++.+..+  ..+.+|||.||..|+..|+..       ...||.  |+..+..
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~-------~~~CP~--Cr~~~~~   62 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA--TTIIECLHSFCKTCIVRYLET-------SKYCPI--CDVQVHK   62 (108)
T ss_dssp             GGTBCTTTSSBCSSE--EEETTTCCEEEHHHHHHHHTS-------CSBCTT--TCCBSCS
T ss_pred             CcCCCccCChHHhCc--CEeCCCCChhhHHHHHHHHHh-------CCcCcC--CCccccc
Confidence            346799999988643  334599999999999999873       268998  8877664

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

Probab=98.00  E-value=5e-06  Score=62.49  Aligned_cols=50  Identities=28%  Similarity=0.660  Sum_probs=39.7

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      ..+.|+||++.+..+.   .++|+|.||..|+..|+..      ....||.  |...+...
T Consensus        77 ~~~~C~IC~~~~~~pv---~~~CgH~fC~~Ci~~~~~~------~~~~CP~--Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQPV---TTECFHNVCKDCLQRSFKA------QVFSCPA--CRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSEE---ECTTSCEEEHHHHHHHHHT------TCCBCTT--TCCBCCTT
T ss_pred             cCCEeecCChhhcCCE---EcCCCCchhHHHHHHHHHh------CCCcCCC--CCccCCCC
Confidence            3468999999876533   2599999999999999983      2468998  88887765

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

Probab=97.94  E-value=4e-07  Score=59.22  Aligned_cols=47  Identities=28%  Similarity=0.729  Sum_probs=35.8

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      .....|+||++.+..    ..++|+|.||..|+..|+.       ....||.  |...+.
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~-------~~~~CP~--Cr~~~~   59 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSD-------RHRNCPI--CRLQMT   59 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSC-------CCSSCHH--HHHCTT
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHH-------CcCcCCC--cCCccc
Confidence            445689999998765    3459999999999999876       2457886  665554

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

Probab=97.91  E-value=2.7e-06  Score=56.97  Aligned_cols=52  Identities=19%  Similarity=0.450  Sum_probs=37.7

Q ss_pred             CceecccCcccccC------------CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           40 RSFVCEICVETKLR------------NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        40 ~~~~C~iC~~~~~~------------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      +..+|+||++++..            +....+.+|+|.|+.+|+..|+...       -.||.  |...+...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~--CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN-------NRCPL--CQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC-------CBCTT--TCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC-------CCCCC--cCCCcchh
Confidence            34458888888743            2234455799999999999998743       27998  88777654

>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=97.89  E-value=1.4e-06  Score=62.66  Aligned_cols=48  Identities=25%  Similarity=0.684  Sum_probs=37.1

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      .+.|+||++.+..+.  .+.+|||.||..|+..|+.         ..||.  |+..+....
T Consensus        22 ~~~C~IC~~~~~~pv--~~~~CgH~fC~~Ci~~~~~---------~~CP~--Cr~~~~~~~   69 (117)
T 1jm7_B           22 LLRCSRCTNILREPV--CLGGCEHIFCSNCVSDCIG---------TGCPV--CYTPAWIQD   69 (117)
T ss_dssp             TTSCSSSCSCCSSCB--CCCSSSCCBCTTTGGGGTT---------TBCSS--SCCBCSCSS
T ss_pred             CCCCCCCChHhhCcc--EeCCCCCHHHHHHHHHHhc---------CCCcC--CCCcCcccc
Confidence            467999999886543  2238999999999999875         67998  888776543

>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=97.89  E-value=2.5e-06  Score=61.07  Aligned_cols=50  Identities=26%  Similarity=0.620  Sum_probs=38.9

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ...+.|+||++.+..+.   .++|+|.||..|+..|+..      ....||.  |...+..
T Consensus        13 ~~~~~C~iC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~------~~~~CP~--Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEILVEPV---TLPCNHTLCKPCFQSTVEK------ASLCCPF--CRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBCSSCE---ECTTSCEECHHHHCCCCCT------TTSBCTT--TCCBCHH
T ss_pred             CCCCCCccCCcccCcee---EcCCCCHHhHHHHHHHHhH------CcCCCCC--CCcccCc
Confidence            44578999999886532   3499999999999988752      2368997  9988875

>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=97.87  E-value=6.1e-06  Score=57.34  Aligned_cols=53  Identities=11%  Similarity=-0.008  Sum_probs=41.4

Q ss_pred             CCCCceecccCcccccCCCceecCCCC-CcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCS-HMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~-H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      ...+.+.|+||++.+..+.   .++|+ |.||+.|+..|+..       ...||.  |+..+..+.
T Consensus        18 ~~p~~~~CpI~~~~m~dPV---~~~cG~htf~r~cI~~~l~~-------~~~cP~--~~~~l~~~~   71 (98)
T 1wgm_A           18 DACDEFLDPIMSTLMCDPV---VLPSSRVTVDRSTIARHLLS-------DQTDPF--NRSPLTMDQ   71 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEE---ECTTTCCEEEHHHHHHHTTT-------SCBCTT--TCSBCCTTT
T ss_pred             cCcHhcCCcCccccccCCe---ECCCCCeEECHHHHHHHHHh-------CCCCCC--CCCCCChhh
Confidence            3456788999999887643   34899 99999999999973       237998  888887654

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=97.86  E-value=5.5e-06  Score=67.12  Aligned_cols=59  Identities=17%  Similarity=0.332  Sum_probs=46.3

Q ss_pred             CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      .....+.|+||++.+..+.  ....|||.||+.|+..|+...     ....||..+|...+....+
T Consensus       177 ~~~~el~CPIcl~~f~DPV--ts~~CGHsFcR~cI~~~~~~~-----~~~~CPvtGCr~~l~~~dL  235 (267)
T 3htk_C          177 GGKIELTCPITCKPYEAPL--ISRKCNHVFDRDGIQNYLQGY-----TTRDCPQAACSQVVSMRDF  235 (267)
T ss_dssp             SSBCCSBCTTTSSBCSSEE--EESSSCCEEEHHHHHHHSTTC-----SCEECSGGGCSCEECGGGE
T ss_pred             CCceeeECcCccCcccCCe--eeCCCCCcccHHHHHHHHHhC-----CCCCCCcccccCcCchhhC
Confidence            3456678999999886543  345999999999999998731     3478999999998887654

>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=97.82  E-value=6.1e-06  Score=57.56  Aligned_cols=54  Identities=9%  Similarity=-0.021  Sum_probs=41.6

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      ......+.|+||++.+..+.+   ++|||.||+.|+..|+..       ...||.  |+..+....
T Consensus        24 ~~~p~~~~CpI~~~~m~dPV~---~~cGhtf~r~~I~~~l~~-------~~~cP~--~~~~l~~~~   77 (100)
T 2kre_A           24 SDAPDEFRDPLMDTLMTDPVR---LPSGTIMDRSIILRHLLN-------SPTDPF--NRQTLTESM   77 (100)
T ss_dssp             SSCSTTTBCTTTCSBCSSEEE---ETTTEEEEHHHHHHHTTS-------CSBCSS--SCCBCCTTS
T ss_pred             ccCcHhhCCcCccCcccCCeE---CCCCCEEchHHHHHHHHc-------CCCCCC--CCCCCChhh
Confidence            344567889999998876543   379999999999999973       247998  888887643

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=97.78  E-value=3e-05  Score=59.67  Aligned_cols=55  Identities=15%  Similarity=0.027  Sum_probs=42.6

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      ......+.|+||++.+..+.   .++|||+||+.|+..|+...   +.   .||.  |+..+....
T Consensus       101 ~~ip~~f~CPI~~elm~DPV---~~~~Ghtfer~~I~~~l~~~---~~---tcP~--t~~~l~~~~  155 (179)
T 2f42_A          101 REIPDYLCGKISFELMREPC---ITPSGITYDRKDIEEHLQRV---GH---FDPV--TRSPLTQDQ  155 (179)
T ss_dssp             CCCCGGGBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHT---CS---BCTT--TCCBCCGGG
T ss_pred             cCCcHhhcccCccccCCCCe---ECCCCCEECHHHHHHHHHhC---CC---CCCC--CcCCCChhh
Confidence            44467788999999887543   34899999999999999842   21   6998  888887754

>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=97.76  E-value=1.8e-05  Score=60.41  Aligned_cols=50  Identities=28%  Similarity=0.761  Sum_probs=38.7

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ..+.|+||++.+..+  ..+.+|+|.||..|+..|+..      ....||.  |+..+..
T Consensus        53 ~~~~C~IC~~~~~~p--~~~~~CgH~fC~~Ci~~~~~~------~~~~CP~--Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKNT--MTTKECLHRFCADCIITALRS------GNKECPT--CRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSSE--EEETTTCCEEEHHHHHHHHHT------TCCBCTT--TCCBCCS
T ss_pred             CCCCCcccChHhhCc--CEeCCCCChhHHHHHHHHHHh------CcCCCCC--CCCcCCC
Confidence            345899999988753  334599999999999999983      1467998  8887753

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=97.72  E-value=1.8e-05  Score=53.51  Aligned_cols=38  Identities=26%  Similarity=0.611  Sum_probs=34.0

Q ss_pred             CCCccCCCCCcceeccCCCcceEE-eccccccccccccc
Q 025608          199 QKWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQL  236 (250)
Q Consensus       199 ~~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~  236 (250)
                      .+++-||+|+..+...++-..++| .|++.||+.|+.+|
T Consensus        23 ~~~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC~~C~~~w   61 (86)
T 2ct7_A           23 PKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQW   61 (86)
T ss_dssp             CCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBC
T ss_pred             CCEeECcCCCchheecCCCCceEeCCCCCccccccCCch
Confidence            345679999999888888888999 89999999999999

>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=97.68  E-value=5.6e-05  Score=62.30  Aligned_cols=56  Identities=14%  Similarity=0.049  Sum_probs=42.7

Q ss_pred             ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      .......+.|+||++.+..+.   ..+|||+||+.|+..|+...   +   ..||.  |+..++...
T Consensus       202 ~~~~~~~~~c~i~~~~~~dPv---~~~~gh~f~~~~i~~~~~~~---~---~~cP~--~~~~~~~~~  257 (281)
T 2c2l_A          202 KRDIPDYLCGKISFELMREPC---ITPSGITYDRKDIEEHLQRV---G---HFNPV--TRSPLTQEQ  257 (281)
T ss_dssp             CCCCCSTTBCTTTCSBCSSEE---ECSSCCEEETTHHHHHHHHT---C---SSCTT--TCCCCCGGG
T ss_pred             CCCCCcccCCcCcCCHhcCCe---ECCCCCEECHHHHHHHHHHC---C---CCCcC--CCCCCchhc
Confidence            345566788999999887653   34899999999999999742   1   23998  888887654

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.65  E-value=5.1e-05  Score=50.50  Aligned_cols=54  Identities=22%  Similarity=0.468  Sum_probs=40.7

Q ss_pred             CCceecccCcccccCCCceecCCCC-----CcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCS-----HMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      .....|.||++++...+.. .++|.     |.|+.+||..|+...     ....||.  |+..+..+
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~-----~~~~Cpl--Cr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSS-----DTRCCEL--CKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHH-----CCSBCSS--SCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhC-----CCCCCCC--CCCeeecC
Confidence            3445799999988655444 35896     999999999999854     2468998  88776543

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=97.59  E-value=3.1e-05  Score=56.51  Aligned_cols=59  Identities=20%  Similarity=0.539  Sum_probs=44.5

Q ss_pred             CCCceecccCcccccCC----CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           38 TSRSFVCEICVETKLRN----ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      +.....|+||++.+...    ......+|+|.||..|+..|+...       -.||.  |...+..+.+..+
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP~--Cr~~~~~~~~~~~  131 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCPT--CRKKINHKRYHPI  131 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHC-------SBCTT--TCCBCCGGGEEEE
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcC-------CCCCC--CCCcCChhcceee
Confidence            45567799999987532    222456999999999999999742       38998  9999988776543

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; NMR {Homo sapiens}

Probab=97.58  E-value=2.7e-05  Score=51.86  Aligned_cols=39  Identities=26%  Similarity=0.575  Sum_probs=35.5

Q ss_pred             CCccCCC--CCcceeccCCCcceEE------eccccccccccccccC
Q 025608          200 KWNRCPN--CKFYVEKKDGCSYIRC------RCGHAFCYHCGVQLST  238 (250)
Q Consensus       200 ~~~~CP~--C~~~i~k~~GCnhm~C------~C~~~FC~~C~~~~~~  238 (250)
                      ..+-||.  |+..|...++...++|      .|++.||+.|+.+|+.
T Consensus        24 ~~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~FC~~C~~~wH~   70 (80)
T 2jmo_A           24 GGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHE   70 (80)
T ss_dssp             SSCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCEETTTTEECCS
T ss_pred             CcEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCeeccccCccccC
Confidence            4789998  9999998889999999      6999999999999964

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=97.55  E-value=6.5e-06  Score=54.09  Aligned_cols=42  Identities=24%  Similarity=0.683  Sum_probs=32.3

Q ss_pred             eecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ..|+||++.+...   .+++|+|. ||.+|+..+           ..||.  |...+..
T Consensus        25 ~~C~iC~~~~~~~---~~~pCgH~~~C~~C~~~~-----------~~CP~--Cr~~i~~   67 (74)
T 4ic3_A           25 KLCKICMDRNIAI---VFVPCGHLVTCKQCAEAV-----------DKCPM--CYTVITF   67 (74)
T ss_dssp             TBCTTTSSSBCCE---EEETTCCBCCCHHHHTTC-----------SBCTT--TCCBCSE
T ss_pred             CCCCCCCCCCCCE---EEcCCCChhHHHHhhhcC-----------ccCCC--cCcCccC
Confidence            4799999876532   23599999 999998866           58998  8776653

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.37  E-value=0.00013  Score=46.88  Aligned_cols=46  Identities=22%  Similarity=0.585  Sum_probs=33.7

Q ss_pred             CCCceecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ......|.||++....   ..+++|+|. ||.+|+..           .-.||.  |...+..
T Consensus        12 ~~~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~-----------~~~CP~--CR~~i~~   58 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY-----------FQQCPM--CRQFVQE   58 (68)
T ss_dssp             CCCSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH-----------CSSCTT--TCCCCCC
T ss_pred             CCCCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc-----------CCCCCC--CCcchhc
Confidence            3445679999986543   345699999 99999983           147998  8776654

>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=97.34  E-value=0.0001  Score=46.81  Aligned_cols=48  Identities=23%  Similarity=0.509  Sum_probs=34.6

Q ss_pred             ceecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ..+|.||++..... ++..++|||. +|.+|+..+...       .-.||.  |...+.
T Consensus         8 ~~~C~IC~~~~~~~-~~~~~pCgH~~~C~~C~~~~~~~-------~~~CPi--CR~~i~   56 (64)
T 2vje_A            8 IEPCVICQGRPKNG-CIVHGKTGHLMACFTCAKKLKKR-------NKPCPV--CRQPIQ   56 (64)
T ss_dssp             GSCCTTTSSSCSCE-EEEETTEEEEEECHHHHHHHHHT-------TCCCTT--TCCCCC
T ss_pred             cCCCCcCCCCCCCE-EEECCCCCChhhHHHHHHHHHHc-------CCcCCC--cCcchh
Confidence            34699999876543 2222499999 899999988752       237998  887664

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.32  E-value=0.00013  Score=47.85  Aligned_cols=43  Identities=23%  Similarity=0.669  Sum_probs=31.9

Q ss_pred             ceecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ..+|+||++.+...   .+++|+|. ||.+|+.+           ...||.  |...+..
T Consensus        25 ~~~C~IC~~~~~~~---~~~pCgH~~~C~~C~~~-----------~~~CP~--Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIAI---VFVPCGHLVTCKQCAEA-----------VDKCPM--CYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCCB---CCSSSCCCCBCHHHHHH-----------CSBCTT--TCCBCCC
T ss_pred             CCCCCcCCCCCCCE---EEecCCCHHHHHHHhhC-----------CCCCcc--CCceecC
Confidence            34699999876542   34699999 99999952           157998  8876654

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=97.31  E-value=0.00017  Score=50.66  Aligned_cols=50  Identities=18%  Similarity=0.416  Sum_probs=37.3

Q ss_pred             ceecccCcccccCCC---------------ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           41 SFVCEICVETKLRNE---------------SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .-.|+||++.+...-               ....++|+|.|+..|+..|+..       ...||.  |...+.+
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-------~~~CP~--Cr~~~~~  101 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-------RQVCPL--DNREWEF  101 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-------CSBCSS--SCSBCCE
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHc-------CCcCcC--CCCccee
Confidence            346999999886431               1334699999999999999873       247997  8877653

>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=97.25  E-value=0.00014  Score=46.01  Aligned_cols=47  Identities=17%  Similarity=0.574  Sum_probs=34.5

Q ss_pred             eecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           42 FVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ..|.||++...... +...+|||. ||.+|...+...       .-.||.  |...+.
T Consensus         8 ~~C~IC~~~~~~~~-~~~~pCgH~~~C~~C~~~~~~~-------~~~CPi--CR~~i~   55 (63)
T 2vje_B            8 KPCSLCEKRPRDGN-IIHGRTGHLVTCFHCARRLKKA-------GASCPI--CKKEIQ   55 (63)
T ss_dssp             SBCTTTSSSBSCEE-EEETTEEEEEECHHHHHHHHHT-------TCBCTT--TCCBCC
T ss_pred             CCCcccCCcCCCeE-EEecCCCCHhHHHHHHHHHHHh-------CCcCCC--cCchhh
Confidence            46999998765332 333599999 999999987752       147998  887764

>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=97.21  E-value=0.00019  Score=47.56  Aligned_cols=42  Identities=29%  Similarity=0.823  Sum_probs=32.1

Q ss_pred             ecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           43 VCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        43 ~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      .|.||++....   ..+++|||. ||.+|+..+           ..||.  |...+...
T Consensus        20 ~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~-----------~~CP~--Cr~~i~~~   62 (79)
T 2yho_A           20 LCMVCCEEEIN---STFCPCGHTVCCESCAAQL-----------QSCPV--CRSRVEHV   62 (79)
T ss_dssp             BCTTTSSSBCC---EEEETTCBCCBCHHHHTTC-----------SBCTT--TCCBCCEE
T ss_pred             EeEEeCcccCc---EEEECCCCHHHHHHHHHhc-----------CcCCC--CCchhhCe
Confidence            69999987653   334599999 999999754           28998  88777653

>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=97.06  E-value=0.00039  Score=59.74  Aligned_cols=48  Identities=29%  Similarity=0.826  Sum_probs=37.3

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      .+|+||++.+..   ....+|+|.||..|+..|+..      ....||.  |...+...
T Consensus       333 ~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~------~~~~CP~--CR~~i~~~  380 (389)
T 2y1n_A          333 QLCKICAENDKD---VKIEPCGHLMCTSCLTSWQES------EGQGCPF--CRCEIKGT  380 (389)
T ss_dssp             SBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHH------TCSBCTT--TCCBCCEE
T ss_pred             CCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhc------CCCCCCC--CCCccCCc
Confidence            589999988754   234599999999999999873      2347998  88777654

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.74  E-value=0.0012  Score=43.04  Aligned_cols=52  Identities=23%  Similarity=0.547  Sum_probs=38.8

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ....+|.||++.+...+  ....|+|.|...|+.+|++.+     ..-.||.  |+..+..
T Consensus        13 ~~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~-----~~~~CP~--Cr~~w~~   64 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSN-----AEPRCPH--CNDYWPH   64 (74)
T ss_dssp             SSSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTC-----SSCCCTT--TCSCCCS
T ss_pred             CCCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhc-----CCCCCCC--CcCcCCC
Confidence            34457999999987543  344999999999999999743     1247997  8776653

>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=96.72  E-value=0.0003  Score=50.22  Aligned_cols=49  Identities=18%  Similarity=0.451  Sum_probs=0.0

Q ss_pred             eecccCcccccCCC---------------ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRNE---------------SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      -.|+||++++...-               .....+|+|.|+..|+..|+...       -.||.  |...+..
T Consensus        49 d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~-------~~CP~--Cr~~~~~  112 (117)
T 4a0k_B           49 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR-------QVCPL--DNREWEF  112 (117)
T ss_dssp             -------------------------------------------------------------------------
T ss_pred             CcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcC-------CcCCC--CCCeeee
Confidence            47999999985421               12234899999999999999852       36997  8776554

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.68  E-value=0.0012  Score=45.63  Aligned_cols=34  Identities=18%  Similarity=0.543  Sum_probs=25.9

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHH
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKY   74 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~   74 (250)
                      ...|+||.+.+..+.+...+.|+|.||..|+..+
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            3679999976443444445799999999999983

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

Probab=96.54  E-value=0.0029  Score=53.21  Aligned_cols=63  Identities=21%  Similarity=0.473  Sum_probs=44.7

Q ss_pred             CCCCceecccCcccccC-CCce----ecCCCCCcchHHHHHHHHHHHhhcC----cccccCCCCCCCCCCCHHH
Q 025608           37 ETSRSFVCEICVETKLR-NESF----SIKGCSHMYCVDCTVKYVDSKLQEN----VTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~-~~~~----~~~~C~H~fC~~Cl~~~~~~~i~~~----~~~i~CP~~~C~~~l~~~~  101 (250)
                      .+....+|+||++.+.. ..++    ....|+|.|...|+..|+.+.-...    ...=.||.  |+..++-..
T Consensus       304 ~ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPy--Cr~pIs~sf  375 (381)
T 3k1l_B          304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPF--CKAKLSTSF  375 (381)
T ss_dssp             CCCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTT--TCCEEEGGG
T ss_pred             cccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCC--CCCcCCccH
Confidence            34566789999998865 3332    1348999999999999999764432    22337997  998877543

>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=95.93  E-value=0.0016  Score=55.39  Aligned_cols=42  Identities=24%  Similarity=0.843  Sum_probs=32.6

Q ss_pred             ceecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ...|+||++.+...   .+++|||. ||..|+..+           ..||.  |...+.
T Consensus       295 ~~~C~IC~~~~~~~---v~lpCgH~~fC~~C~~~~-----------~~CP~--CR~~i~  337 (345)
T 3t6p_A          295 ERTCKVCMDKEVSV---VFIPCGHLVVCQECAPSL-----------RKCPI--CRGIIK  337 (345)
T ss_dssp             TCBCTTTSSSBCCE---EEETTCCEEECTTTGGGC-----------SBCTT--TCCBCC
T ss_pred             CCCCCccCCcCCce---EEcCCCChhHhHHHHhcC-----------CcCCC--CCCCcc
Confidence            46799999977542   33499999 999999855           47998  887665

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=95.71  E-value=0.0084  Score=37.23  Aligned_cols=39  Identities=31%  Similarity=0.775  Sum_probs=32.6

Q ss_pred             CeecCCCCCCCCceecCccCccCcccCCc--ccchhccccCcccC
Q 025608          127 QKFYCPFKDCSALLIDDAGEAIRESECPN--CHRLFCAQCKVAWH  169 (250)
Q Consensus       127 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H  169 (250)
                      ....||  .|+..+..+.+  -+.+.|..  |+..||+.|..+|.
T Consensus         5 ~~k~CP--~C~~~Iek~~G--CnhmtC~~~~C~~~FCw~C~~~~~   45 (60)
T 1wd2_A            5 NTKECP--KCHVTIEKDGG--CNHMVCRNQNCKAEFCWVCLGPWE   45 (60)
T ss_dssp             CCCCCT--TTCCCCSSCCS--CCSSSCCSSGGGSCCSSSSCSCSG
T ss_pred             cceECc--CCCCeeEeCCC--CCcEEECCCCcCCEEeeCcCCCcc
Confidence            345898  99999888765  57799988  99999999999873

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=95.51  E-value=0.03  Score=34.65  Aligned_cols=49  Identities=22%  Similarity=0.472  Sum_probs=34.6

Q ss_pred             CceecccCcccccCCCceecCCCC--C---cchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           40 RSFVCEICVETKLRNESFSIKGCS--H---MYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ....|.||+++... ..  ..+|.  +   .|..+||.+|+...-     ...||.  |+..+.
T Consensus         5 ~~~~CrIC~~~~~~-~l--~~PC~C~gs~~~~H~~Cl~~W~~~~~-----~~~C~~--C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEELGN-ER--FRACGCTGELENVHRSCLSTWLTISR-----NTACQI--CGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSC-CC--CCSCCCSSGGGSCCHHHHHHHHHHHT-----CSBCTT--TCCBCC
T ss_pred             CCCEeEEeecCCCC-ce--ecCcCCCCchhhhHHHHHHHHHHhCC-----CCccCC--CCCeee
Confidence            34569999987533 22  34765  4   899999999998541     368998  876654

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=95.20  E-value=0.015  Score=39.73  Aligned_cols=33  Identities=21%  Similarity=0.517  Sum_probs=25.2

Q ss_pred             cccCcccccCCCceecCCCCCcchHHHHHHHHHHH
Q 025608           44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSK   78 (250)
Q Consensus        44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~   78 (250)
                      |++|.-  +....-++.+|.|.||-+|...+.+..
T Consensus         4 C~~C~~--Pi~iygRmIPCkHvFCydCa~~~~~~~   36 (101)
T 3vk6_A            4 CDKCGL--PIKVYGRMIPCKHVFCYDCAILHEKKG   36 (101)
T ss_dssp             CTTTCS--BCSEEEEEETTCCEEEHHHHHHHHHTT
T ss_pred             cCccCC--CeEEEeeeccccccHHHHHHHHHHhcc
Confidence            788854  434445678999999999999988743

>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=94.81  E-value=0.025  Score=35.18  Aligned_cols=53  Identities=15%  Similarity=0.204  Sum_probs=39.0

Q ss_pred             ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc
Q 025608           41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD  104 (250)
Q Consensus        41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  104 (250)
                      .+.|+|+++.+..+.  ...++||.|++.++.+|+...   +    .||.  .+..|..+++..
T Consensus         3 ~~~CpIs~~~m~dPV--~~~~sG~~yer~~I~~~l~~~---~----~cP~--t~~~L~~~~Lip   55 (61)
T 2bay_A            3 HMLCAISGKVPRRPV--LSPKSRTIFEKSLLEQYVKDT---G----NDPI--TNEPLSIEEIVE   55 (61)
T ss_dssp             -CCCTTTCSCCSSEE--EETTTTEEEEHHHHHHHHHHH---S----BCTT--TCCBCCGGGCEE
T ss_pred             eEEecCCCCCCCCCE--EeCCCCcEEcHHHHHHHHHhC---C----CCcC--CcCCCChhhcEE
Confidence            367999999887542  222899999999999999842   2    3887  777787766543

>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=94.68  E-value=0.069  Score=34.59  Aligned_cols=52  Identities=21%  Similarity=0.464  Sum_probs=38.2

Q ss_pred             CCCCceecccCcccccCCCceecCC-CCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           37 ETSRSFVCEICVETKLRNESFSIKG-CSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        37 ~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      .+...+.|.+|.+.+.+..+....+ =.|.||-.|-+.+++.+-.  ...|.||.
T Consensus        11 ~~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q~~--~~EvyCPS   63 (93)
T 2cs3_A           11 ANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGA--TGEVYCPS   63 (93)
T ss_dssp             CSCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHS--SSCCCCTT
T ss_pred             CCCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhcCC--CCcEECCC
Confidence            3456678999999888766543211 1399999999999998743  36788886

>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=94.57  E-value=0.0075  Score=41.56  Aligned_cols=43  Identities=26%  Similarity=0.585  Sum_probs=33.8

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|.-.+.     +-+++ .||+.||+.|...|-... ...||.|.+
T Consensus        23 ~~C~IC~~~~~-----~p~~~~~CgH~FC~~Ci~~~~~~~-~~~CP~Cr~   66 (100)
T 3lrq_A           23 FRCFICMEKLR-----DARLCPHCSKLCCFSCIRRWLTEQ-RAQCPHCRA   66 (100)
T ss_dssp             TBCTTTCSBCS-----SEEECTTTCCEEEHHHHHHHHHHT-CSBCTTTCC
T ss_pred             CCCccCCcccc-----CccccCCCCChhhHHHHHHHHHHC-cCCCCCCCC
Confidence            68999998876     36788 999999999999994322 256999964

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.99  E-value=0.032  Score=35.61  Aligned_cols=44  Identities=32%  Similarity=0.769  Sum_probs=32.7

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccC-CCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLST-VSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~-~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++-.||+.||+.|...|-. ......||.|.+
T Consensus        21 ~~C~IC~~~~~~-----~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~   65 (73)
T 2ysl_A           21 VICPICLDILQK-----PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKT   65 (73)
T ss_dssp             CBCTTTCSBCSS-----EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCC
T ss_pred             CEeccCCcccCC-----eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCC
Confidence            689999987652     33338999999999999953 234557999974

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

Probab=93.90  E-value=0.04  Score=33.00  Aligned_cols=45  Identities=27%  Similarity=0.473  Sum_probs=32.5

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+...+.  -+.- .||+.||..|+..|-..  ...||.|.+
T Consensus         6 ~~C~IC~~~~~~~~~--~~~~~~C~H~f~~~Ci~~w~~~--~~~CP~Cr~   51 (55)
T 1iym_A            6 VECAVCLAELEDGEE--ARFLPRCGHGFHAECVDMWLGS--HSTCPLCRL   51 (55)
T ss_dssp             CCCTTTCCCCCTTSC--CEECSSSCCEECTTHHHHTTTT--CCSCSSSCC
T ss_pred             CcCccCCccccCCCc--eEECCCCCCcccHHHHHHHHHc--CCcCcCCCC
Confidence            578888887765432  3444 59999999999999543  346999964

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=93.63  E-value=0.019  Score=37.01  Aligned_cols=44  Identities=25%  Similarity=0.570  Sum_probs=32.7

Q ss_pred             ccCCCCCcceeccCCCcceEEe-ccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCR-CGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~-C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++=. ||+.||+.|...|-.......||.|.+
T Consensus        16 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~   60 (74)
T 2yur_A           16 LLCLICKDIMTD-----AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ   60 (74)
T ss_dssp             GSCSSSCCCCTT-----CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCC
T ss_pred             CCCcCCChHHhC-----CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCC
Confidence            689999887653     35555 999999999999953333457999964

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=93.53  E-value=0.025  Score=37.11  Aligned_cols=33  Identities=27%  Similarity=0.787  Sum_probs=24.0

Q ss_pred             ccCCCCCcceeccCCCcceEE-ecccc-----ccccccccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQL  236 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~  236 (250)
                      ..||.|+..+..++|  ...| .|+..     ||--|++++
T Consensus         3 ~~CP~C~~~l~~~~~--~~~C~~C~~~~~~~afCPeCgq~L   41 (81)
T 2jrp_A            3 ITCPVCHHALERNGD--TAHCETCAKDFSLQALCPDCRQPL   41 (81)
T ss_dssp             CCCSSSCSCCEECSS--EEECTTTCCEEEEEEECSSSCSCC
T ss_pred             CCCCCCCCccccCCC--ceECccccccCCCcccCcchhhHH
Confidence            589999999998877  5557 66643     566666665

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

Probab=93.48  E-value=0.034  Score=36.91  Aligned_cols=48  Identities=29%  Similarity=0.599  Sum_probs=33.2

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccC-CCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLST-VSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~-~~h~~~~~~~~~  250 (250)
                      ..||-|...+.....- -+.-.||+.||+.|...|-. ......||.|.+
T Consensus        16 ~~C~IC~~~~~~~~~~-~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~   64 (88)
T 2ct2_A           16 LECPICMESFTEEQLR-PKLLHCGHTICRQCLEKLLASSINGVRCPFCSK   64 (88)
T ss_dssp             CBCTTTCCBCCTTSSC-EEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCC
T ss_pred             CCCccCCccccccCCC-eEECCCCChhhHHHHHHHHHcCCCCcCCCCCCC
Confidence            6899998877654211 12228999999999999932 223467999974

>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=93.20  E-value=0.042  Score=32.84  Aligned_cols=45  Identities=24%  Similarity=0.604  Sum_probs=32.7

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+...+  +.+.- .|++.||+.|...|-...  ..||.|.+
T Consensus         6 ~~C~IC~~~~~~~~--~~~~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~   51 (55)
T 2ecm_A            6 SGCPICLEDIHTSR--VVAHVLPCGHLLHRTCYEEMLKEG--YRCPLCSG   51 (55)
T ss_dssp             CSCTTTCCCCCTTT--SCEEECTTSCEEETTHHHHHHHHT--CCCTTSCC
T ss_pred             CcCcccChhhcCCC--cCeEecCCCCcccHHHHHHHHHcC--CcCCCCCC
Confidence            57888887664322  34566 899999999999994323  56999974

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.11  E-value=0.038  Score=34.21  Aligned_cols=42  Identities=33%  Similarity=0.799  Sum_probs=31.2

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccC-CCCCcCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLST-VSHGYYCPSC  248 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~-~~h~~~~~~~  248 (250)
                      ..||-|...+..     -++-.||+.||+.|+..|-. ......||.|
T Consensus        21 ~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           21 VICPICLDILQK-----PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CBCTTTCSBCSS-----CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CCCCcCCchhCC-----eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            689999887653     33348999999999999943 2344569987

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=92.96  E-value=0.046  Score=39.89  Aligned_cols=42  Identities=29%  Similarity=0.660  Sum_probs=31.7

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|.-.+..     -++-.|||.||+.|...|-...  ..||.|.+
T Consensus        54 ~~C~iC~~~~~~-----~~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~   95 (138)
T 4ayc_A           54 LQCIICSEYFIE-----AVTLNCAHSFCSYCINEWMKRK--IECPICRK   95 (138)
T ss_dssp             SBCTTTCSBCSS-----EEEETTSCEEEHHHHHHHTTTC--SBCTTTCC
T ss_pred             CCCcccCcccCC-----ceECCCCCCccHHHHHHHHHcC--CcCCCCCC
Confidence            479999887642     3445899999999999995433  45999964

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

Probab=92.88  E-value=0.024  Score=36.30  Aligned_cols=42  Identities=33%  Similarity=0.643  Sum_probs=31.6

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++- .||+.||+.|...|-..  ...||.|.+
T Consensus        16 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~--~~~CP~Cr~   58 (72)
T 2djb_A           16 ILCSICKGYLID-----ATTITECLHTFCKSCIVRHFYY--SNRCPKCNI   58 (72)
T ss_dssp             GSCTTTSSCCSS-----CEECSSSCCEECHHHHHHHHHH--CSSCTTTCC
T ss_pred             CCCCCCChHHHC-----cCEECCCCCHHHHHHHHHHHHc--CCcCCCcCc
Confidence            689999887654     4555 89999999999888432  346999864

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

Probab=92.58  E-value=0.054  Score=34.45  Aligned_cols=42  Identities=26%  Similarity=0.593  Sum_probs=31.1

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++-.||+.||+.|...|-...  ..||.|.+
T Consensus        16 ~~C~IC~~~~~~-----~~~~~CgH~fC~~Ci~~~~~~~--~~CP~Cr~   57 (71)
T 2d8t_A           16 PECAICLQTCVH-----PVSLPCKHVFCYLCVKGASWLG--KRCALCRQ   57 (71)
T ss_dssp             CBCSSSSSBCSS-----EEEETTTEEEEHHHHHHCTTCS--SBCSSSCC
T ss_pred             CCCccCCcccCC-----CEEccCCCHHHHHHHHHHHHCC--CcCcCcCc
Confidence            689999876643     2444899999999999985333  56999964

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=92.53  E-value=0.043  Score=37.44  Aligned_cols=42  Identities=26%  Similarity=0.638  Sum_probs=32.5

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++- .||+.||..|...|-...  ..||.|+.
T Consensus        23 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~~--~~CP~Cr~   65 (99)
T 2y43_A           23 LRCGICFEYFNI-----AMIIPQCSHNYCSLCIRKFLSYK--TQCPTCCV   65 (99)
T ss_dssp             TBCTTTCSBCSS-----EEECTTTCCEEEHHHHHHHHTTC--CBCTTTCC
T ss_pred             CCcccCChhhCC-----cCEECCCCCHhhHHHHHHHHHCC--CCCCCCCC
Confidence            589999887653     4666 799999999999995433  46999974

>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=92.52  E-value=0.049  Score=37.84  Aligned_cols=42  Identities=33%  Similarity=0.686  Sum_probs=33.3

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++- .||+.||+.|...|-...  ..||.|.+
T Consensus        16 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~~--~~CP~Cr~   58 (108)
T 2ckl_A           16 LMCVLCGGYFID-----ATTIIECLHSFCKTCIVRYLETS--KYCPICDV   58 (108)
T ss_dssp             TBCTTTSSBCSS-----EEEETTTCCEEEHHHHHHHHTSC--SBCTTTCC
T ss_pred             CCCccCChHHhC-----cCEeCCCCChhhHHHHHHHHHhC--CcCcCCCc
Confidence            689999887653     5777 999999999999995433  56999964

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

Probab=92.44  E-value=0.05  Score=35.59  Aligned_cols=47  Identities=30%  Similarity=0.745  Sum_probs=32.2

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|.-++... .-.-+.|.|||.||..|+..+... ..+.||.|.+
T Consensus        12 ~~CpICle~~~~~-d~~~~p~~CGH~fC~~Cl~~~~~~-~~~~CP~CR~   58 (78)
T 1e4u_A           12 VECPLCMEPLEID-DINFFPCTCGYQICRFCWHRIRTD-ENGLCPACRK   58 (78)
T ss_dssp             CBCTTTCCBCCTT-TTTCCSSTTSCCCCHHHHHHHTTS-SCSBCTTTCC
T ss_pred             CcCCccCccCccc-cccccccCCCCCcCHHHHHHHHhc-CCCCCCCCCC
Confidence            6899998866422 122333679999999998887432 3457999964

>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=92.10  E-value=0.055  Score=34.11  Aligned_cols=44  Identities=27%  Similarity=0.545  Sum_probs=31.3

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|...+....   .+.- .||+.||+.|...|-...  ..||.|.+
T Consensus        15 ~~C~IC~~~~~~~~---~~~~~~C~H~fc~~Ci~~~~~~~--~~CP~Cr~   59 (69)
T 2kiz_A           15 EKCTICLSILEEGE---DVRRLPCMHLFHQVCVDQWLITN--KKCPICRV   59 (69)
T ss_dssp             CSBTTTTBCCCSSS---CEEECTTSCEEEHHHHHHHHHHC--SBCTTTCS
T ss_pred             CCCeeCCccccCCC---cEEEeCCCCHHHHHHHHHHHHcC--CCCcCcCc
Confidence            68999987664332   2444 899999999999994322  24999963

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=91.94  E-value=0.027  Score=37.89  Aligned_cols=44  Identities=25%  Similarity=0.570  Sum_probs=32.0

Q ss_pred             ccCCCCCcceeccCCCcceEEe-ccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCR-CGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~-C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|..++..     -++-. ||+.||..|+..|-.......||.|.+
T Consensus        14 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~   58 (92)
T 3ztg_A           14 LLCLICKDIMTD-----AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ   58 (92)
T ss_dssp             TEETTTTEECSS-----CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCC
T ss_pred             CCCCCCChhhcC-----ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCC
Confidence            689999876652     35555 999999999988843223357999964

>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=91.73  E-value=0.056  Score=40.63  Aligned_cols=43  Identities=28%  Similarity=0.673  Sum_probs=33.6

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++. .||+.||+.|...|-... ...||.|.+
T Consensus        55 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~~-~~~CP~Cr~   98 (165)
T 2ckl_B           55 LMCPICLDMLKN-----TMTTKECLHRFCADCIITALRSG-NKECPTCRK   98 (165)
T ss_dssp             HBCTTTSSBCSS-----EEEETTTCCEEEHHHHHHHHHTT-CCBCTTTCC
T ss_pred             CCCcccChHhhC-----cCEeCCCCChhHHHHHHHHHHhC-cCCCCCCCC
Confidence            489999887763     5777 999999999999994322 346999974

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

Probab=91.69  E-value=0.056  Score=33.77  Aligned_cols=43  Identities=28%  Similarity=0.755  Sum_probs=31.4

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+...     ++=.||+.||+.|...|-. .....||.|++
T Consensus        16 ~~C~IC~~~~~~p-----~~~~CgH~fC~~Ci~~~~~-~~~~~CP~Cr~   58 (66)
T 2ecy_A           16 YKCEKCHLVLCSP-----KQTECGHRFCESCMAALLS-SSSPKCTACQE   58 (66)
T ss_dssp             EECTTTCCEESSC-----CCCSSSCCCCHHHHHHHHT-TSSCCCTTTCC
T ss_pred             CCCCCCChHhcCe-----eECCCCCHHHHHHHHHHHH-hCcCCCCCCCc
Confidence            6899998876532     2228999999999999953 23346999974

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

Probab=91.56  E-value=0.074  Score=33.34  Aligned_cols=42  Identities=36%  Similarity=0.756  Sum_probs=30.5

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -..- .||+.||+.|...|-...  ..||.|++
T Consensus         6 ~~C~IC~~~~~~-----~~~~~~C~H~fc~~Ci~~~~~~~--~~CP~Cr~   48 (68)
T 1chc_A            6 ERCPICLEDPSN-----YSMALPCLHAFCYVCITRWIRQN--PTCPLCKV   48 (68)
T ss_dssp             CCCSSCCSCCCS-----CEEETTTTEEESTTHHHHHHHHS--CSTTTTCC
T ss_pred             CCCeeCCccccC-----CcEecCCCCeeHHHHHHHHHhCc--CcCcCCCh
Confidence            579999887642     2345 899999999998884322  46999864

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=91.42  E-value=0.067  Score=34.61  Aligned_cols=44  Identities=25%  Similarity=0.611  Sum_probs=31.7

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCC-----CCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTV-----SHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~-----~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++-.||+.||..|...|-..     .....||.|.+
T Consensus        13 ~~C~IC~~~~~~-----p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~   61 (79)
T 2egp_A           13 VTCPICLELLTE-----PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGI   61 (79)
T ss_dssp             CEETTTTEECSS-----CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCC
T ss_pred             CCCcCCCcccCC-----eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCC
Confidence            679999876543     233489999999999988433     22457999964

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=91.34  E-value=0.051  Score=34.40  Aligned_cols=48  Identities=29%  Similarity=0.604  Sum_probs=33.8

Q ss_pred             CccCCCCCcceecc-CCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          201 WNRCPNCKFYVEKK-DGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       201 ~~~CP~C~~~i~k~-~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ...||=|...+... .+=..+.- .||+.||+.|...|-...  ..||.|.+
T Consensus        10 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~   59 (71)
T 3ng2_A           10 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA--NTCPTCRK   59 (71)
T ss_dssp             CCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC--SBCTTTCC
T ss_pred             CCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC--CCCCCCCC
Confidence            36899999876653 22234445 899999999999994323  36999964

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

Probab=91.23  E-value=0.054  Score=33.39  Aligned_cols=47  Identities=30%  Similarity=0.610  Sum_probs=32.1

Q ss_pred             ccCCCCCcceeccC-CCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKD-GCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~-GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+.... +=..+.- .||+.||..|...|-..  ...||.|.+
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--~~~CP~Cr~   52 (64)
T 2xeu_A            4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--ANTCPTCRK   52 (64)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH--CSBCTTTCC
T ss_pred             CCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc--CCCCCCCCc
Confidence            57888887665431 2233344 89999999999999432  236999964

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

Probab=91.12  E-value=0.053  Score=34.01  Aligned_cols=47  Identities=30%  Similarity=0.600  Sum_probs=32.9

Q ss_pred             ccCCCCCcceeccCC-CcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDG-CSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~G-Cnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..... =..+.- .||+.||..|...|-..  ...||.|.+
T Consensus        16 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--~~~CP~Cr~   64 (69)
T 2ea6_A           16 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--ANTCPTCRK   64 (69)
T ss_dssp             CCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH--CSSCTTTCC
T ss_pred             CCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc--CCCCCCCCC
Confidence            689999887665422 123344 89999999999999432  236999964

>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=91.11  E-value=0.064  Score=38.25  Aligned_cols=43  Identities=26%  Similarity=0.573  Sum_probs=31.6

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|.-.+..     -++=.|||.||..|...|-. .+...||.|.+
T Consensus        53 ~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~-~~~~~CP~Cr~   95 (124)
T 3fl2_A           53 FQCICCQELVFR-----PITTVCQHNVCKDCLDRSFR-AQVFSCPACRY   95 (124)
T ss_dssp             TBCTTTSSBCSS-----EEECTTSCEEEHHHHHHHHH-TTCCBCTTTCC
T ss_pred             CCCCcCChHHcC-----cEEeeCCCcccHHHHHHHHh-HCcCCCCCCCc
Confidence            589999887662     23348999999999988843 33446999964

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=91.09  E-value=0.21  Score=32.19  Aligned_cols=44  Identities=32%  Similarity=0.582  Sum_probs=31.1

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|...+....   .+.= .|++.||+.|+..|-...  ..||.|.+
T Consensus        16 ~~C~IC~~~~~~~~---~~~~~~C~H~fc~~Ci~~~~~~~--~~CP~Cr~   60 (78)
T 2ect_A           16 LECPVCKEDYALGE---SVRQLPCNHLFHDSCIVPWLEQH--DSCPVCRK   60 (78)
T ss_dssp             CCCTTTTSCCCTTS---CEEECTTSCEEETTTTHHHHTTT--CSCTTTCC
T ss_pred             CCCeeCCccccCCC---CEEEeCCCCeecHHHHHHHHHcC--CcCcCcCC
Confidence            68999987665432   2222 799999999999995322  46999964

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=90.91  E-value=0.062  Score=35.20  Aligned_cols=44  Identities=25%  Similarity=0.615  Sum_probs=31.8

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCC----CCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTV----SHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~----~h~~~~~~~~~  250 (250)
                      ..||-|...+...     +.-.||+.||+.|...|-..    .....||.|.+
T Consensus        20 ~~C~IC~~~~~~p-----~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~   67 (85)
T 2ecw_A           20 VTCPICLELLKEP-----VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRV   67 (85)
T ss_dssp             TSCTTTCSCCSSC-----EECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCC
T ss_pred             CCCcCCChhhCcc-----eeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCC
Confidence            5899998876532     34489999999999988322    12457999964

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

Probab=90.86  E-value=0.053  Score=34.87  Aligned_cols=44  Identities=25%  Similarity=0.594  Sum_probs=32.2

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|...+....   .+.. .|++.||+.|...|-...  ..||.|.+
T Consensus        24 ~~C~IC~~~~~~~~---~~~~l~C~H~fh~~Ci~~w~~~~--~~CP~Cr~   68 (75)
T 1x4j_A           24 TLCVVCMCDFESRQ---LLRVLPCNHEFHAKCVDKWLKAN--RTCPICRA   68 (75)
T ss_dssp             CEETTTTEECCBTC---EEEEETTTEEEETTHHHHHHHHC--SSCTTTCC
T ss_pred             CCCeECCcccCCCC---eEEEECCCCHhHHHHHHHHHHcC--CcCcCcCC
Confidence            57998987665433   4455 899999999999994322  36999964

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=90.79  E-value=0.11  Score=31.21  Aligned_cols=42  Identities=29%  Similarity=0.789  Sum_probs=30.6

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCC-CCCcCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTV-SHGYYCPSC  248 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~-~h~~~~~~~  248 (250)
                      ..||-|...+...     +.-.||+.||+.|...|-.. .....||.|
T Consensus        16 ~~C~IC~~~~~~p-----~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           16 ASCSVCLEYLKEP-----VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CBCSSSCCBCSSC-----CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             CCCccCCcccCcc-----EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            6899998876542     23389999999999999322 244569987

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=90.60  E-value=0.096  Score=33.84  Aligned_cols=43  Identities=14%  Similarity=0.219  Sum_probs=31.9

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|..++..     -++-.||+.||..|...|-.. ....||.|++
T Consensus         9 ~~C~IC~~~~~~-----Pv~~~CgH~fc~~Ci~~~~~~-~~~~CP~C~~   51 (78)
T 1t1h_A            9 FRCPISLELMKD-----PVIVSTGQTYERSSIQKWLDA-GHKTCPKSQE   51 (78)
T ss_dssp             SSCTTTSCCCSS-----EEEETTTEEEEHHHHHHHHTT-TCCBCTTTCC
T ss_pred             CCCCCccccccC-----CEEcCCCCeecHHHHHHHHHH-CcCCCCCCcC
Confidence            589999887653     344589999999999998532 2346999974

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=90.27  E-value=0.065  Score=33.36  Aligned_cols=47  Identities=28%  Similarity=0.604  Sum_probs=27.6

Q ss_pred             ccCCCCCc-ceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKF-YVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~-~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|.. .+....- ..+.=.||+.||+.|...|-.. ....||.|++
T Consensus         4 ~~C~IC~~~~~~~~~~-~~~~~~CgH~fC~~Ci~~~~~~-~~~~CP~Cr~   51 (65)
T 1g25_A            4 QGCPRCKTTKYRNPSL-KLMVNVCGHTLCESCVDLLFVR-GAGNCPECGT   51 (65)
T ss_dssp             TCCSTTTTHHHHCSSC-CEEECTTCCCEEHHHHHHHHHT-TSSSCTTTCC
T ss_pred             CcCCcCCCCccCCCcc-CeecCCCCCHhHHHHHHHHHHc-CCCcCCCCCC
Confidence            46777776 4332210 0011268889999998888321 2345999874

>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=90.20  E-value=0.38  Score=33.73  Aligned_cols=40  Identities=28%  Similarity=0.668  Sum_probs=31.2

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++= .||+.||+.|...|-.    ..||.|.+
T Consensus        23 ~~C~IC~~~~~~-----pv~~~~CgH~fC~~Ci~~~~~----~~CP~Cr~   63 (117)
T 1jm7_B           23 LRCSRCTNILRE-----PVCLGGCEHIFCSNCVSDCIG----TGCPVCYT   63 (117)
T ss_dssp             TSCSSSCSCCSS-----CBCCCSSSCCBCTTTGGGGTT----TBCSSSCC
T ss_pred             CCCCCCChHhhC-----ccEeCCCCCHHHHHHHHHHhc----CCCcCCCC
Confidence            689999887653     3444 8999999999999954    56999964

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

Probab=90.20  E-value=0.057  Score=34.56  Aligned_cols=45  Identities=31%  Similarity=0.630  Sum_probs=31.7

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+.....  .+.-.|++.||+.|...|-...  ..||.|.+
T Consensus        16 ~~C~IC~~~~~~~~~--~~~~~C~H~f~~~Ci~~~~~~~--~~CP~Cr~   60 (74)
T 2ep4_A           16 ELCAVCLEDFKPRDE--LGICPCKHAFHRKCLIKWLEVR--KVCPLCNM   60 (74)
T ss_dssp             CBCSSSCCBCCSSSC--EEEETTTEEEEHHHHHHHHHHC--SBCTTTCC
T ss_pred             CCCcCCCcccCCCCc--EEEcCCCCEecHHHHHHHHHcC--CcCCCcCc
Confidence            689999887665432  1223799999999999994322  26999964

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

Probab=90.07  E-value=0.065  Score=35.01  Aligned_cols=42  Identities=24%  Similarity=0.596  Sum_probs=30.9

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++=.||+.||+.|...|-..  ...||.|.+
T Consensus        16 ~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~--~~~CP~Cr~   57 (81)
T 2csy_A           16 FRCFICRQAFQN-----PVVTKCRHYFCESCALEHFRA--TPRCYICDQ   57 (81)
T ss_dssp             SBCSSSCSBCCS-----EEECTTSCEEEHHHHHHHHHH--CSBCSSSCC
T ss_pred             CCCcCCCchhcC-----eeEccCCCHhHHHHHHHHHHC--CCcCCCcCc
Confidence            689999887643     233389999999999988532  346999864

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=90.04  E-value=0.26  Score=28.97  Aligned_cols=28  Identities=25%  Similarity=0.558  Sum_probs=22.7

Q ss_pred             CccCCCCCc-ceeccCCCcceEE-eccccc
Q 025608          201 WNRCPNCKF-YVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       201 ~~~CP~C~~-~i~k~~GCnhm~C-~C~~~F  228 (250)
                      ...||.|+. .+.-+..=..+.| .||..|
T Consensus         5 ~~~CP~C~~~~l~~d~~~gelvC~~CG~v~   34 (50)
T 1pft_A            5 QKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             cEeCcCCCCcceEEcCCCCeEECcccCCcc
Confidence            468999998 7777777778999 998865

>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=89.69  E-value=0.22  Score=34.43  Aligned_cols=44  Identities=27%  Similarity=0.724  Sum_probs=31.1

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCC-CCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTV-SHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~-~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++-.||+.||+.|...|-.. .....||.|..
T Consensus        22 ~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~   66 (112)
T 1jm7_A           22 LECPICLELIKE-----PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKN   66 (112)
T ss_dssp             TSCSSSCCCCSS-----CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSC
T ss_pred             CCCcccChhhcC-----eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCC
Confidence            589999886642     122379999999999988432 22346999963

>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=89.68  E-value=0.073  Score=32.72  Aligned_cols=43  Identities=28%  Similarity=0.753  Sum_probs=34.6

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      ..|=.|...+...+   -..| +|+..||.-|-.=++..-|.  ||.|.
T Consensus        16 ~~C~~C~~~~~~~~---~y~C~~C~~~FC~dCD~fiHe~Lh~--CPgC~   59 (59)
T 1z60_A           16 RFCYGCQGELKDQH---VYVCAVCQNVFCVDCDVFVHDSLHS--CPGCI   59 (59)
T ss_dssp             CEETTTTEECTTSE---EECCTTTTCCBCHHHHHTTTTTSCS--SSTTC
T ss_pred             CcccccCcccCCCc---cEECCccCcCcccchhHHHHhhccC--CcCCC
Confidence            46888888775333   2779 99999999998888888887  99984

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

Probab=89.64  E-value=0.1  Score=34.98  Aligned_cols=44  Identities=30%  Similarity=0.406  Sum_probs=31.8

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+...+   .+.- .||+.||+.|...|-...  ..||.|.+
T Consensus        41 ~~C~IC~~~~~~~~---~~~~l~C~H~Fh~~Ci~~wl~~~--~~CP~Cr~   85 (91)
T 2l0b_A           41 MCCPICCSEYVKGD---VATELPCHHYFHKPCVSIWLQKS--GTCPVCRC   85 (91)
T ss_dssp             SEETTTTEECCTTC---EEEEETTTEEEEHHHHHHHHTTT--CBCTTTCC
T ss_pred             CCCcccChhhcCCC---cEEecCCCChHHHHHHHHHHHcC--CcCcCcCc
Confidence            57999987665433   2333 799999999999995322  36999964

>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=89.03  E-value=0.23  Score=34.66  Aligned_cols=43  Identities=21%  Similarity=0.546  Sum_probs=31.1

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++=.||+.||..|...|-.. ....||.|.+
T Consensus        16 ~~C~iC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~-~~~~CP~Cr~   58 (115)
T 3l11_A           16 CQCGICMEILVE-----PVTLPCNHTLCKPCFQSTVEK-ASLCCPFCRR   58 (115)
T ss_dssp             HBCTTTCSBCSS-----CEECTTSCEECHHHHCCCCCT-TTSBCTTTCC
T ss_pred             CCCccCCcccCc-----eeEcCCCCHHhHHHHHHHHhH-CcCCCCCCCc
Confidence            489999877653     222289999999999999532 2357999964

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

Probab=88.65  E-value=0.24  Score=32.35  Aligned_cols=47  Identities=23%  Similarity=0.651  Sum_probs=30.8

Q ss_pred             ccCCCCCcceec----------cCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEK----------KDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k----------~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..|+=|...++.          .+.+..+.-.|++.|+..|..+|-...  ..||.|.+
T Consensus        16 ~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~   72 (81)
T 2ecl_A           16 DTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN--NRCPLCQQ   72 (81)
T ss_dssp             SCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC--CBCTTTCC
T ss_pred             CCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC--CCCCCcCC
Confidence            356666665543          233333333799999999999995433  36999974

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=88.21  E-value=0.15  Score=33.62  Aligned_cols=29  Identities=28%  Similarity=0.609  Sum_probs=25.8

Q ss_pred             CccCCCCCcceeccCCCcceEE-ecccccc
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAFC  229 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC  229 (250)
                      .-.||+|+....+..+=..+.| .|++.|-
T Consensus        27 ~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           27 DHACPNCGEDRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             CEECSSSCCEEEEEEETTEEEETTTCCEEE
T ss_pred             cCcCCCCCCcceeccCCCeEECCCCCCEec
Confidence            4799999999999988889999 9999874

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.09  E-value=0.17  Score=33.01  Aligned_cols=44  Identities=27%  Similarity=0.667  Sum_probs=31.5

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCC----CCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTV----SHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~----~h~~~~~~~~~  250 (250)
                      ..||-|...+...     ++-.||+.||..|+..|-..    .....||.|.+
T Consensus        20 ~~C~IC~~~~~~p-----~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~   67 (85)
T 2ecv_A           20 VTCPICLELLTQP-----LSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRI   67 (85)
T ss_dssp             CCCTTTCSCCSSC-----BCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCC
T ss_pred             CCCCCCCcccCCc-----eeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCC
Confidence            6899998876532     23389999999999988321    22457999963

>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=87.92  E-value=0.087  Score=37.22  Aligned_cols=43  Identities=28%  Similarity=0.692  Sum_probs=31.2

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+...     ++-.||+.||+.|...|-.... ..||.|.+
T Consensus        19 ~~C~IC~~~~~~p-----~~~~CgH~fC~~Ci~~~~~~~~-~~CP~Cr~   61 (118)
T 3hct_A           19 YECPICLMALREA-----VQTPCGHRFCKACIIKSIRDAG-HKCPVDNE   61 (118)
T ss_dssp             GBCTTTCSBCSSE-----EECTTSCEEEHHHHHHHHHHHC-SBCTTTCC
T ss_pred             CCCCcCChhhcCe-----EECCcCChhhHHHHHHHHhhCC-CCCCCCCC
Confidence            5899999876532     4458999999999988842222 26999863

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=87.81  E-value=0.32  Score=30.74  Aligned_cols=29  Identities=17%  Similarity=0.160  Sum_probs=24.5

Q ss_pred             CCccCCCCCcceeccCCCcceEE-eccccc
Q 025608          200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~F  228 (250)
                      .+..||.|+..++-..+...+.| .||..|
T Consensus         7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2jr6_A            7 DILVCPVTKGRLEYHQDKQELWSRQAKLAY   36 (68)
T ss_dssp             CCCBCSSSCCBCEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            45799999999988888889999 887765

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=87.00  E-value=0.27  Score=29.67  Aligned_cols=28  Identities=29%  Similarity=0.521  Sum_probs=20.2

Q ss_pred             CccCCCCCcceeccCCCcceEE-eccccc
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~F  228 (250)
                      .+.||+|+..+.-...-+.+.| +|++.+
T Consensus        18 ~~fCPkCG~~~~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           18 HRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             cccCcCCCCceeEeccCCEEECCCCCCEE
Confidence            3789999984432233468999 999875

>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=86.75  E-value=0.19  Score=30.85  Aligned_cols=36  Identities=31%  Similarity=0.821  Sum_probs=26.1

Q ss_pred             cCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCC
Q 025608          130 YCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGI  172 (250)
Q Consensus       130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~  172 (250)
                      .|-  +|...+...     ....|+.|+..||..|..-.|..+
T Consensus        17 ~C~--~C~~~~~~~-----~~y~C~~C~~~FC~dCD~fiHe~L   52 (59)
T 1z60_A           17 FCY--GCQGELKDQ-----HVYVCAVCQNVFCVDCDVFVHDSL   52 (59)
T ss_dssp             EET--TTTEECTTS-----EEECCTTTTCCBCHHHHHTTTTTS
T ss_pred             ccc--ccCcccCCC-----ccEECCccCcCcccchhHHHHhhc
Confidence            465  676665321     136799999999999999888664

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=85.99  E-value=0.6  Score=37.30  Aligned_cols=52  Identities=25%  Similarity=0.540  Sum_probs=39.5

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      ...+|.||.+-....  .....|++.|...|+.+|++..     ....||.  |+..++.+
T Consensus       179 ~i~~C~iC~~iv~~g--~~C~~C~~~~H~~C~~~~~~~~-----~~~~CP~--C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSN-----AEPRCPH--CNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSC--EECSSSCCEECHHHHHHHTTTC-----SSCBCTT--TCCBCCSC
T ss_pred             CCCcCcchhhHHhCC--cccCccChHHHHHHHHHHHHhC-----CCCCCCC--CCCCCCCC
Confidence            366799999988754  3344599999999999998742     3458996  88877655

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=85.92  E-value=0.35  Score=28.54  Aligned_cols=27  Identities=26%  Similarity=0.583  Sum_probs=19.2

Q ss_pred             CccCCCCCc-ceeccCCCcceEE-eccccc
Q 025608          201 WNRCPNCKF-YVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       201 ~~~CP~C~~-~i~k~~GCnhm~C-~C~~~F  228 (250)
                      .+.||.|+. .++...+ +.+.| +||+.+
T Consensus        19 ~k~CP~CG~~~fm~~~~-~R~~C~kCG~t~   47 (50)
T 3j20_Y           19 NKFCPRCGPGVFMADHG-DRWACGKCGYTE   47 (50)
T ss_dssp             SEECSSSCSSCEEEECS-SEEECSSSCCEE
T ss_pred             cccCCCCCCceEEecCC-CeEECCCCCCEE
Confidence            489999998 3343333 78899 888653

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

Probab=85.42  E-value=0.2  Score=31.52  Aligned_cols=40  Identities=28%  Similarity=0.614  Sum_probs=29.1

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      ..||-|...+..      +.=.|++.||+.|...|-.  ....||.|.
T Consensus        16 ~~C~IC~~~~~~------~~~~CgH~fc~~Ci~~~~~--~~~~CP~Cr   55 (70)
T 2ecn_A           16 EECCICMDGRAD------LILPCAHSFCQKCIDKWSD--RHRNCPICR   55 (70)
T ss_dssp             CCCSSSCCSCCS------EEETTTEEECHHHHHHSSC--CCSSCHHHH
T ss_pred             CCCeeCCcCccC------cccCCCCcccHHHHHHHHH--CcCcCCCcC
Confidence            689999886543      3348999999999998854  234588763

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

Probab=84.83  E-value=0.5  Score=28.31  Aligned_cols=39  Identities=28%  Similarity=0.628  Sum_probs=24.8

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|.......     ++=.||+.||+.|...+     ...||.|.+
T Consensus         7 ~~C~IC~~~~~~p-----~~l~CgH~fC~~Ci~~~-----~~~CP~Cr~   45 (56)
T 1bor_A            7 LRCQQCQAEAKCP-----KLLPCLHTLCSGCLEAS-----GMQCPICQA   45 (56)
T ss_dssp             SSCSSSCSSCBCC-----SCSTTSCCSBTTTCSSS-----SSSCSSCCS
T ss_pred             CCceEeCCccCCe-----EEcCCCCcccHHHHccC-----CCCCCcCCc
Confidence            5677776655421     11168888999998773     235888863

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=84.63  E-value=1.2  Score=28.27  Aligned_cols=37  Identities=30%  Similarity=0.628  Sum_probs=27.6

Q ss_pred             ccCCCCCcceeccCCCcceEE-ecccc-ccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHA-FCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~-FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|.....      ...= .||+. ||+.|...|      ..||.|.+
T Consensus        25 ~~C~iC~~~~~------~~~~~pCgH~~~C~~C~~~~------~~CP~Cr~   63 (74)
T 4ic3_A           25 KLCKICMDRNI------AIVFVPCGHLVTCKQCAEAV------DKCPMCYT   63 (74)
T ss_dssp             TBCTTTSSSBC------CEEEETTCCBCCCHHHHTTC------SBCTTTCC
T ss_pred             CCCCCCCCCCC------CEEEcCCCChhHHHHhhhcC------ccCCCcCc
Confidence            58999887543      2334 89999 999998888      45898863

>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=83.71  E-value=0.25  Score=34.55  Aligned_cols=43  Identities=33%  Similarity=0.786  Sum_probs=31.1

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++-.||+.||+.|...|-... ...||.|.+
T Consensus        24 ~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~~-~~~CP~Cr~   66 (116)
T 1rmd_A           24 ISCQICEHILAD-----PVETSCKHLFCRICILRCLKVM-GSYCPSCRY   66 (116)
T ss_dssp             TBCTTTCSBCSS-----EEECTTSCEEEHHHHHHHHHHT-CSBCTTTCC
T ss_pred             CCCCCCCcHhcC-----cEEcCCCCcccHHHHHHHHhHC-cCcCCCCCC
Confidence            589999887653     2334899999999998884321 345999864

>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=81.98  E-value=0.24  Score=37.23  Aligned_cols=43  Identities=28%  Similarity=0.692  Sum_probs=31.9

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|..++...     +++.||+.||..|...|-.... ..||.|..
T Consensus        19 ~~C~IC~~~~~~p-----v~~~CgH~fC~~Ci~~~~~~~~-~~CP~Cr~   61 (170)
T 3hcs_A           19 YECPICLMALREA-----VQTPCGHRFCKACIIKSIRDAG-HKCPVDNE   61 (170)
T ss_dssp             GBCTTTCSBCSSE-----EECTTSCEEEHHHHHHHHHHHC-SBCTTTCC
T ss_pred             CCCCCCChhhcCc-----EECCCCCHHHHHHHHHHHHhCC-CCCCCCcc
Confidence            5899999887643     6679999999999998832211 26998863

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.55  E-value=1.1  Score=28.85  Aligned_cols=46  Identities=22%  Similarity=0.493  Sum_probs=36.4

Q ss_pred             CCccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      .+..|+-|+..|..     -+.| .|++.|=..|+.+|-...+...||.|++
T Consensus        14 ~i~~C~IC~~~i~~-----g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~   60 (74)
T 2ct0_A           14 AVKICNICHSLLIQ-----GQSCETCGIRMHLPCVAKYFQSNAEPRCPHCND   60 (74)
T ss_dssp             SSCBCSSSCCBCSS-----SEECSSSCCEECHHHHHHHSTTCSSCCCTTTCS
T ss_pred             CCCcCcchhhHccc-----CCccCCCCchhhHHHHHHHHHhcCCCCCCCCcC
Confidence            45799999998874     3677 9999999999999954444467999974

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=81.51  E-value=0.46  Score=32.34  Aligned_cols=24  Identities=21%  Similarity=0.646  Sum_probs=15.1

Q ss_pred             ccCCCCCcceecc---CCCcceEE-ecc
Q 025608          202 NRCPNCKFYVEKK---DGCSYIRC-RCG  225 (250)
Q Consensus       202 ~~CP~C~~~i~k~---~GCnhm~C-~C~  225 (250)
                      .-||.|+.+|.--   -=|+|+.| .|-
T Consensus         2 hfC~~C~~Pi~iygRmIPCkHvFCydCa   29 (101)
T 3vk6_A            2 HFCDKCGLPIKVYGRMIPCKHVFCYDCA   29 (101)
T ss_dssp             CBCTTTCSBCSEEEEEETTCCEEEHHHH
T ss_pred             eecCccCCCeEEEeeeccccccHHHHHH
Confidence            4689999987633   24555555 444

>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=80.38  E-value=0.46  Score=35.06  Aligned_cols=43  Identities=23%  Similarity=0.559  Sum_probs=30.8

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||-|...+..     -++=.||+.||+.|...|-.. ....||.|..
T Consensus        79 ~~C~IC~~~~~~-----pv~~~CgH~fC~~Ci~~~~~~-~~~~CP~Cr~  121 (150)
T 1z6u_A           79 FMCVCCQELVYQ-----PVTTECFHNVCKDCLQRSFKA-QVFSCPACRH  121 (150)
T ss_dssp             TBCTTTSSBCSS-----EEECTTSCEEEHHHHHHHHHT-TCCBCTTTCC
T ss_pred             CEeecCChhhcC-----CEEcCCCCchhHHHHHHHHHh-CCCcCCCCCc
Confidence            589999886642     233489999999999888432 3346999863

---

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	250
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	1e-07
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-07
d2ct7a1	73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	3e-07

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (107), Expect = 1e-07
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)

Query: 203 RCPNCKFYVEKKDGCSYIRCR---CGHAFCYHCGVQLSTVSHGYYCPSCNK 250
            CP C   +EK  GC+++ CR   C   FC+ C          +Y  +CN+
Sbjct: 8   ECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWY--NCNR 56

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 3/92 (3%)

Query: 38  TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQE-NVTSIGCPVTDC--G 94
           +S S  C++C+      +  +I  C  ++C  C  +YV+  ++E   T+I CP   C   
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ 61

Query: 95  GSLEPEYCRDILPEEAFDKWGKALCESLIPGA 126
           G L+      ++  E   ++ K   E   P +
Sbjct: 62  GHLQENEIECMVAAEIMQRYKKLQFERSGPSS 93

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 3e-07
 Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 1/59 (1%)

Query: 188 EDIILMKLAQNQKWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYC 245
           + +    L ++ K+  C  C F    +       C +C   FC  C  Q      G  C
Sbjct: 5   KKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQHRGRSC 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	250
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.76
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.69
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.14
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.13
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.6
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.55
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	98.49
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.49
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.32
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.27
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.25
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.18
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	98.18
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.18
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.15
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.08
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.05
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	97.9
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	97.35
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	97.14
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	95.62
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	95.35
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	94.64
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	94.62
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	94.53
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	93.9
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	92.32
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	91.34
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	90.29
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	89.96
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	89.4
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	89.0
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	86.85
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	85.64
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	85.1
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	84.43
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	84.42
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	83.81
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	82.48

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-19  Score=113.32  Aligned_cols=50  Identities=34%  Similarity=0.861  Sum_probs=42.5

Q ss_pred             CCCccCCCCCcceeccCCCcceEEe---ccccccccccccccCCCCCcCCCCCCC
Q 025608          199 QKWNRCPNCKFYVEKKDGCSYIRCR---CGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       199 ~~~~~CP~C~~~i~k~~GCnhm~C~---C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      .++|+||+|+++|+|++|||||+|.   |+++|||+|+++|.+  |..+.++|||
T Consensus         4 ~ntK~CP~C~~~ieK~~GCnhM~C~~~~C~~~fCw~C~~~~~~--~~~~~~~C~~   56 (60)
T d1wd2a_           4 ANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEP--HGSAWYNCNR   56 (60)
T ss_dssp             CCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGG--GGTSSSSSCS
T ss_pred             hcCcCCCCCCCeEEECCCCCCeEeCCCCCCCeEECCCCCcccc--CCCCCCCCcC
Confidence            3569999999999999999999993   999999999999964  3444566775

>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=99.69  E-value=1.9e-17  Score=114.19  Aligned_cols=86  Identities=24%  Similarity=0.488  Sum_probs=75.8

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcC-cccccCCCCCCCC--CCCHHHHhccCChHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQEN-VTSIGCPVTDCGG--SLEPEYCRDILPEEAFDKWG  115 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~--~l~~~~i~~~l~~~~~~~~~  115 (250)
                      ....+|+||+++++.++++.+.+|+|.||.+||+.|++.+|.++ ..+|+||...|+.  .+...+|+.+|+++.+++|.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky~   82 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQRYK   82 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHHSCHHHHHHHH
T ss_pred             CCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCCCCCcccCHHHHHHhCCHHHHHHHH
Confidence            45678999999999888888889999999999999999999875 5789999988864  58899999999999999999


Q ss_pred             HHHHhhccC
Q 025608          116 KALCESLIP  124 (250)
Q Consensus       116 ~~~~~~~~~  124 (250)
                      ++..+.+..
T Consensus        83 ~~~l~~~~~   91 (94)
T d1wima_          83 KLQFERSGP   91 (94)
T ss_dssp             HHHHHSSCS
T ss_pred             HHHHHhccc
Confidence            998876543

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=1.8e-12  Score=84.10  Aligned_cols=64  Identities=36%  Similarity=0.840  Sum_probs=52.9

Q ss_pred             HHHHHHhhccCCCC-eecCCCCCCCCceecCccCccCcccCCcccchhccccCccc---CCCCCchhHhhhc
Q 025608          114 WGKALCESLIPGAQ-KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAW---HAGIECADFQKLH  181 (250)
Q Consensus       114 ~~~~~~~~~~~~~~-~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~~  181 (250)
                      |++++.+.+|.... ..|||  +|+++++.+++  .+.+.|+.|+..||+.|+.+|   |.|.+|+++++|+
T Consensus         3 Y~~~l~~~~l~~~~~~k~CP--~C~~~~~~~~~--~~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~wk   70 (73)
T d2ct7a1           3 FHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE--QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWK   70 (73)
T ss_dssp             SSSCCCCSCCCSCCCEECCS--SSCCCEECCCS--CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCCC--CCCCEeEECCC--CCEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHHH
Confidence            45556666666654 56998  89999988765  467999999999999999999   9999999998874

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=6.5e-12  Score=81.37  Aligned_cols=44  Identities=25%  Similarity=0.604  Sum_probs=39.6

Q ss_pred             hcCCCccCCCCCcceeccCCCcceEE-eccccccccccccccCCCC
Q 025608          197 QNQKWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSH  241 (250)
Q Consensus       197 ~~~~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h  241 (250)
                      .+.+++.||+|+.+|++++||++|+| .|++.|||.|+.+|.. .|
T Consensus        14 ~~~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~~C~~~w~~-~H   58 (73)
T d2ct7a1          14 RDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEE-QH   58 (73)
T ss_dssp             SCCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCT-TT
T ss_pred             HCCCCCCCCCCCCEeEECCCCCEEEcCCCCCeECcccCcchhc-CC
Confidence            45567999999999999999999999 9999999999999953 45

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.60  E-value=5e-09  Score=62.74  Aligned_cols=50  Identities=20%  Similarity=0.403  Sum_probs=37.7

Q ss_pred             eecccCcccccCC-CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRN-ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ++|+||++++... ..+...+|+|.||.+|+.+|+...      ..+||.  |...++.
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~------~~~CP~--CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDE------NGLCPA--CRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTS------CCBCTT--TCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhc------CCCCCc--cCCcCCC
Confidence            4799999998543 334456899999999999997632      247998  8877654

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.55  E-value=3.3e-08  Score=68.03  Aligned_cols=68  Identities=21%  Similarity=0.511  Sum_probs=48.5

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc-cCChHHHHHHHHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD-ILPEEAFDKWGKAL  118 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~~~~  118 (250)
                      ++|+||++.+..+.   .++|||.||.+|+..|+...    .....||.  |+..+..+.++. ..-.+.++++.+..
T Consensus        22 l~CpIC~~~~~~pv---~~~CgH~fC~~Ci~~~~~~~----~~~~~CP~--Cr~~~~~~~l~~n~~l~~~ve~l~~~~   90 (103)
T d1jm7a_          22 LECPICLELIKEPV---STKCDHIFCKFCMLKLLNQK----KGPSQCPL--CKNDITKRSLQESTRFSQLVEELLKII   90 (103)
T ss_dssp             TSCSSSCCCCSSCC---BCTTSCCCCSHHHHHHHHSS----SSSCCCTT--TSCCCCTTTCBCCCSSSHHHHHHHHHH
T ss_pred             cCCCccCchhCCeE---EcCCCCchhhHHHHHHHHHC----CCCCcCcC--CCCcCChhhCCcCHHHHHHHHHHHHHH
Confidence            46999999886543   34899999999999998732    23468998  998888776542 22345566665443

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.49  E-value=1.1e-08  Score=67.75  Aligned_cols=54  Identities=22%  Similarity=0.544  Sum_probs=41.2

Q ss_pred             CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc
Q 025608           40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD  104 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  104 (250)
                      ..+.|+||++.+..+   ..++|||.||.+|+.+|++..      .-.||.  |+..+...++..
T Consensus        22 ~~l~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~------~~~CP~--Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILADP---VETSCKHLFCRICILRCLKVM------GSYCPS--CRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHT------CSBCTT--TCCBCCGGGCBC
T ss_pred             cCcCCccCCcchhcc---eecCCCChhhHHHHHHHHhhC------CCcCcc--cCCCCChhhccC
Confidence            446799999877643   345999999999999999732      126998  888888776543

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=2.3e-08  Score=62.68  Aligned_cols=54  Identities=26%  Similarity=0.522  Sum_probs=39.3

Q ss_pred             eecccCccccc--CCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608           42 FVCEICVETKL--RNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR  103 (250)
Q Consensus        42 ~~C~iC~~~~~--~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  103 (250)
                      .+|+||++++.  .+......+|+|.||.+|+.+|+...      .-.||.  |+..+....++
T Consensus         4 ~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~------~~~CP~--CR~~i~~~~~~   59 (65)
T d1g25a_           4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRG------AGNCPE--CGTPLRKSNFR   59 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTT------SSSCTT--TCCCCSSCCCE
T ss_pred             CCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcC------cCCCCC--CCcCccccccc
Confidence            46999998752  23334456999999999999999732      126998  98888765543

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=98.32  E-value=1e-07  Score=57.44  Aligned_cols=47  Identities=21%  Similarity=0.600  Sum_probs=36.2

Q ss_pred             eecccCcccccCCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608           42 FVCEICVETKLRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL   97 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l   97 (250)
                      .+|+||++++..++. ..+..|+|.||.+|+.+|+..+       -.||.  |+..+
T Consensus         6 ~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~-------~~CP~--CR~~i   53 (55)
T d1iyma_           6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH-------STCPL--CRLTV   53 (55)
T ss_dssp             CCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC-------CSCSS--SCCCS
T ss_pred             CCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhC-------CcCCC--CCCEe
Confidence            469999999975443 4455799999999999998632       26998  77654

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.27  E-value=4.8e-07  Score=63.12  Aligned_cols=54  Identities=22%  Similarity=0.373  Sum_probs=39.9

Q ss_pred             eecccCcccccCC---------------CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRN---------------ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~---------------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      .+|+||++++...               ....+++|+|.||.+||..|+...-  ....+.||.  |+.++..
T Consensus        26 ~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~--~~~~~~CP~--CR~~~~~   94 (114)
T d1v87a_          26 EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN--KDGSLQCPS--CKTIYGE   94 (114)
T ss_dssp             CEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC--CSSCCBCTT--TCCBSSS
T ss_pred             ccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcC--cCCCCcccc--ccchhcc
Confidence            4699999987432               2344679999999999999998542  234678998  8776643

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.25  E-value=4.4e-07  Score=58.96  Aligned_cols=47  Identities=30%  Similarity=0.854  Sum_probs=35.8

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      ..|+||++.+..   ..+++|||.||.+|+..|+...      .-.||.  |+..+..
T Consensus        24 ~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~------~~~CP~--Cr~~i~~   70 (79)
T d1fbva4          24 QLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESE------GQGCPF--CRCEIKG   70 (79)
T ss_dssp             TBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTT------CCSCTT--TCCCCCC
T ss_pred             CCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHC------cCcCCC--CCcCccC
Confidence            359999987653   3356999999999999998732      235998  8877754

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.18  E-value=4.4e-07  Score=58.86  Aligned_cols=66  Identities=18%  Similarity=0.279  Sum_probs=47.2

Q ss_pred             CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh-ccCChHHHHHHH
Q 025608           39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR-DILPEEAFDKWG  115 (250)
Q Consensus        39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~  115 (250)
                      ...+.|+||++.+..+.   .++|||.||+.|+.+|+...      .-.||.  |+..+..+++. ++.-.+.++.|.
T Consensus         6 P~~l~CpIc~~~m~dPV---~~~cgh~fc~~ci~~~~~~~------~~~cP~--~~~~l~~~~l~pN~~L~~~I~~~~   72 (78)
T d1t1ha_           6 PEYFRCPISLELMKDPV---IVSTGQTYERSSIQKWLDAG------HKTCPK--SQETLLHAGLTPNYVLKSLIALWC   72 (78)
T ss_dssp             SSSSSCTTTSCCCSSEE---EETTTEEEEHHHHHHHHTTT------CCBCTT--TCCBCSSCCCEECTTTHHHHHHHH
T ss_pred             CccCCCcCcCchhhCce---EccCCCcchHHHHHHHHHHC------CCCCCc--ccccCCcccccchHHHHHHHHHHH
Confidence            45688999999887643   34899999999999998732      235887  77777765543 444556666664

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=98.18  E-value=6.1e-07  Score=56.51  Aligned_cols=46  Identities=26%  Similarity=0.670  Sum_probs=35.9

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      -+|+||++.+...  ...++|+|.||.+|+.+|+...       -.||.  |+..+.
T Consensus         6 d~C~IC~~~~~~~--~~~~~C~H~Fc~~Ci~~w~~~~-------~~CP~--CR~~i~   51 (68)
T d1chca_           6 ERCPICLEDPSNY--SMALPCLHAFCYVCITRWIRQN-------PTCPL--CKVPVE   51 (68)
T ss_dssp             CCCSSCCSCCCSC--EEETTTTEEESTTHHHHHHHHS-------CSTTT--TCCCCC
T ss_pred             CCCccCCcCccCC--cEEeCCCCcCcHHHHHHHHHhC-------CcCCC--CCcchH
Confidence            3699999988543  3456999999999999999742       36998  887654

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=2.5e-07  Score=55.84  Aligned_cols=48  Identities=19%  Similarity=0.540  Sum_probs=35.7

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE  100 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  100 (250)
                      ..+.++|+||++.+....   +++|+|.||..|+.+          ....||.  |+..++..
T Consensus         3 e~~~l~C~IC~~~~~~p~---~lpCgH~fC~~Ci~~----------~~~~CP~--Cr~~~~~~   50 (56)
T d1bora_           3 EFQFLRCQQCQAEAKCPK---LLPCLHTLCSGCLEA----------SGMQCPI--CQAPWPLG   50 (56)
T ss_dssp             SCCCSSCSSSCSSCBCCS---CSTTSCCSBTTTCSS----------SSSSCSS--CCSSSSCC
T ss_pred             ccCCCCCcccCcccCCCE---EecCCCHHhHHHHHc----------CCCcCcC--CCCcccCC
Confidence            345578999999886543   459999999999842          3457998  88776643

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.15  E-value=7.6e-07  Score=53.76  Aligned_cols=52  Identities=17%  Similarity=0.238  Sum_probs=40.8

Q ss_pred             ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608           43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI  105 (250)
Q Consensus        43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  105 (250)
                      .|+||++.+..+  .....|||.||.+|+.+|+...   +    .||.  |+..++.+++..+
T Consensus         2 ~C~Ic~~~~~~P--v~~~~cGh~fc~~cI~~~l~~~---~----~CP~--c~~~l~~~dLipi   53 (56)
T d2baya1           2 LCAISGKVPRRP--VLSPKSRTIFEKSLLEQYVKDT---G----NDPI--TNEPLSIEEIVEI   53 (56)
T ss_dssp             CCTTTCSCCSSE--EEETTTTEEEEHHHHHHHHHHH---S----BCTT--TCCBCCGGGCEEC
T ss_pred             CCccCCchHHhc--CccCCCCCcccHHHHHHHHhhc---c----CCCc--cCCcCCHHhceeC
Confidence            599999987643  3344799999999999999953   1    5998  9999988876543

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.08  E-value=9.3e-07  Score=57.52  Aligned_cols=54  Identities=15%  Similarity=0.010  Sum_probs=41.4

Q ss_pred             CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ..+.+.|+||++.+..+.   .++|||+||++|+.+|+...      .-.||.  |+..++.+++
T Consensus         4 iP~~l~CpIc~~l~~dPv---~~~cGhtfc~~ci~~~l~~~------~~~cP~--c~~~l~~~~l   57 (80)
T d2c2la2           4 IPDYLCGKISFELMREPC---ITPSGITYDRKDIEEHLQRV------GHFNPV--TRSPLTQEQL   57 (80)
T ss_dssp             CCSTTBCTTTCSBCSSEE---ECSSCCEEETTHHHHHHHHT------CSSCTT--TCCCCCGGGC
T ss_pred             CCccccCcCcCchhhhhc---ccCCcCeecHHHHHHHHhcC------CccCCC--cccccccccc
Confidence            356678999999887643   35999999999999998632      236897  8888876654

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.05  E-value=1.9e-07  Score=63.27  Aligned_cols=47  Identities=26%  Similarity=0.728  Sum_probs=35.9

Q ss_pred             eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608           42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY  101 (250)
Q Consensus        42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  101 (250)
                      ++|+||++.+..+.  .+.+|||.||.+|+.+|+..         .||.  |+..+....
T Consensus        23 l~C~IC~~~~~~pv--~~~~CgH~fC~~Ci~~~~~~---------~CP~--Cr~~~~~~~   69 (97)
T d1jm7b_          23 LRCSRCTNILREPV--CLGGCEHIFCSNCVSDCIGT---------GCPV--CYTPAWIQD   69 (97)
T ss_dssp             TSCSSSCSCCSSCB--CCCSSSCCBCTTTGGGGTTT---------BCSS--SCCBCSCSS
T ss_pred             CCCccCCchhhcCc--eeCCCCCchhHHHHHHHHhc---------cccc--cCCcCchhh
Confidence            57999999987543  33489999999999988631         4998  887766544

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=97.90  E-value=7.4e-06  Score=49.95  Aligned_cols=52  Identities=19%  Similarity=0.308  Sum_probs=37.1

Q ss_pred             CceecccCcccccCCCce--ecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608           40 RSFVCEICVETKLRNESF--SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE   98 (250)
Q Consensus        40 ~~~~C~iC~~~~~~~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~   98 (250)
                      ....|.||++++....+.  ....|+|.|+.+||..|+...-     ..+||.  |+..+.
T Consensus         5 d~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~-----~~~CP~--Cr~~~~   58 (60)
T d1vyxa_           5 DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISR-----NTACQI--CGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHT-----CSBCTT--TCCBCC
T ss_pred             CCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCC-----CCCCcc--cCCeee
Confidence            445699999987654333  2334569999999999997542     247998  877654

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.35  E-value=6.1e-05  Score=49.46  Aligned_cols=49  Identities=18%  Similarity=0.451  Sum_probs=35.6

Q ss_pred             eecccCcccccCCC---------------ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608           42 FVCEICVETKLRNE---------------SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP   99 (250)
Q Consensus        42 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~   99 (250)
                      -+|+||++++....               ....++|+|.|+.+||..|++.+       -.||.  |...+..
T Consensus        22 d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~--CR~~~~~   85 (88)
T d3dplr1          22 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR-------QVCPL--DNREWEF   85 (88)
T ss_dssp             CCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTC-------SBCSS--SCSBCCE
T ss_pred             CcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHC-------CcCCC--CCCcccc
Confidence            35999988764322               13345899999999999999742       25998  8877654

>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=97.14  E-value=0.00014  Score=48.73  Aligned_cols=56  Identities=9%  Similarity=0.020  Sum_probs=39.1

Q ss_pred             cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608           36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC  102 (250)
Q Consensus        36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  102 (250)
                      ......|.|+||.+.+..+.+  +..|+|.||+.|+.+|+..   ++    .||.  |+..+..+.+
T Consensus        17 ~~~P~~f~CPI~~~lm~dPV~--~~~~~~ty~r~~I~~~l~~---~~----~~P~--~~~~l~~~~L   72 (98)
T d1wgma_          17 ADACDEFLDPIMSTLMCDPVV--LPSSRVTVDRSTIARHLLS---DQ----TDPF--NRSPLTMDQI   72 (98)
T ss_dssp             CSCCTTTBCTTTCSBCSSEEE--CTTTCCEEEHHHHHHHTTT---SC----BCTT--TCSBCCTTTS
T ss_pred             cCCcHHhCCcCchhHHHHHHh--cccccchhhHHHHHHHHHh---cC----Cccc--ccccccchhh
Confidence            344567899999998876432  2234568999999999862   21    5887  7777776544

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.62  E-value=0.0046  Score=36.91  Aligned_cols=38  Identities=32%  Similarity=0.792  Sum_probs=31.3

Q ss_pred             CeecCCCCCCCCceecCccCccCcccCC--cccchhccccCccc
Q 025608          127 QKFYCPFKDCSALLIDDAGEAIRESECP--NCHRLFCAQCKVAW  168 (250)
Q Consensus       127 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~  168 (250)
                      ....||  .|+..+....+  -+.+.|.  .|+..||+.|+++|
T Consensus         5 ntK~CP--~C~~~ieK~~G--CnhM~C~~~~C~~~fCw~C~~~~   44 (60)
T d1wd2a_           5 NTKECP--KCHVTIEKDGG--CNHMVCRNQNCKAEFCWVCLGPW   44 (60)
T ss_dssp             CCCCCT--TTCCCCSSCCS--CCSSSCCSSGGGSCCSSSSCSCS
T ss_pred             cCcCCC--CCCCeEEECCC--CCCeEeCCCCCCCeEECCCCCcc
Confidence            356898  99999888765  4778994  69999999999976

>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=95.35  E-value=0.019  Score=34.65  Aligned_cols=51  Identities=22%  Similarity=0.472  Sum_probs=37.5

Q ss_pred             CCCceecccCcccccCCCceecCC-CCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608           38 TSRSFVCEICVETKLRNESFSIKG-CSHMYCVDCTVKYVDSKLQENVTSIGCPV   90 (250)
Q Consensus        38 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   90 (250)
                      +...+.|.+|-+.+.+..+....+ =.|.||-.|-+.+++.+..+  ..|.||.
T Consensus         5 ~~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~q~~~--~evyCPS   56 (80)
T d2cs3a1           5 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGAT--GEVYCPS   56 (80)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSS--SCCCCTT
T ss_pred             CCCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHhcCCC--CcEECCC
Confidence            344578999999887766543211 13999999999999988554  5788886

>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=94.64  E-value=0.005  Score=37.37  Aligned_cols=47  Identities=28%  Similarity=0.639  Sum_probs=33.2

Q ss_pred             ccCCCCCcceeccCCCcceEEecccccccccccccc-CCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS-TVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~-~~~h~~~~~~~~~  250 (250)
                      ..||=|...+.....-.-+.-.||+.||..|...|- ..++  .||.|.+
T Consensus         4 ~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~--~CP~CR~   51 (65)
T d1g25a_           4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAG--NCPECGT   51 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSS--SCTTTCC
T ss_pred             CCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcC--CCCCCCc
Confidence            578888776554444444445899999999999994 3233  5999964

>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=94.62  E-value=0.0099  Score=39.04  Aligned_cols=40  Identities=28%  Similarity=0.668  Sum_probs=31.8

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|..++..     -++. .||+.||..|...|-.    ..||.|+.
T Consensus        23 l~C~IC~~~~~~-----pv~~~~CgH~fC~~Ci~~~~~----~~CP~Cr~   63 (97)
T d1jm7b_          23 LRCSRCTNILRE-----PVCLGGCEHIFCSNCVSDCIG----TGCPVCYT   63 (97)
T ss_dssp             TSCSSSCSCCSS-----CBCCCSSSCCBCTTTGGGGTT----TBCSSSCC
T ss_pred             CCCccCCchhhc-----CceeCCCCCchhHHHHHHHHh----ccccccCC
Confidence            589999998753     3676 8999999999999952    24999963

>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=94.53  E-value=0.0064  Score=37.21  Aligned_cols=42  Identities=36%  Similarity=0.774  Sum_probs=32.5

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|.-.+.     +.... .||+.||+.|...|-.  +...||.|++
T Consensus         6 d~C~IC~~~~~-----~~~~~~~C~H~Fc~~Ci~~w~~--~~~~CP~CR~   48 (68)
T d1chca_           6 ERCPICLEDPS-----NYSMALPCLHAFCYVCITRWIR--QNPTCPLCKV   48 (68)
T ss_dssp             CCCSSCCSCCC-----SCEEETTTTEEESTTHHHHHHH--HSCSTTTTCC
T ss_pred             CCCccCCcCcc-----CCcEEeCCCCcCcHHHHHHHHH--hCCcCCCCCc
Confidence            57999987664     24678 9999999999999943  2346999974

>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=93.90  E-value=0.018  Score=38.22  Aligned_cols=44  Identities=27%  Similarity=0.719  Sum_probs=32.2

Q ss_pred             ccCCCCCcceeccCCCcceEEecccccccccccccc-CCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS-TVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~-~~~h~~~~~~~~~  250 (250)
                      ..||=|.-++..     -++-.|||.||..|...|- .......||.|++
T Consensus        22 l~CpIC~~~~~~-----pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~   66 (103)
T d1jm7a_          22 LECPICLELIKE-----PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKN   66 (103)
T ss_dssp             TSCSSSCCCCSS-----CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSC
T ss_pred             cCCCccCchhCC-----eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCC
Confidence            579999987753     2444799999999988873 2334457999963

>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=92.32  E-value=0.066  Score=30.92  Aligned_cols=45  Identities=29%  Similarity=0.527  Sum_probs=33.1

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|...++..+.  -++. .|++.|++.|...|-.. + ..||.|.+
T Consensus         6 ~~C~ICl~~~~~~~~--~~~l~~C~H~Fh~~Ci~~Wl~~-~-~~CP~CR~   51 (55)
T d1iyma_           6 VECAVCLAELEDGEE--ARFLPRCGHGFHAECVDMWLGS-H-STCPLCRL   51 (55)
T ss_dssp             CCCTTTCCCCCTTSC--CEECSSSCCEECTTHHHHTTTT-C-CSCSSSCC
T ss_pred             CCCeEECccccCCCE--EEEeCCCCCcccHHHHHHHHHh-C-CcCCCCCC
Confidence            468888887765443  2455 69999999999999533 3 36999964

>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=91.34  E-value=0.075  Score=30.84  Aligned_cols=39  Identities=28%  Similarity=0.632  Sum_probs=28.9

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ..||=|...+.     +.++-.||+.||..|...+     ...||.|++
T Consensus         7 l~C~IC~~~~~-----~p~~lpCgH~fC~~Ci~~~-----~~~CP~Cr~   45 (56)
T d1bora_           7 LRCQQCQAEAK-----CPKLLPCLHTLCSGCLEAS-----GMQCPICQA   45 (56)
T ss_dssp             SSCSSSCSSCB-----CCSCSTTSCCSBTTTCSSS-----SSSCSSCCS
T ss_pred             CCCcccCcccC-----CCEEecCCCHHhHHHHHcC-----CCcCcCCCC
Confidence            58999987654     2355589999999998765     335999964

>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=90.29  E-value=0.025  Score=36.18  Aligned_cols=42  Identities=31%  Similarity=0.787  Sum_probs=31.0

Q ss_pred             ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608          202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN  249 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~  249 (250)
                      ..||=|.-++..     -++=.||+.||+.|...|-. .+...||.|.
T Consensus        24 l~C~IC~~~~~~-----pv~~~CgH~FC~~Ci~~~~~-~~~~~CP~Cr   65 (86)
T d1rmda2          24 ISCQICEHILAD-----PVETSCKHLFCRICILRCLK-VMGSYCPSCR   65 (86)
T ss_dssp             TBCTTTCSBCSS-----EEECTTSCEEEHHHHHHHHH-HTCSBCTTTC
T ss_pred             cCCccCCcchhc-----ceecCCCChhhHHHHHHHHh-hCCCcCcccC
Confidence            589999887652     23348999999999999842 2334599996

>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=89.96  E-value=0.04  Score=32.14  Aligned_cols=43  Identities=28%  Similarity=0.737  Sum_probs=34.5

Q ss_pred             CccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCC
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSC  248 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~  248 (250)
                      .+.|-.|...+...   ..+.| +|+..||--|-.=++..-|.  ||.|
T Consensus        15 ~~~C~gC~~~l~~~---~~y~C~~C~~~FC~dCD~fiHe~lh~--CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKDQ---HVYVCAVCQNVFCVDCDVFVHDSLHS--CPGC   58 (59)
T ss_dssp             CCEETTTTEECTTS---EEECCTTTTCCBCHHHHHTTTTTSCS--SSTT
T ss_pred             CCCccCCCCcCCCC---ceEECcCCCCccccccchhhhhhhcC--CCCC
Confidence            47888898766422   34889 99999999998888877888  9987

>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=89.40  E-value=0.16  Score=31.62  Aligned_cols=43  Identities=28%  Similarity=0.682  Sum_probs=31.3

Q ss_pred             CccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ...||=|.....+      +.= .||+.||..|...|-. ++...||-|++
T Consensus        23 ~~~C~IC~~~~~~------~~~~~CgH~fC~~Ci~~wl~-~~~~~CP~Cr~   66 (79)
T d1fbva4          23 FQLCKICAENDKD------VKIEPCGHLMCTSCLTSWQE-SEGQGCPFCRC   66 (79)
T ss_dssp             TTBCTTTSSSBCC------EECSSSCCEECHHHHHHHHH-TTCCSCTTTCC
T ss_pred             CCCCccCCCcCCC------eEEeCCCCeeeHHHHHHHHH-HCcCcCCCCCc
Confidence            3579999875542      344 8999999999999842 34456999974

>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=89.00  E-value=0.056  Score=30.80  Aligned_cols=28  Identities=36%  Similarity=0.978  Sum_probs=21.6

Q ss_pred             EeccccccccccccccCCCCCcCCCCCCC
Q 025608          222 CRCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       222 C~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      +.||+.||..|...|.. .+...||.|.+
T Consensus        20 ~~CgH~~c~~C~~~w~~-~~~~~CP~CR~   47 (52)
T d1ur6b_          20 CTCGYQICRFCWHRIRT-DENGLCPACRK   47 (52)
T ss_dssp             SSSSCCCCHHHHHHHTT-TSCCBCTTTCC
T ss_pred             cCCCCccchHHHHHHHh-hcCCCCCccCC
Confidence            47999999999999953 23336999964

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=86.85  E-value=0.13  Score=29.26  Aligned_cols=27  Identities=30%  Similarity=0.550  Sum_probs=19.7

Q ss_pred             ccCCCCCcceeccCCCcceEE-eccccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHAF  228 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~F  228 (250)
                      +.||+|+.-+.-..-=|.++| +|++..
T Consensus        19 k~CP~CG~GvFmA~H~dR~~CGKCgyTe   46 (55)
T d2k4xa1          19 RFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             CCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             CcCcCCCCcEEeeecCCCccccCCcccE
Confidence            789999874444444479999 998753

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.64  E-value=0.68  Score=28.75  Aligned_cols=61  Identities=18%  Similarity=0.443  Sum_probs=39.7

Q ss_pred             ecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCCccCCCCC
Q 025608          129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCK  208 (250)
Q Consensus       129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C~  208 (250)
                      ..|-  -|+--+-.... ....+.|..|+...|..|..          |.                  .+...+.||.|+
T Consensus        17 q~Cq--iCGd~VG~~~~-Ge~FVAC~eC~FPvCrpCyE----------YE------------------rkeG~q~CpqCk   65 (93)
T d1weoa_          17 QFCE--ICGDQIGLTVE-GDLFVACNECGFPACRPCYE----------YE------------------RREGTQNCPQCK   65 (93)
T ss_dssp             CBCS--SSCCBCCBCSS-SSBCCSCSSSCCCCCHHHHH----------HH------------------HHTSCSSCTTTC
T ss_pred             chhh--hcccccccCCC-CCEEEEecccCCccchHHHH----------HH------------------HhccCccCcccC
Confidence            3555  45543333321 23668999999999977753          21                  123348999999


Q ss_pred             cceeccCCCcce
Q 025608          209 FYVEKKDGCSYI  220 (250)
Q Consensus       209 ~~i~k~~GCnhm  220 (250)
                      ++..+..|+-.|
T Consensus        66 t~Ykr~kgsprv   77 (93)
T d1weoa_          66 TRYKRLRGSPRV   77 (93)
T ss_dssp             CCCCCCTTCCCC
T ss_pred             ChhhhhcCCCCC
Confidence            999988887544

>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=85.10  E-value=0.11  Score=33.00  Aligned_cols=29  Identities=31%  Similarity=0.684  Sum_probs=22.9

Q ss_pred             eEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          220 IRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       220 m~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      +.. .||+.|+..|+.+|-.. + ..||-|.+
T Consensus        52 ~~~~~C~H~FH~~Ci~~Wl~~-~-~~CP~CR~   81 (88)
T d3dplr1          52 VAWGVCNHAFHFHCISRWLKT-R-QVCPLDNR   81 (88)
T ss_dssp             EEEETTSCEEEHHHHHHHHTT-C-SBCSSSCS
T ss_pred             eEEccccCcccHHHHHHHHHH-C-CcCCCCCC
Confidence            456 79999999999999543 3 25999975

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.43  E-value=0.13  Score=26.96  Aligned_cols=26  Identities=27%  Similarity=0.742  Sum_probs=19.4

Q ss_pred             cCCCCCCCCceecCccCccCcccCCcccchh
Q 025608          130 YCPFKDCSALLIDDAGEAIRESECPNCHRLF  160 (250)
Q Consensus       130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~  160 (250)
                      .||  .|+..+.+.++   ..+.||.|+..|
T Consensus         5 ~CP--~C~seytYedg---~l~vCPeC~hEW   30 (38)
T d2akla2           5 PCP--QCNSEYTYEDG---ALLVCPECAHEW   30 (38)
T ss_dssp             CCT--TTCCCCCEECS---SSEEETTTTEEE
T ss_pred             cCC--CCCCcceEcCC---CEEECCcccCcC
Confidence            577  89888777665   557898888764

>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=84.42  E-value=0.062  Score=31.57  Aligned_cols=50  Identities=16%  Similarity=0.194  Sum_probs=30.9

Q ss_pred             CCccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608          200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK  250 (250)
Q Consensus       200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~  250 (250)
                      ....|+=|....... -=.--.| .|++.|+..|+..|-..+....||.|+.
T Consensus         5 d~~~C~IC~~~~~~~-~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~   55 (60)
T d1vyxa_           5 DVPVCWICNEELGNE-RFRACGCTGELENVHRSCLSTWLTISRNTACQICGV   55 (60)
T ss_dssp             SCCEETTTTEECSCC-CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCC
T ss_pred             CCCCCccCCccCCCc-eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCC
Confidence            345677776533211 0111235 7889999999999953344456999974

>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=83.81  E-value=0.24  Score=32.87  Aligned_cols=33  Identities=27%  Similarity=0.633  Sum_probs=23.2

Q ss_pred             cceEE--eccccccccccccccCC---CCCcCCCCCCC
Q 025608          218 SYIRC--RCGHAFCYHCGVQLSTV---SHGYYCPSCNK  250 (250)
Q Consensus       218 nhm~C--~C~~~FC~~C~~~~~~~---~h~~~~~~~~~  250 (250)
                      +...+  .|++.|+..|+..|-..   .....||.|.+
T Consensus        53 ~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~   90 (114)
T d1v87a_          53 MVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT   90 (114)
T ss_dssp             SCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCC
T ss_pred             ccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccc
Confidence            34445  79999999999998421   22346999963

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=82.48  E-value=0.35  Score=29.01  Aligned_cols=33  Identities=33%  Similarity=0.978  Sum_probs=26.9

Q ss_pred             ccCCCCCcceeccCCCcceEE-ecccc-----ccccccccc
Q 025608          202 NRCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQL  236 (250)
Q Consensus       202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~  236 (250)
                      ..||.|...++..+|  +.+| .|...     ||--|.+++
T Consensus         3 ~~CP~C~~eL~~~~~--~~~C~~C~~~~~~~a~CPdC~~~L   41 (71)
T d2jnea1           3 LHCPQCQHVLDQDNG--HARCRSCGEFIEMKALCPDCHQPL   41 (71)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEEEEEEECTTTCSBC
T ss_pred             CcCCCccCcccccCC--CEehhhhhhhheeEEeCCccccHH
Confidence            589999999999887  9999 88765     577776665