Citrus Sinensis ID: 024938

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260
Protein Sequence
MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccEEccccccccHHHHHHHHHHHccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccEEEEEEHccccccEEEcccccccHHHHHHHHccccccccccccccccccEEEEEccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
meqnlfepetgyateedaslkqkwsptsaptnvpekdgsffecnicldsaqdpvvtlcghlycwpciykwlhvqtssldadeqqqncpvckanisvaslvplygrggissasdskkpnlgevvpsrphpsalntsvtssststrhqtQQLHSdffqsqapafhnpqyfphhygshaalassslggmatisffnplmgmlggmtlerifggsttslftypsqsllvsnnprirRQEMELDKSLNRVSLFLFCCLVLCLLLF
Flexible Loop (DISEMBL)
meqnlfepetgyateedaslkqkwspTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGIssasdskkpnlgevvpsrphpsalnTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF
Low Complexity Region (SEG)
MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNtsvtssststRHQTQQLHSDFFQSQAPAFHNPQYFPhhygshaalassslggMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSlflfcclvlclllf
Disordered region (IsUnstruct)
**************************************SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRG*******************************************************FHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVS***********LDKSLNRVSLFLFCCLVLCLLL*
Disordered Region (DISOPRED)
******************************************CNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTS****DEQQQNCPVCKANISVASLVPL***********************************************************F************************ATISFFNPLMGMLGGMTLERIFGGSTTSL**************************LNRVSLFLFCCLVLCLLLF
Disordered Region (DISEMBL)
********************************VPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVP**************************HSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF
Disordered Region (DISPRO)
*************************************GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRG************************************TRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHi
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF
Positional Conservation
no confident homologs detected

---

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	260	2.2.26 [Sep-21-2011]
Q6R567	252	E3 ubiquitin-protein liga	N/A	no	0.873	0.900	0.452	6e-49
Q8GUK7	243	E3 ubiquitin-protein liga	yes	no	0.853	0.913	0.442	1e-48
O64425	249	E3 ubiquitin-protein liga	no	no	0.85	0.887	0.402	2e-43
P93030	193	E3 ubiquitin-protein liga	no	no	0.661	0.891	0.358	4e-31
Q09463	235	RING finger protein 5 OS=	yes	no	0.388	0.429	0.467	4e-20
Q99942	180	E3 ubiquitin-protein liga	yes	no	0.307	0.444	0.457	1e-18
Q91YT2	192	E3 ubiquitin-protein liga	yes	no	0.296	0.401	0.466	2e-18
Q568Y3	192	E3 ubiquitin-protein liga	yes	no	0.296	0.401	0.466	2e-18
Q96GF1	192	E3 ubiquitin-protein liga	no	no	0.296	0.401	0.466	2e-18
Q5RFK9	192	E3 ubiquitin-protein liga	no	no	0.296	0.401	0.466	3e-18

>sp|Q6R567|RMA1_CAPAN E3 ubiquitin-protein ligase RMA1H1 OS=Capsicum annuum GN=RMA1H1 PE=1 SV=1

 Score =  194 bits (492), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 109/241 (45%), Positives = 148/241 (61%), Gaps = 14/241 (5%)

Query: 23  KWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQT-SSLDAD 81
           KW   S    V E     F+CNICLD   +PV+TLCGHLYCWPCIYKW++ Q+ SS ++D
Sbjct: 23  KWK--SMNDEVEENISGGFDCNICLDCVHEPVITLCGHLYCWPCIYKWIYFQSVSSENSD 80

Query: 82  EQQQNCPVCKANISVASLVPLYGRGGISSA-SDSKKPNLGEVVPSRPHPSALNTSVTSSS 140
           +QQ  CPVCKA +S  +L+PLYGRGG S+  S+ K PNLG V+P RP PS          
Sbjct: 81  QQQPQCPVCKAEVSEKTLIPLYGRGGQSTKPSEGKAPNLGIVIPQRP-PSPRCGGHFLLP 139

Query: 141 TSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLG 200
           T+  + +Q L    +Q Q+         P + GS+ +    S GG AT +       M+G
Sbjct: 140 TTDSNPSQLLQRRGYQQQSQTRQ-----PAYQGSYMSSPMLSPGG-ATANMLQ--HSMIG 191

Query: 201 GMTLERIFGGSTTSLFTYP-SQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLL 259
            +   RIFG S+T+++TYP S +L +S++PR+RRQ  + D+SL R+  FLFCC V CL+L
Sbjct: 192 EVAYARIFGNSSTTMYTYPNSYNLAISSSPRMRRQLSQADRSLGRICFFLFCCFVTCLIL 251

Query: 260 F 260
           F
Sbjct: 252 F 252

E3 ubiquitin-protein ligase required for aquaporin levels regulation.
Capsicum annuum (taxid: 4072)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q8GUK7|RMA3_ARATH E3 ubiquitin-protein ligase RMA3 OS=Arabidopsis thaliana GN=RMA3 PE=1 SV=1

 Score =  192 bits (489), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 112/253 (44%), Positives = 146/253 (57%), Gaps = 31/253 (12%)

Query: 1   MEQNLF-EPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCG 59
           ME N F   +   A +     KQK + T+APT     +   F+CNICLD+A DPVVTLCG
Sbjct: 1   MEGNFFIRSDAQRAHDNGFIAKQKPNLTTAPTAGQANESGCFDCNICLDTAHDPVVTLCG 60

Query: 60  HLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSAS---DSKK 116
           HL+CWPCIYKWLHVQ SS+  D+ Q NCPVCK+NI++ SLVPLYGRG  S +S     K+
Sbjct: 61  HLFCWPCIYKWLHVQLSSVSVDQHQNNCPVCKSNITITSLVPLYGRGMSSPSSTFGSKKQ 120

Query: 117 PNLGEVVPSRPHPSALNTSVTSSST---STRHQTQQLHSDFFQSQAPAFHNPQYFPHHYG 173
             L   +P RP PSAL   +TS+S+   S +HQT           +P+FHN QY P  + 
Sbjct: 121 DALSTDIPRRPAPSALRNPITSASSLNPSLQHQT----------LSPSFHNHQYSPRGF- 169

Query: 174 SHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRR 233
                 S+ L     +SF  P++GM G +   RIFG  T ++   P QS          +
Sbjct: 170 --TTTESTDLANAVMMSFLYPVIGMFGDLVYTRIFGTFTNTI-AQPYQS----------Q 216

Query: 234 QEMELDKSLNRVS 246
           + M+ +KSLNRVS
Sbjct: 217 RMMQREKSLNRVS 229

E3 ubiquitin-protein ligase.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O64425|RMA1_ARATH E3 ubiquitin-protein ligase RMA1 OS=Arabidopsis thaliana GN=RMA1 PE=1 SV=1

 Score =  175 bits (444), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 97/241 (40%), Positives = 141/241 (58%), Gaps = 20/241 (8%)

Query: 22  QKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQT-SSLDA 80
           +K  P +      + D S F+CNICLDS Q+PVVTLCGHL+CWPCI+KWL VQ+ S+ D 
Sbjct: 27  KKPEPITVSVPSDDTDDSNFDCNICLDSVQEPVVTLCGHLFCWPCIHKWLDVQSFSTSDE 86

Query: 81  DEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSS 140
            ++ + CPVCK+ +S ++LVPLYGRG  ++  + K       VP RP        + +S 
Sbjct: 87  YQRHRQCPVCKSKVSHSTLVPLYGRGRCTTQEEGKNS-----VPKRPVGPVYRLEMPNSP 141

Query: 141 TSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLG 200
            ++        +D   SQ   F++PQ    +Y     ++S+SL   A +   +P+M M+G
Sbjct: 142 YAS--------TDLRLSQRVHFNSPQ--EGYYPVSGVMSSNSLSYSAVL---DPVMVMVG 188

Query: 201 GMTLERIFGGSTTSLFTYP-SQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLL 259
            M   R+FG      F YP + +L  ++ PR+RR+ M+ DKSL R+  F  CC+VLCLLL
Sbjct: 189 EMVATRLFGTRVMDRFAYPDTYNLAGTSGPRMRRRIMQADKSLGRIFFFFMCCVVLCLLL 248

Query: 260 F 260
           F
Sbjct: 249 F 249

E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of aquaporin PIP2-1. Forms a ubiquitin ligase complex in cooperation with the E2 enzymes UCB8/UCB10.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P93030|RMA2_ARATH E3 ubiquitin-protein ligase RMA2 OS=Arabidopsis thaliana GN=RMA2 PE=1 SV=1

 Score =  135 bits (339), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 113/229 (49%), Gaps = 57/229 (24%)

Query: 38  GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSS------LDADEQQQNCPVCK 91
           G  F+CNICLD  +DPVVTLCGHL+CWPCI+KW +   +S       D   +   CPVCK
Sbjct: 16  GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCK 75

Query: 92  ANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLH 151
           +++S A+LVP+YGRG        K P  G  VPSRP         T      R   Q+L 
Sbjct: 76  SDVSEATLVPIYGRG-------QKAPQSGSNVPSRP---------TGPVYDLRGVGQRLG 119

Query: 152 SDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGS 211
               +SQ   +  P                           +P+MG++  M   R+FG S
Sbjct: 120 EG--ESQRYMYRMP---------------------------DPVMGVVCEMVYRRLFGES 150

Query: 212 TTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF 260
           ++++  Y         N R RR+ M+ ++SL+RV LFL C + +CL LF
Sbjct: 151 SSNMAPYRDM------NVRSRRRAMQAEESLSRVYLFLLCFMFMCLFLF 193

E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of the auxin-binding protein ERABP1.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q09463|RNF5_CAEEL RING finger protein 5 OS=Caenorhabditis elegans GN=rnf-5 PE=1 SV=1

 Score = 98.6 bits (244), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 51/109 (46%), Positives = 65/109 (59%), Gaps = 8/109 (7%)

Query: 25  SPTSAPTNVPEKDGSF-FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQ 83
           +P+  PT+   KD S  FECNICLD+A+D VV+LCGHL+CWPC+ +W       LD    
Sbjct: 7   APSEEPTSSSNKDESARFECNICLDAAKDAVVSLCGHLFCWPCLSQW-------LDTRPN 59

Query: 84  QQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSAL 132
            Q CPVCK+ I    +VP+YGRGG SS    K P   +   S P P + 
Sbjct: 60  NQVCPVCKSAIDGNKVVPIYGRGGDSSDPRKKVPPRPKGQRSEPPPQSF 108

Caenorhabditis elegans (taxid: 6239)

>sp|Q99942|RNF5_HUMAN E3 ubiquitin-protein ligase RNF5 OS=Homo sapiens GN=RNF5 PE=1 SV=1

 Score = 93.6 bits (231), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/94 (45%), Positives = 58/94 (61%), Gaps = 14/94 (14%)

Query: 13  ATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLH 72
           A EED   +        P       G+ FECNICL++A++ VV++CGHLYCWPC+++WL 
Sbjct: 4   AEEEDGGPE-------GPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLE 56

Query: 73  VQTSSLDADEQQQNCPVCKANISVASLVPLYGRG 106
            +        ++Q CPVCKA IS   +VPLYGRG
Sbjct: 57  TRP-------ERQECPVCKAGISREKVVPLYGRG 83

Has E2-dependent E3 ubiquitin-protein ligase activity. May function together with E2 ubiquitin-conjugating enzymes UBE2D1/UBCH5A and UBE2D2/UBC4. Mediates ubiquitination of PXN/paxillin and Salmonella type III secreted protein sopA. May be involved in regulation of cell motility and localization of PXN/paxillin. Mediates the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD; the ubiquitination appears to involve E2 ubiquitin-conjugating enzyme UBE2N. Mediates the 'Lys-48'-linked polyubiquitination of TMEM173 at 'Lys-150' leading to its proteasomal degradation; the ubiquitination occurrs in mitochondria after viral transfection and regulates antiviral responses.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q91YT2|RN185_MOUSE E3 ubiquitin-protein ligase RNF185 OS=Mus musculus GN=Rnf185 PE=2 SV=1

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 13/90 (14%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
           S FECNICLD+A+D V++LCGHL+CWPC+++WL  + +       +Q CPVCKA IS   
Sbjct: 35  STFECNICLDTAKDAVISLCGHLFCWPCLHQWLETRPN-------RQVCPVCKAGISRDK 87

Query: 99  LVPLYGRGGISSASDSKKPNLGEVVPSRPH 128
           ++PLYGRG        +K       P RP 
Sbjct: 88  VIPLYGRGSTGQQDPREK------TPPRPQ 111

Mitochondrial E3 ubiquitin-protein ligase that regulates selective mitochondrial autophagy by mediating 'Lys-63'-linked polyubiquitination of BNIP1.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q568Y3|RN185_RAT E3 ubiquitin-protein ligase RNF185 OS=Rattus norvegicus GN=Rnf185 PE=2 SV=1

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 13/90 (14%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
           S FECNICLD+A+D V++LCGHL+CWPC+++WL  + +       +Q CPVCKA IS   
Sbjct: 35  STFECNICLDTAKDAVISLCGHLFCWPCLHQWLETRPN-------RQVCPVCKAGISRDK 87

Query: 99  LVPLYGRGGISSASDSKKPNLGEVVPSRPH 128
           ++PLYGRG        +K       P RP 
Sbjct: 88  VIPLYGRGSTGQQDPREK------TPPRPQ 111

Mitochondrial E3 ubiquitin-protein ligase that regulates selective mitochondrial autophagy by mediating 'Lys-63'-linked polyubiquitination of BNIP1.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q96GF1|RN185_HUMAN E3 ubiquitin-protein ligase RNF185 OS=Homo sapiens GN=RNF185 PE=1 SV=1

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 13/90 (14%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
           S FECNICLD+A+D V++LCGHL+CWPC+++WL  + +       +Q CPVCKA IS   
Sbjct: 35  STFECNICLDTAKDAVISLCGHLFCWPCLHQWLETRPN-------RQVCPVCKAGISRDK 87

Query: 99  LVPLYGRGGISSASDSKKPNLGEVVPSRPH 128
           ++PLYGRG        +K       P RP 
Sbjct: 88  VIPLYGRGSTGQQDPREK------TPPRPQ 111

Mitochondrial E3 ubiquitin-protein ligase that regulates selective mitochondrial autophagy by mediating 'Lys-63'-linked polyubiquitination of BNIP1.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5RFK9|RN185_PONAB E3 ubiquitin-protein ligase RNF185 OS=Pongo abelii GN=RNF185 PE=2 SV=1

 Score = 92.4 bits (228), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 13/90 (14%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
           S FECNICLD+A+D V++LCGHL+CWPC+++WL  + +       +Q CPVCKA IS   
Sbjct: 35  STFECNICLDTAKDAVISLCGHLFCWPCLHQWLETRPN-------RQVCPVCKAGISRDK 87

Query: 99  LVPLYGRGGISSASDSKKPNLGEVVPSRPH 128
           ++PLYGRG        +K       P RP 
Sbjct: 88  VIPLYGRGSTGQQDPREK------TPPRPQ 111

Mitochondrial E3 ubiquitin-protein ligase that regulates selective mitochondrial autophagy by mediating 'Lys-63'-linked polyubiquitination of BNIP1.

Pongo abelii (taxid: 9601)

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	260
449446936	261	PREDICTED: E3 ubiquitin-protein ligase R	0.992	0.988	0.536	4e-71
449531287	261	PREDICTED: E3 ubiquitin-protein ligase R	0.992	0.988	0.532	1e-70
225461411	253	PREDICTED: E3 ubiquitin-protein ligase R	0.946	0.972	0.513	5e-69
224128161	228	predicted protein [Populus trichocarpa]	0.873	0.995	0.568	1e-67
255573345	265	rnf5, putative [Ricinus communis] gi|223	0.926	0.909	0.539	3e-67
224114956	228	predicted protein [Populus trichocarpa]	0.873	0.995	0.560	1e-64
328929994	250	MAKIBISHI 1 [Medicago truncatula]	0.896	0.932	0.527	3e-64
388507976	248	unknown [Lotus japonicus]	0.888	0.931	0.535	5e-62
302143025	308	unnamed protein product [Vitis vinifera]	0.780	0.659	0.467	2e-56
358249238	246	uncharacterized protein LOC100817526 [Gl	0.880	0.930	0.485	2e-54

>gi|449446936|ref|XP_004141226.1| PREDICTED: E3 ubiquitin-protein ligase RMA3-like [Cucumis sativus]

 Score =  273 bits (699), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 141/263 (53%), Positives = 177/263 (67%), Gaps = 5/263 (1%)

Query: 1   MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGH 60
           MEQN   PE    +E+D SLKQ W   S  + + E     F+CNICLDSA DPVVTLCGH
Sbjct: 1   MEQNYSVPEAYLESEQDVSLKQNWKSISTQSTISEDANGCFDCNICLDSAADPVVTLCGH 60

Query: 61  LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLG 120
           LYCWPCIYKWLHVQ SS +  E  QNCPVCKA+I+ +SLVPLYGRG  +S S+SKK +LG
Sbjct: 61  LYCWPCIYKWLHVQISS-NEPENTQNCPVCKASITPSSLVPLYGRGTSNSDSESKKSHLG 119

Query: 121 EVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHH-YGSHAALA 179
             VP RP PS +NT   S+S+ST + +Q+LHS++ +S +   ++ QYFP   YG+ A+ +
Sbjct: 120 MAVPRRPPPS-MNTPSHSNSSSTLYPSQELHSNYIRSPSHPIYHQQYFPQATYGNFASYS 178

Query: 180 SSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNP--RIRRQEME 237
            S LG     S  NP +GM G     RIFG    +L  Y   +  +S N   R+RRQEM+
Sbjct: 179 PSYLGNAVITSLLNPTIGMFGETVFTRIFGSVDGNLLPYSPYNNSISGNASTRMRRQEMQ 238

Query: 238 LDKSLNRVSLFLFCCLVLCLLLF 260
           LDKSLNRVS+FLFCC ++CLLLF
Sbjct: 239 LDKSLNRVSIFLFCCFIICLLLF 261

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449531287|ref|XP_004172618.1| PREDICTED: E3 ubiquitin-protein ligase RMA3-like [Cucumis sativus]

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 140/263 (53%), Positives = 176/263 (66%), Gaps = 5/263 (1%)

Query: 1   MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGH 60
           MEQN   PE    +E+D SLKQ W   S  + + E     F+CNICLDSA DPVVTLCGH
Sbjct: 1   MEQNYSVPEAYLESEQDVSLKQNWKSISTQSTISEDANGCFDCNICLDSAADPVVTLCGH 60

Query: 61  LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLG 120
           LYCWPCIYKWLHVQ SS +  E  QNCPVCKA+I+ +SLVPLYGRG  +S S+SKK +LG
Sbjct: 61  LYCWPCIYKWLHVQISS-NEPENTQNCPVCKASITPSSLVPLYGRGTSNSDSESKKSHLG 119

Query: 121 EVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHH-YGSHAALA 179
             VP RP PS +NT   S+S+S  + +Q+LHS++ +S +   ++ QYFP   YG+ A+ +
Sbjct: 120 MAVPRRPPPS-MNTPSHSNSSSALYPSQELHSNYIRSPSHPIYHQQYFPQATYGNFASYS 178

Query: 180 SSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNP--RIRRQEME 237
            S LG     S  NP +GM G     RIFG    +L  Y   +  +S N   R+RRQEM+
Sbjct: 179 PSYLGNAVITSLLNPTIGMFGETVFTRIFGSVDGNLLPYSPYNNSISGNASTRMRRQEMQ 238

Query: 238 LDKSLNRVSLFLFCCLVLCLLLF 260
           LDKSLNRVS+FLFCC ++CLLLF
Sbjct: 239 LDKSLNRVSIFLFCCFIICLLLF 261

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461411|ref|XP_002282248.1| PREDICTED: E3 ubiquitin-protein ligase RMA1H1-like [Vitis vinifera]

 Score =  266 bits (681), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 136/265 (51%), Positives = 175/265 (66%), Gaps = 19/265 (7%)

Query: 1   MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGH 60
           +EQ+  E    + ++ D SL++KW   SA     E     F+CNICLDSA DPVVTLCGH
Sbjct: 3   LEQDFPELAAQHESDGDVSLQKKWKAISASEAASENSNGSFDCNICLDSAHDPVVTLCGH 62

Query: 61  LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLG 120
           LYCWPCIYKWLHVQ++S    EQQQNCPVCKANIS  SLVPLYGRG   S S++KK ++G
Sbjct: 63  LYCWPCIYKWLHVQSTS-PVTEQQQNCPVCKANISHTSLVPLYGRGPSPSESETKKLHVG 121

Query: 121 EVVPSRPHPSALNTSVTSSSTST--RHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAAL 178
             +P RP    ++T +T++++++   H ++ LH + FQS +      QYFPH YG +AA 
Sbjct: 122 PAIPRRPPAHGVHTLITTTTSASLNSHPSRHLHPNPFQSHS------QYFPHPYGGYAAT 175

Query: 179 ASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYP---SQSLLVSNNPRIRRQE 235
            +         S  NP +GM G M   R+FG S TSLF YP   +  L+ S NPR+RRQE
Sbjct: 176 PT-------LTSVLNPTIGMFGEMVFSRMFGSSDTSLFAYPYPNTYPLMASANPRMRRQE 228

Query: 236 MELDKSLNRVSLFLFCCLVLCLLLF 260
           M+LD+ LNRVS+FLFCC +LCLL F
Sbjct: 229 MQLDRCLNRVSIFLFCCFILCLLSF 253

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128161|ref|XP_002329096.1| predicted protein [Populus trichocarpa] gi|222869765|gb|EEF06896.1| predicted protein [Populus trichocarpa]

 Score =  262 bits (669), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 132/232 (56%), Positives = 160/232 (68%), Gaps = 5/232 (2%)

Query: 21  KQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDA 80
           KQK      PT V + D  +FECNICLDSA DPVVTLCGHLYCWPCIYKWLHV+TSS DA
Sbjct: 1   KQKHKLIPVPTAVSDNDSGYFECNICLDSAHDPVVTLCGHLYCWPCIYKWLHVKTSSPDA 60

Query: 81  DEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSS 140
            +QQ +CPVCKA+IS  SLVPLYGRG  +S S SKK     V+P RP PS LNT     +
Sbjct: 61  SQQQPSCPVCKADISPNSLVPLYGRGPSTSESKSKKDPADVVIPRRPLPSELNT----VN 116

Query: 141 TSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLG 200
            +T  Q +QLHS+FF  Q  +F + QYF   +G +AAL SS+LGG     F NP++GM  
Sbjct: 117 ANTSPQNRQLHSNFFNPQPQSFQHQQYFHDPHGGYAALTSSNLGGTVMTGFLNPMLGMFN 176

Query: 201 GMTLERIFGGSTTSLFTYP-SQSLLVSNNPRIRRQEMELDKSLNRVSLFLFC 251
            M   R FG S T++F  P +  L+ SN+PR+RRQE++LDKSLNRVS+F  C
Sbjct: 177 EMVFTRNFGTSITNMFARPYTNPLMGSNSPRMRRQEVQLDKSLNRVSIFFLC 228

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573345|ref|XP_002527599.1| rnf5, putative [Ricinus communis] gi|223533016|gb|EEF34780.1| rnf5, putative [Ricinus communis]

 Score =  261 bits (666), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 138/256 (53%), Positives = 175/256 (68%), Gaps = 15/256 (5%)

Query: 1   MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGH 60
           ME   FE +  +  EED ++KQKW   SA T + E D   F CNICLDSA DPVVTLCGH
Sbjct: 1   MEPRFFEHDMHFDAEEDLTVKQKWKSVSAATGLSEDDDDCFSCNICLDSANDPVVTLCGH 60

Query: 61  LYCWPCIYKWLHVQTSSLDADEQQQ--NCPVCKANISVASLVPLYGRGGISSASDSKKPN 118
           LYCWPCIYKWL V+ +S D DEQQQ  +CPVCKANIS  S+VPLYGRG   S S++KK +
Sbjct: 61  LYCWPCIYKWLQVKRTSSDVDEQQQQPSCPVCKANISSNSMVPLYGRGTSQSNSETKKGS 120

Query: 119 LGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFF----QSQAPAFHNPQYFPHHYGS 174
           +   +P RP P A+NTS+T++S      +QQLH +FF    QSQ  +FH+ +YF   YG 
Sbjct: 121 VDAAIPRRP-PPAMNTSITNTS----QLSQQLHPNFFQSHSQSQPQSFHHQRYFTDRYGG 175

Query: 175 HAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYP---SQSLLVS-NNPR 230
           + ALAS++LG  A    F+P++GM G +   R FG S TSLF Y    S SL+ S N+PR
Sbjct: 176 YGALASTNLGAAAMTQIFSPMIGMFGELIFSRTFGTSNTSLFAYSYPNSNSLMGSYNSPR 235

Query: 231 IRRQEMELDKSLNRVS 246
           +RRQEM+L++SLNRV+
Sbjct: 236 MRRQEMQLEQSLNRVT 251

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114956|ref|XP_002316902.1| predicted protein [Populus trichocarpa] gi|222859967|gb|EEE97514.1| predicted protein [Populus trichocarpa]

 Score =  252 bits (643), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 130/232 (56%), Positives = 160/232 (68%), Gaps = 5/232 (2%)

Query: 21  KQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDA 80
           +QK+    AP  V + D   FECNICLDSA DPVVT CGHLYCWPC+YKWLHV+TSS DA
Sbjct: 1   EQKYKSIPAPAAVSDNDSDLFECNICLDSAHDPVVTFCGHLYCWPCMYKWLHVKTSSPDA 60

Query: 81  DEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSS 140
            +QQ +CPVCKA IS  SLVPLYGRG  SS S S   ++   +P RP PS LNT     S
Sbjct: 61  VQQQPSCPVCKAAISPTSLVPLYGRGPPSSESKSMGSSVDAALPRRPLPSGLNT----VS 116

Query: 141 TSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLG 200
            +T  Q++Q HS+ F  Q+ +F + QYF   +G +AA+ SS+L       FFNP+MGM  
Sbjct: 117 PNTSRQSRQPHSNSFNPQSQSFQHQQYFHDPHGGYAAMTSSNLRSTVMTGFFNPMMGMFN 176

Query: 201 GMTLERIFGGSTTSLFTYP-SQSLLVSNNPRIRRQEMELDKSLNRVSLFLFC 251
            M   RIFG S T++F +P +  L+ SNNPR+RRQEM+LDKSLNRVS+FLFC
Sbjct: 177 EMGCSRIFGTSVTNMFAHPYTNPLMGSNNPRMRRQEMQLDKSLNRVSIFLFC 228

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|328929994|gb|AEB69786.1| MAKIBISHI 1 [Medicago truncatula]

 Score =  250 bits (639), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 125/237 (52%), Positives = 157/237 (66%), Gaps = 4/237 (1%)

Query: 10  TGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYK 69
           T + + ++ SLKQKW  T+  T +   + + F+CNICL+SA DPVVTLCGHLYCWPCIYK
Sbjct: 4   TCFGSNDEVSLKQKWKSTTEDTTISSGENNCFDCNICLESANDPVVTLCGHLYCWPCIYK 63

Query: 70  WLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHP 129
           WL+VQ+SS++ D Q   CPVCKA IS  SLVPLYGRG  +S ++S K  +G  +P RP P
Sbjct: 64  WLNVQSSSVEPDTQP-TCPVCKAVISHTSLVPLYGRGKSNSETESNKLQVGLGIPHRPPP 122

Query: 130 SALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATI 189
             LN  +TS+  S     QQLH ++FQSQ+   H   Y PH YG H A     LGG A  
Sbjct: 123 YNLNALLTSNRPSNLRHEQQLHPNYFQSQSRPIHYQHYIPHLYGGHGANGLHYLGGAAMT 182

Query: 190 SFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVS 246
           SF NP+MG+ G M   R+FG S  +LF YP      S +PR+RRQEM++DKSLNRVS
Sbjct: 183 SFVNPVMGLFGEMVSTRMFGVSDANLFAYPRNG---STSPRMRRQEMQIDKSLNRVS 236

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507976|gb|AFK42054.1| unknown [Lotus japonicus]

 Score =  243 bits (621), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 127/237 (53%), Positives = 157/237 (66%), Gaps = 6/237 (2%)

Query: 10  TGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYK 69
           T + +  + S KQK   TSA + +   D   F+CNICL+SA DPVVTLCGHLYCWPCIYK
Sbjct: 4   TYFDSNGEVSPKQKLKSTSAESPISSSDNGCFDCNICLESAHDPVVTLCGHLYCWPCIYK 63

Query: 70  WLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHP 129
           WL VQ+SS + D QQQ CP+CKA IS  SLVPLYGRG  +S S+SKK  +G  +P RP P
Sbjct: 64  WLSVQSSSAEPD-QQQTCPICKAEISHTSLVPLYGRGTSNSESESKKLQMGLGIPQRPPP 122

Query: 130 SALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATI 189
             LN  +TS+  S  H  +QL+  +F SQ+   H  Q++   YG+H A     LGG A  
Sbjct: 123 YNLNAMLTSNRASNPHLGEQLYPSYFHSQSQPLHYQQHY--LYGTHGANGLPYLGGTAMT 180

Query: 190 SFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVS 246
           SFFNP++GM G M L RIFG S  +LF YP      S +PR+RRQEM++DKSLNRVS
Sbjct: 181 SFFNPVIGMFGEMVLTRIFGVSDANLFPYPHSG---SGSPRMRRQEMQIDKSLNRVS 234

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143025|emb|CBI20320.3| unnamed protein product [Vitis vinifera]

 Score =  224 bits (572), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/263 (46%), Positives = 148/263 (56%), Gaps = 60/263 (22%)

Query: 1   MEQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGH 60
           +EQ+  E    + ++ D SL++KW   SA     E     F+CNICLDSA DPVVTLCGH
Sbjct: 103 LEQDFPELAAQHESDGDVSLQKKWKAISASEAASENSNGSFDCNICLDSAHDPVVTLCGH 162

Query: 61  LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLG 120
           LYCWPCIYKWLHVQ++S    EQQQNCPVCKANIS  SLVPLYGRG   S S++KK ++G
Sbjct: 163 LYCWPCIYKWLHVQSTS-PVTEQQQNCPVCKANISHTSLVPLYGRGPSPSESETKKLHVG 221

Query: 121 EVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALAS 180
             +P RP                                PA          +G H  L  
Sbjct: 222 PAIPRRP--------------------------------PA----------HGVHTVL-- 237

Query: 181 SSLGGMATISFFNPLMGMLGGMTLERIFGGSTTSLFTYP---SQSLLVSNNPRIRRQEME 237
                       NP +GM G M   R+FG S TSLF YP   +  L+ S NPR+RRQEM+
Sbjct: 238 ------------NPTIGMFGEMVFSRMFGSSDTSLFAYPYPNTYPLMASANPRMRRQEMQ 285

Query: 238 LDKSLNRVSLFLFCCLVLCLLLF 260
           LD+ LNRVS+FLFCC +LCLL F
Sbjct: 286 LDRCLNRVSIFLFCCFILCLLSF 308

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358249238|ref|NP_001240271.1| uncharacterized protein LOC100817526 [Glycine max] gi|255640217|gb|ACU20399.1| unknown [Glycine max]

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 115/237 (48%), Positives = 152/237 (64%), Gaps = 8/237 (3%)

Query: 12  YATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWL 71
           + +  + SLKQK    SA   +   +   F+CNIC++SA DPVVTLCGHLYCWPCIYKWL
Sbjct: 6   FDSNGEVSLKQKSKSISAEPTISTSEYDCFDCNICMESAHDPVVTLCGHLYCWPCIYKWL 65

Query: 72  HVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSA 131
            VQ+SS++   QQQ CPVCK+ IS  S+VPLYG G  +S S++KK  +   +P R  P +
Sbjct: 66  DVQSSSVEP-YQQQTCPVCKSEISHTSVVPLYGCGTSNSESNAKKLQMSLGIPHRQPPCS 124

Query: 132 LNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISF 191
           LN  +TS  +   H +QQLH  +FQ+Q+  FH  Q+    YGS+       LGG +  SF
Sbjct: 125 LNAMLTSPRSRISHPSQQLHPSYFQTQSRPFHYQQF----YGSYGTNGLPYLGGASMTSF 180

Query: 192 FNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLF 248
           FN ++ M G M L RIFG S  +LF  P   L  S + R+RRQEM++DKSLNR+S+F
Sbjct: 181 FNTVIDMFGEMVLTRIFGISDANLFANP---LNGSGSSRMRRQEMQIDKSLNRLSIF 234

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	260
TAIR|locus:2124004	243	RMA3 "RING membrane-anchor 3"	0.823	0.880	0.436	1.9e-42
UNIPROTKB|Q6R567	252	RMA1H1 "E3 ubiquitin-protein l	0.815	0.841	0.415	1.6e-40
TAIR|locus:2123663	193	RMA2 "RING membrane-anchor 2"	0.319	0.430	0.520	7.6e-29
TAIR|locus:2016437	226	AT1G19310 [Arabidopsis thalian	0.353	0.407	0.57	6.6e-28
TAIR|locus:2128746	249	RMA1 "RING membrane-anchor 1"	0.780	0.815	0.344	3.5e-27
TAIR|locus:2049023	227	AT2G23780 [Arabidopsis thalian	0.380	0.436	0.473	2.1e-25
TAIR|locus:2037294	137	AT1G74990 [Arabidopsis thalian	0.438	0.832	0.440	2.6e-22
WB|WBGene00004381	235	rnf-5 [Caenorhabditis elegans	0.384	0.425	0.472	2.4e-21
UNIPROTKB|Q09463	235	rnf-5 "RING finger protein 5"	0.384	0.425	0.472	2.4e-21
TAIR|locus:2095833	436	AT3G58030 [Arabidopsis thalian	0.311	0.185	0.478	1.1e-20

TAIR|locus:2124004 RMA3 "RING membrane-anchor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 449 (163.1 bits), Expect = 1.9e-42, P = 1.9e-42
 Identities = 100/229 (43%), Positives = 129/229 (56%)

Query:     1 MEQNLFEPETGYATEEDASL-KQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCG 59
             ME N F         ++  + KQK + T+APT     +   F+CNICLD+A DPVVTLCG
Sbjct:     1 MEGNFFIRSDAQRAHDNGFIAKQKPNLTTAPTAGQANESGCFDCNICLDTAHDPVVTLCG 60

Query:    60 HLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASD--SKKP 117
             HL+CWPCIYKWLHVQ SS+  D+ Q NCPVCK+NI++ SLVPLYGRG  S +S   SKK 
Sbjct:    61 HLFCWPCIYKWLHVQLSSVSVDQHQNNCPVCKSNITITSLVPLYGRGMSSPSSTFGSKKQ 120

Query:   118 N-LGEVVPSRPHPSALNXXXXXXXXXXRHQTQQLHSDFFQSQAPAFHNPQYFPXXXXXXX 176
             + L   +P RP PSAL            + + Q H    Q+ +P+FHN QY P       
Sbjct:   121 DALSTDIPRRPAPSALRNPITSASSL--NPSLQ-H----QTLSPSFHNHQYSPRGFTTTE 173

Query:   177 XXXXXXXXXMATISFFNPLMGMLGGMTLERIFGGSTTSLFT-YPSQSLL 224
                      M   SF  P++GM G +   RIFG  T ++   Y SQ ++
Sbjct:   174 STDLANAVMM---SFLYPVIGMFGDLVYTRIFGTFTNTIAQPYQSQRMM 219

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

UNIPROTKB|Q6R567 RMA1H1 "E3 ubiquitin-protein ligase RMA1H1" [Capsicum annuum (taxid:4072)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 94/226 (41%), Positives = 127/226 (56%)

Query:    23 KWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQT-SSLDAD 81
             KW   S    V E     F+CNICLD   +PV+TLCGHLYCWPCIYKW++ Q+ SS ++D
Sbjct:    23 KWK--SMNDEVEENISGGFDCNICLDCVHEPVITLCGHLYCWPCIYKWIYFQSVSSENSD 80

Query:    82 EQQQNCPVCKANISVASLVPLYGRGGISSA-SDSKKPNLGEVVPSRPHPSALNXXXXXXX 140
             +QQ  CPVCKA +S  +L+PLYGRGG S+  S+ K PNLG V+P RP PS          
Sbjct:    81 QQQPQCPVCKAEVSEKTLIPLYGRGGQSTKPSEGKAPNLGIVIPQRP-PSPRCGGHFLLP 139

Query:   141 XXXRHQTQQLHSDFFQSQAPAFHNPQYFPXXXXXXXXXXXXXXXXMATISFFNPLMGMLG 200
                 + +Q L    +Q Q+     P Y                  M   S       M+G
Sbjct:   140 TTDSNPSQLLQRRGYQQQSQT-RQPAYQGSYMSSPMLSPGGATANMLQHS-------MIG 191

Query:   201 GMTLERIFGGSTTSLFTYP-SQSLLVSNNPRIRRQEMELDKSLNRV 245
              +   RIFG S+T+++TYP S +L +S++PR+RRQ  + D+SL R+
Sbjct:   192 EVAYARIFGNSSTTMYTYPNSYNLAISSSPRMRRQLSQADRSLGRI 237

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

GO:0005515 "protein binding" evidence=IPI

GO:0005789 "endoplasmic reticulum membrane" evidence=IDA

GO:0006970 "response to osmotic stress" evidence=IEP

GO:0009409 "response to cold" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009611 "response to wounding" evidence=IEP

GO:0009723 "response to ethylene stimulus" evidence=IEP

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

TAIR|locus:2123663 RMA2 "RING membrane-anchor 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 7.6e-29, Sum P(2) = 7.6e-29
 Identities = 50/96 (52%), Positives = 65/96 (67%)

Query:    38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSS---LDA-DEQQQ--NCPVCK 91
             G  F+CNICLD  +DPVVTLCGHL+CWPCI+KW +   +S   +D  D +++   CPVCK
Sbjct:    16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCK 75

Query:    92 ANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRP 127
             +++S A+LVP+YGRG        K P  G  VPSRP
Sbjct:    76 SDVSEATLVPIYGRG-------QKAPQSGSNVPSRP 104

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2016437 AT1G19310 [Arabidopsis thaliana (taxid:3702)]

 Score = 285 (105.4 bits), Expect = 6.6e-28, Sum P(2) = 6.6e-28
 Identities = 57/100 (57%), Positives = 65/100 (65%)

Query:    28 SAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNC 87
             S+  +    D S FECNICLD AQDP+VTLCGHL+CWPC+YKWLH+ + S D       C
Sbjct:     8 SSGNDTNNNDSSNFECNICLDLAQDPIVTLCGHLFCWPCLYKWLHLHSQSKD-------C 60

Query:    88 PVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRP 127
             PVCKA I    LVPLYGRG  SSA    K   G  VP+RP
Sbjct:    61 PVCKAVIEEDRLVPLYGRGK-SSADPRSKSIPGLEVPNRP 99

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2128746 RMA1 "RING membrane-anchor 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 80/232 (34%), Positives = 116/232 (50%)

Query:    21 KQKWSPTSAPTNVP--EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQT-SS 77
             K K  P     +VP  + D S F+CNICLDS Q+PVVTLCGHL+CWPCI+KWL VQ+ S+
Sbjct:    25 KSK-KPEPITVSVPSDDTDDSNFDCNICLDSVQEPVVTLCGHLFCWPCIHKWLDVQSFST 83

Query:    78 LDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNXXXX 137
              D  ++ + CPVCK+ +S ++LVPLYGRG  ++  + K       VP RP          
Sbjct:    84 SDEYQRHRQCPVCKSKVSHSTLVPLYGRGRCTTQEEGKNS-----VPKRPVGPVYRLEMP 138

Query:   138 XXXXXXRHQTQQLHSDFFQSQAPAFHNPQ--YFPXXXXXXXXXXXXXXXXMATISFFNPL 195
                      +    +D   SQ   F++PQ  Y+P                   +     +
Sbjct:   139 --------NSPYASTDLRLSQRVHFNSPQEGYYPVSGVMSSNSLSYSAVLDPVMVMVGEM 190

Query:   196 MG--MLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRV 245
             +   + G   ++R F    T    Y   +L  ++ PR+RR+ M+ DKSL R+
Sbjct:   191 VATRLFGTRVMDR-FAYPDT----Y---NLAGTSGPRMRRRIMQADKSLGRI 234

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0032527 "protein exit from endoplasmic reticulum" evidence=IMP

GO:0016020 "membrane" evidence=IDA

GO:0032940 "secretion by cell" evidence=IGI

TAIR|locus:2049023 AT2G23780 [Arabidopsis thaliana (taxid:3702)]

 Score = 261 (96.9 bits), Expect = 2.1e-25, Sum P(2) = 2.1e-25
 Identities = 53/112 (47%), Positives = 69/112 (61%)

Query:    17 DASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTS 76
             ++S    +S ++  TN     G  FECNIC + AQDP+VTLCGHL+CWPC+Y+WLH  + 
Sbjct:     5 ESSTSTSYSDSNNDTN---DQGGDFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSH 61

Query:    77 SLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSKK-PNLGEVVPSRP 127
             S       Q CPVCKA +    LVPLYGRG   +   SK+ P L   +P+RP
Sbjct:    62 S-------QECPVCKAVVQDDKLVPLYGRGKNQTDPRSKRYPGLR--IPNRP 104

GO:0005634 "nucleus" evidence=ISM

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

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

TAIR|locus:2037294 AT1G74990 [Arabidopsis thaliana (taxid:3702)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 56/127 (44%), Positives = 70/127 (55%)

Query:    31 TNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
             TN  +   + F CNICL+ A++P+VTLCGHL+CWPC+YKWLH  + S        +CPVC
Sbjct:     7 TNEEDDASNNFGCNICLELAREPIVTLCGHLFCWPCLYKWLHYHSKS-------NHCPVC 59

Query:    91 KANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNXXXXXXXXXXRHQTQQL 150
             KA +   +LVPLYG G  SS   SK  N G  VP+RP  +A            RH     
Sbjct:    60 KALVKEDTLVPLYGMGKPSSDPRSKL-NSGVTVPNRP--AATRTETARPRLEQRHHGSSF 116

Query:   151 ---HSDF 154
                HS F
Sbjct:   117 FGGHSSF 123

GO:0005737 "cytoplasm" evidence=ISM

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

WB|WBGene00004381 rnf-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 51/108 (47%), Positives = 65/108 (60%)

Query:    25 SPTSAPTNVPEKDGSF-FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQ 83
             +P+  PT+   KD S  FECNICLD+A+D VV+LCGHL+CWPC+ +WL       D    
Sbjct:     7 APSEEPTSSSNKDESARFECNICLDAAKDAVVSLCGHLFCWPCLSQWL-------DTRPN 59

Query:    84 QQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSA 131
              Q CPVCK+ I    +VP+YGRGG SS    K P   +   S P P +
Sbjct:    60 NQVCPVCKSAIDGNKVVPIYGRGGDSSDPRKKVPPRPKGQRSEPPPQS 107

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005680 "anaphase-promoting complex" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0055120 "striated muscle dense body" evidence=IDA

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0055002 "striated muscle cell development" evidence=IMP

GO:0030054 "cell junction" evidence=IDA

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

UNIPROTKB|Q09463 rnf-5 "RING finger protein 5" [Caenorhabditis elegans (taxid:6239)]

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 51/108 (47%), Positives = 65/108 (60%)

Query:    25 SPTSAPTNVPEKDGSF-FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQ 83
             +P+  PT+   KD S  FECNICLD+A+D VV+LCGHL+CWPC+ +WL       D    
Sbjct:     7 APSEEPTSSSNKDESARFECNICLDAAKDAVVSLCGHLFCWPCLSQWL-------DTRPN 59

Query:    84 QQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSA 131
              Q CPVCK+ I    +VP+YGRGG SS    K P   +   S P P +
Sbjct:    60 NQVCPVCKSAIDGNKVVPIYGRGGDSSDPRKKVPPRPKGQRSEPPPQS 107

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2095833 AT3G58030 [Arabidopsis thaliana (taxid:3702)]

 Score = 248 (92.4 bits), Expect = 1.1e-20, P = 1.1e-20
 Identities = 44/92 (47%), Positives = 60/92 (65%)

Query:    37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV 96
             DG+FF+CNICLD +++PV+T CGHLYCWPC+Y+WL +     DA E    CPVCK  ++ 
Sbjct:   133 DGNFFDCNICLDLSKEPVLTCCGHLYCWPCLYQWLQIS----DAKE----CPVCKGEVTS 184

Query:    97 ASLVPLYGRGGISSASDSKKPNLGEVVPSRPH 128
              ++ P+YGRG      +    +L   VP RPH
Sbjct:   185 KTVTPIYGRGNHKREIEE---SLDTKVPMRPH 213

GO:0005634 "nucleus" evidence=ISM

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8GUK7	RMA3_ARATH	6, ., 3, ., 2, ., -	0.4426	0.8538	0.9135	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.107.139.1 hypothetical protein (228 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	260
PLN03208	193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	1e-39
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	6e-11
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-10
smart00184	40	smart00184, RING, Ring finger	2e-08
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-08
COG5574	271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	8e-08
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	5e-06
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	1e-04
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	1e-04
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	2e-04
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	3e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.003
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	0.004

>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional

 Score =  135 bits (342), Expect = 1e-39
 Identities = 81/229 (35%), Positives = 113/229 (49%), Gaps = 57/229 (24%)

Query: 38  GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSS------LDADEQQQNCPVCK 91
           G  F+CNICLD  +DPVVTLCGHL+CWPCI+KW +   +S       D   +   CPVCK
Sbjct: 16  GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCK 75

Query: 92  ANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLH 151
           +++S A+LVP+YGRG        K P  G  VPSRP         +      R   Q+L 
Sbjct: 76  SDVSEATLVPIYGRG-------QKAPQSGSNVPSRP---------SGPVYDLRGVGQRLG 119

Query: 152 SDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISFFNPLMGMLGGMTLERIFGGS 211
               +SQ   +  P                           +P+MG++  M   R+FG S
Sbjct: 120 EG--ESQRYMYRMP---------------------------DPVMGVVCEMVYRRLFGES 150

Query: 212 TTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF 260
           ++++  Y         N R RR+ M+ ++SL+RV LFL C + +CL LF
Sbjct: 151 SSNMAPYRDM------NVRSRRRAMQAEESLSRVYLFLLCFMFMCLFLF 193

Length = 193

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

 Score = 55.9 bits (135), Expect = 6e-11
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 10/54 (18%)

Query: 42 ECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI 94
          EC ICL+  ++PVV L CGH++C  CI KWL            +  CP+C+  I
Sbjct: 1  ECPICLEEFREPVVLLPCGHVFCRSCIDKWL---------KSGKNTCPLCRTPI 45

Length = 45

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

 Score = 54.0 bits (130), Expect = 3e-10
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 11/53 (20%)

Query: 41 FECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA 92
           EC ICLD  +DPVV   CGH++C  CI ++L          +++  CP+C+ 
Sbjct: 3  LECPICLDLLRDPVVLTPCGHVFCRECILRYL----------KKKSKCPICRT 45

Length = 45

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

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 10/49 (20%)

Query: 43 CNICLD-SAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
          C ICL+   +DPV+  CGH +C  CI KWL         +     CP+C
Sbjct: 1  CPICLEEYLKDPVILPCGHTFCRSCIRKWL---------ESGNNTCPIC 40

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

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

 Score = 48.5 bits (116), Expect = 3e-08
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 13/55 (23%)

Query: 41 FECNICLDS---AQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA 92
           EC ICLD     ++ VV  CGH++   C+ KWL               CP+C+A
Sbjct: 1  DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWL----------RSSNTCPLCRA 45

Length = 46

>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 51.8 bits (124), Expect = 8e-08
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 17/79 (21%)

Query: 14  TEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHV 73
           T+E+ S K           +P  D   ++C +CL+  + P  T CGHL+C  C+      
Sbjct: 198 TKENLSKKNGLP------FIPLAD---YKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTK 248

Query: 74  QTSSLDADEQQQNCPVCKA 92
           +        + + CP+C+A
Sbjct: 249 K--------KYEFCPLCRA 259

Length = 271

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

 Score = 42.1 bits (99), Expect = 5e-06
 Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 10/49 (20%)

Query: 43 CNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
          C ICL+  +DPV  L CGHL+C  CI  WL         +     CP+C
Sbjct: 1  CPICLEEPKDPVTILPCGHLFCSKCILSWL---------ESGNVTCPLC 40

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

>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18

 Score = 42.7 bits (100), Expect = 1e-04
 Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 12/78 (15%)

Query: 15 EEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQ 74
          E D +    W  T  P+  P    +   C+IC D    PV+T C H +C  CI + L  Q
Sbjct: 3  ELDITDSSDWLTTPIPSLYPLD--TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQ 60

Query: 75 TSSLDADEQQQNCPVCKA 92
                      CP+C+A
Sbjct: 61 P----------KCPLCRA 68

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 25/78 (32%), Positives = 32/78 (41%), Gaps = 12/78 (15%)

Query: 15 EEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQ 74
          E DA+    W+ T  P+ +   D S   C IC      P  T CGH +C  CI + L   
Sbjct: 2  ELDATDPSDWNQTKIPS-LKGLD-SMLRCRICDCRISIPCETTCGHTFCSLCIRRHLG-- 57

Query: 75 TSSLDADEQQQNCPVCKA 92
                   Q  CPVC+ 
Sbjct: 58 --------TQPFCPVCRE 67

Length = 391

>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 4/41 (9%)

Query: 39 SFFECNICL----DSAQDPVVTLCGHLYCWPCIYKWLHVQT 75
          S F C I      D    PV+  CGH+Y    + K      
Sbjct: 9  SIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGG 49

This zinc-finger is the dimerisation motif for LisH proteins, and is also a typical RING-type of plant ubiquitin ligases. Length = 55

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

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 12/55 (21%)

Query: 42 ECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
           C ICL+  ++ V   CGHL  C  C  +              ++ CP+C+  I 
Sbjct: 4  LCVICLERPRNVVFLPCGHLCLCEECAKRLR-----------SKKKCPICRQPIE 47

Length = 49

>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 7/44 (15%)

Query: 54 VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA 97
          V   C H +   CI KWL  +TS       +  CP+C+     A
Sbjct: 48 VWGKCKHNFHMHCILKWLATETS-------KGLCPMCRQTFVFA 84

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. Length = 85

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 12/51 (23%)

Query: 43 CNICLDSAQD--PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
          C  C     D   V   CGH +   CI +WL          + +  CP+C+
Sbjct: 33 CPECKSPGDDCPVVWGECGHAFHLHCISRWL----------KTRNTCPLCR 73

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	260
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	100.0
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.25
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.24
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.2
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.14
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.1
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	99.08
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.03
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.03
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.02
PHA02929	238	N1R/p28-like protein; Provisional	99.01
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.99
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.91
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.84
PHA02926	242	zinc finger-like protein; Provisional	98.79
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.77
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.76
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.73
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.72
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.7
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.62
PF14634	44	zf-RING_5: zinc-RING finger domain	98.6
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.56
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.53
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.42
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.4
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.4
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.28
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.27
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.17
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.03
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.99
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.93
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.79
COG5152	259	Uncharacterized conserved protein, contains RING a	97.77
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.7
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.67
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.6
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.59
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.59
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.52
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.43
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.41
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.36
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	97.27
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.21
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.14
KOG2660	331	consensus Locus-specific chromosome binding protei	97.12
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	97.11
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.11
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	97.09
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	97.0
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.97
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.96
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.96
KOG0825	1134	consensus PHD Zn-finger protein [General function	96.95
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.84
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.7
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.56
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.42
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.24
KOG4367	699	consensus Predicted Zn-finger protein [Function un	96.11
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.0
PF04641	260	Rtf2: Rtf2 RING-finger	95.85
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	95.59
KOG4739	233	consensus Uncharacterized protein involved in syna	95.54
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	95.44
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.37
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.04
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.66
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	94.58
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.51
COG5236	493	Uncharacterized conserved protein, contains RING Z	94.32
KOG3002	299	consensus Zn finger protein [General function pred	93.88
PHA03096	284	p28-like protein; Provisional	93.74
KOG4445	368	consensus Uncharacterized conserved protein, conta	93.64
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	93.53
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	93.42
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.16
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	92.92
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.8
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	92.49
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	92.42
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	91.83
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	91.68
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	91.61
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	91.55
PHA02825	162	LAP/PHD finger-like protein; Provisional	91.23
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	91.23
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	90.87
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	90.38
PHA02862	156	5L protein; Provisional	90.06
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	89.41
COG5109	396	Uncharacterized conserved protein, contains RING Z	89.11
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	88.44
COG5175	480	MOT2 Transcriptional repressor [Transcription]	87.93
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	87.85
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.5
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	86.93
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	82.68
KOG1940	276	consensus Zn-finger protein [General function pred	82.66
KOG3899	381	consensus Uncharacterized conserved protein [Funct	81.5

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=100.00  E-value=4.5e-50  Score=341.85  Aligned_cols=173  Identities=45%  Similarity=0.930  Sum_probs=139.3

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCcc-------ccccCcCCCCcccccccccccccccCCCC
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLD-------ADEQQQNCPVCKANISVASLVPLYGRGGI  108 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~-------~~~~~~~CPvCr~~v~~~~l~p~~~~~~~  108 (260)
                      +..+.++|+||++.+.+|++|+|||.|||.||.+|+...+.+.+       ..+.. .||+||..+...+++|+|+++..
T Consensus        14 ~~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~-~CPvCR~~Is~~~LvPiygrg~~   92 (193)
T PLN03208         14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPP-KCPVCKSDVSEATLVPIYGRGQK   92 (193)
T ss_pred             cCCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCC-cCCCCCCcCChhcEEEeeccCCC
Confidence            44567999999999999999999999999999999986433221       11234 89999999999999999999874


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCccccccccCCCCCCCCCCCCCCCCCCCCccccccCCCCccc
Q 024938          109 SSASDSKKPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMAT  188 (260)
Q Consensus       109 ~~~~~~~~~~~~~~ip~RP~~~~~~~~~~~~s~s~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  188 (260)
                      .       .+.+..+|+||.+++.+.         ++.++++.      ++   +++.|.                   +
T Consensus        93 ~-------~~~~~~iP~rp~~~~~~~---------~~~~~~~~------~~---~~~~~~-------------------~  128 (193)
T PLN03208         93 A-------PQSGSNVPSRPSGPVYDL---------RGVGQRLG------EG---ESQRYM-------------------Y  128 (193)
T ss_pred             C-------CCCCCCCCcCCCCCccCC---------CCcccccc------cc---ccceee-------------------e
Confidence            3       344566999998876552         22223331      11   111111                   1


Q ss_pred             hhcccccccccccceeecccCCCCCCCCCCCCCCCCCCCChhhHhHHhHHHHHhHHHHHHHHHHHHHHHhhC
Q 024938          189 ISFFNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF  260 (260)
Q Consensus       189 ~~~~~~~~g~f~~~v~~~~fg~~~~~~~~~~~~~~~~~~~pr~r~~~~~~~~~l~ri~~fl~~~~~lcll~f  260 (260)
                       ++++|++||||||||+||||++.+|+|+|||+      +||||||+||+|||||||+|||||||+||||||
T Consensus       129 -~~~~p~~g~~~~~~~~r~fg~~~~~~~~~~~~------~~r~r~~~~q~~~sl~r~~~f~~c~~~~~~~~f  193 (193)
T PLN03208        129 -RMPDPVMGVVCEMVYRRLFGESSSNMAPYRDM------NVRSRRRAMQAEESLSRVYLFLLCFMFMCLFLF  193 (193)
T ss_pred             -ccCCccccchhhhhhhhhhCCccccccccccC------chHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhC
Confidence             37889999999999999999999999999996      899999999999999999999999999999998

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

Probab=100.00  E-value=1.7e-37  Score=269.07  Aligned_cols=187  Identities=38%  Similarity=0.736  Sum_probs=137.9

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccCCCCCCCCCCC
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASDSK  115 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~~~~~~~~~~~  115 (260)
                      .....|+|+||||..+|||+|.|||+|||+||++|++.+.      ..+ .|||||+.|+.++++|+|++|....+.+++
T Consensus        43 ~~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~------~~~-~cPVCK~~Vs~~~vvPlYGrG~~~~~~~~~  115 (230)
T KOG0823|consen   43 RDGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRP------NSK-ECPVCKAEVSIDTVVPLYGRGSKKPSDPRK  115 (230)
T ss_pred             CCCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcC------CCe-eCCccccccccceEEeeeccCCCCCCCccc
Confidence            3567899999999999999999999999999999999876      335 899999999999999999999977666655


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCccccccccCCCCCCCCCCCCCCCCCCCCc-cccccCCCCccchhcccc
Q 024938          116 KPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHA-ALASSSLGGMATISFFNP  194 (260)
Q Consensus       116 ~~~~~~~ip~RP~~~~~~~~~~~~s~s~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~  194 (260)
                      +.     +|+||.++|.++.+.+...+..                 +..+++. ...+-++ ..-|.+.|....+   .+
T Consensus       116 ~~-----vP~RP~~~R~e~~~p~~~~~~~-----------------~g~r~~g-~~~~~~~~~~f~~s~~i~~~~---~~  169 (230)
T KOG0823|consen  116 KD-----VPPRPAGQRYESKRPTPQNRGN-----------------HGFRFFG-FRLGEESSNRFMYSFGIGLFG---DP  169 (230)
T ss_pred             cc-----CCCCCCCccccccCCCCccccc-----------------ccccccc-ccccccCCcceeEEeecccCC---Cc
Confidence            54     8999999998876555211110                 0111100 0000001 1112223322211   68


Q ss_pred             cccccccceeecccCCCCCCCCCCCCCCCCCCCChhhHhHHhHHHHHhHHHHHHHHHHHHHHHhhC
Q 024938          195 LMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF  260 (260)
Q Consensus       195 ~~g~f~~~v~~~~fg~~~~~~~~~~~~~~~~~~~pr~r~~~~~~~~~l~ri~~fl~~~~~lcll~f  260 (260)
                      |+|||++++++++||+.++.+ +  .++  +...+|.++++||.|++|+|+.+|++|++++||+++
T Consensus       170 v~~~~p~~~~~~lf~~~~~~~-~--~~~--~~~~~~~~~r~~q~e~~ls~~f~~~~~~~~~~l~~~  230 (230)
T KOG0823|consen  170 VMGLFPFGLYTRLFGTDETFP-A--DTP--RPSPARPLGRQMQRENSLSRVFLFLACFFVSWLLVI  230 (230)
T ss_pred             eeeeccccceeeecCCCCCcc-c--cCC--CCCCCccccccchhhcccccchhhhhhhheeeeeeC
Confidence            999999999999999998755 2  111  224578888889999999999999999999999875

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

Probab=99.25  E-value=3.4e-12  Score=84.07  Aligned_cols=42  Identities=38%  Similarity=0.941  Sum_probs=32.0

Q ss_pred             ccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           43 CNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        43 C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      |+||++.+.+||.++|||.||..||.+|.+...      ...+.||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~------~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPS------GSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSS------SST---SSS
T ss_pred             CCccchhhCCccccCCcCHHHHHHHHHHHHccC------CcCCCCcCC
Confidence            899999999999999999999999999997543      221489987

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

Probab=99.24  E-value=4.3e-12  Score=113.94  Aligned_cols=56  Identities=30%  Similarity=1.006  Sum_probs=49.4

Q ss_pred             CCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPL  102 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~  102 (260)
                      .+....|.+|++...+|.-|+|||+|||.||..|...+.          .||+||..+...+++-+
T Consensus       236 ~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~----------eCPlCR~~~~pskvi~L  291 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKA----------ECPLCREKFQPSKVICL  291 (293)
T ss_pred             CCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHcccc----------CCCcccccCCCcceeee
Confidence            445689999999999999999999999999999998764          89999999988776543

>smart00504 Ubox Modified RING finger domain

Probab=99.20  E-value=1.6e-11  Score=86.69  Aligned_cols=55  Identities=31%  Similarity=0.526  Sum_probs=49.2

Q ss_pred             cccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           40 FFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        40 ~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ++.|+||.+.+.+||+++|||.||..||.+|+..+         . .||+|+..+..++++++..
T Consensus         1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~---------~-~cP~~~~~~~~~~l~~~~~   55 (63)
T smart00504        1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLSH---------G-TDPVTGQPLTHEDLIPNLA   55 (63)
T ss_pred             CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHC---------C-CCCCCcCCCChhhceeCHH
Confidence            46899999999999999999999999999999863         4 8999999998888887753

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

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

Probab=99.14  E-value=2.2e-11  Score=102.49  Aligned_cols=59  Identities=36%  Similarity=0.863  Sum_probs=50.5

Q ss_pred             CCCCcccccccccCCCC--cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQD--PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~--Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .-++.+.|||||+.+.+  |+.|.|||+||..||+..++..         . .||+|++.|..+.+.++|.
T Consensus       127 ~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~---------~-~CP~C~kkIt~k~~~rI~L  187 (187)
T KOG0320|consen  127 RKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT---------N-KCPTCRKKITHKQFHRIYL  187 (187)
T ss_pred             ccccccCCCceecchhhccccccccchhHHHHHHHHHHHhC---------C-CCCCcccccchhhheeccC
Confidence            34567999999999876  5669999999999999999876         4 9999999999988888763

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

Probab=99.10  E-value=4.3e-11  Score=77.29  Aligned_cols=38  Identities=58%  Similarity=1.290  Sum_probs=32.8

Q ss_pred             ccccccCCCCc-EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           43 CNICLDSAQDP-VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        43 C~ICld~~~~P-vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      |+||++.+.+| ++++|||.||+.||.+|++.+         . .||+|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~---------~-~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKN---------P-KCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCT---------S-B-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHCc---------C-CCcCC
Confidence            89999999999 579999999999999999863         4 99988

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

Probab=99.08  E-value=4.5e-11  Score=114.54  Aligned_cols=81  Identities=27%  Similarity=0.713  Sum_probs=65.2

Q ss_pred             chhHhhhcCCCCCCCCCCCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           17 DASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        17 ~~~~~~~wk~~~~~~~~~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +.+....|+.+.......     ...||||++...-|+.|.|||+||++||..++...    .....+ .||+|+..|..
T Consensus       168 dpD~p~~~e~i~qv~~~t-----~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s----~~~~~~-~CPiC~s~I~~  237 (513)
T KOG2164|consen  168 DPDAPVDWEDIFQVYGST-----DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYS----AIKGPC-SCPICRSTITL  237 (513)
T ss_pred             CCccccchHHhhhhhcCc-----CCcCCcccCCCCcccccccCceeeHHHHHHHHhhh----cccCCc-cCCchhhhccc
Confidence            455566676666554322     78999999999999999999999999999988754    123345 99999999999


Q ss_pred             ccccccccCCC
Q 024938           97 ASLVPLYGRGG  107 (260)
Q Consensus        97 ~~l~p~~~~~~  107 (260)
                      +++.+.+.+.+
T Consensus       238 kdl~pv~~e~~  248 (513)
T KOG2164|consen  238 KDLLPVFIEDD  248 (513)
T ss_pred             cceeeeeeccc
Confidence            99999998876

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.03  E-value=1.2e-10  Score=110.38  Aligned_cols=71  Identities=31%  Similarity=0.649  Sum_probs=56.3

Q ss_pred             hhhcCCCCCCCCCCCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           21 KQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        21 ~~~wk~~~~~~~~~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      .-.|.......  .+.++..+.|+||++.+.+|++++|||.||..||..|+...         . .||+|+..+....+.
T Consensus         9 ~tDw~~t~~~~--l~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~---------~-~CP~Cr~~~~~~~Lr   76 (397)
T TIGR00599         9 SSDWLTTPIPS--LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQ---------P-KCPLCRAEDQESKLR   76 (397)
T ss_pred             chhhccCCccc--ccccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCC---------C-CCCCCCCccccccCc
Confidence            34565554322  35677889999999999999999999999999999999754         3 899999998765555


Q ss_pred             ccc
Q 024938          101 PLY  103 (260)
Q Consensus       101 p~~  103 (260)
                      .++
T Consensus        77 ~N~   79 (397)
T TIGR00599        77 SNW   79 (397)
T ss_pred             cch
Confidence            444

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

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

Probab=99.03  E-value=9e-11  Score=77.63  Aligned_cols=40  Identities=43%  Similarity=1.096  Sum_probs=34.1

Q ss_pred             cccccccCCC---CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcc
Q 024938           42 ECNICLDSAQ---DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK   91 (260)
Q Consensus        42 ~C~ICld~~~---~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr   91 (260)
                      +|+||++.+.   ..+.++|||.||..||.+|++.+         . +||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~---------~-~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN---------N-SCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS---------S-B-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC---------C-cCCccC
Confidence            6999999984   45678999999999999999865         4 999997

...

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

Probab=99.02  E-value=1.7e-10  Score=78.39  Aligned_cols=47  Identities=36%  Similarity=0.916  Sum_probs=40.1

Q ss_pred             CcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ++..|.||++...+.+.++|||. ||..|+.+|++..         + .||+||+++.
T Consensus         1 ~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~---------~-~CP~Cr~~i~   48 (50)
T PF13920_consen    1 EDEECPICFENPRDVVLLPCGHLCFCEECAERLLKRK---------K-KCPICRQPIE   48 (50)
T ss_dssp             -HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTT---------S-BBTTTTBB-S
T ss_pred             CcCCCccCCccCCceEEeCCCChHHHHHHhHHhcccC---------C-CCCcCChhhc
Confidence            35789999999999999999999 9999999999844         4 9999999875

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.01  E-value=2.2e-10  Score=101.90  Aligned_cols=50  Identities=30%  Similarity=0.858  Sum_probs=41.4

Q ss_pred             CCCCcccccccccCCCCc--------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           36 KDGSFFECNICLDSAQDP--------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~P--------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....+.+|+||++.+.++        ++++|+|.||..||.+|+..+         . +||+||..+.
T Consensus       170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~---------~-tCPlCR~~~~  227 (238)
T PHA02929        170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK---------N-TCPVCRTPFI  227 (238)
T ss_pred             cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcC---------C-CCCCCCCEee
Confidence            345578999999987653        556899999999999999865         3 9999999875

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

Probab=98.99  E-value=2.2e-10  Score=84.04  Aligned_cols=58  Identities=28%  Similarity=0.472  Sum_probs=46.5

Q ss_pred             CCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .+.|.|+|+.+.+.+||+++|||+|+..||.+|+....        . .||+|+..+...+++++..
T Consensus         2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~--------~-~~P~t~~~l~~~~l~pn~~   59 (73)
T PF04564_consen    2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNG--------G-TDPFTRQPLSESDLIPNRA   59 (73)
T ss_dssp             SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTS--------S-B-TTT-SB-SGGGSEE-HH
T ss_pred             CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCC--------C-CCCCCCCcCCcccceECHH
Confidence            36799999999999999999999999999999999632        5 9999999999999988764

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 ....

>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=98.91  E-value=9.6e-10  Score=71.35  Aligned_cols=40  Identities=45%  Similarity=1.214  Sum_probs=35.4

Q ss_pred             ccccccCCCCcE-EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           43 CNICLDSAQDPV-VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        43 C~ICld~~~~Pv-vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      |+||++.+.+++ +++|||.||..||.+|++...       .. .||+|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~-------~~-~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSG-------SV-KCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTS-------SS-BTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHhcC-------Cc-cCCcC
Confidence            899999999999 899999999999999999532       24 89988

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

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

Probab=98.84  E-value=2.9e-09  Score=68.93  Aligned_cols=44  Identities=50%  Similarity=1.284  Sum_probs=36.9

Q ss_pred             cccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           42 ECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        42 ~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      +|+||++.+.+++.+. |||.||..|+.+|+....        . .||+|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~--------~-~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGK--------N-TCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCc--------C-CCCCCCCcC
Confidence            5999999998777665 999999999999998622        4 899998753

>PHA02926 zinc finger-like protein; Provisional

Probab=98.79  E-value=3.3e-09  Score=92.55  Aligned_cols=57  Identities=25%  Similarity=0.764  Sum_probs=43.3

Q ss_pred             CCCCcccccccccCCCC---------cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           36 KDGSFFECNICLDSAQD---------PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~---------Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..+.+.+|+||+|...+         ++..+|+|.||..||.+|.+.+.   +.+..+ .||+||..+..
T Consensus       166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~---~~~~~r-sCPiCR~~f~~  231 (242)
T PHA02926        166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR---ETGASD-NCPICRTRFRN  231 (242)
T ss_pred             hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc---ccCcCC-cCCCCcceeee
Confidence            45567899999998643         35568999999999999998542   122335 89999998763

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

Probab=98.77  E-value=3e-09  Score=94.74  Aligned_cols=53  Identities=30%  Similarity=0.879  Sum_probs=46.3

Q ss_pred             CCcccccccccCCCCcEEccCCCccCHHHHHH-hhhhhcCCccccccCcCCCCcccccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYK-WLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~-wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      ..++.|.||++....|..++|||+|||.||.. |-..+.        . .||+||+.+..+++
T Consensus       213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~--------~-~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKY--------E-FCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCCcccccccchhhHHHHHHHHHhhcc--------c-cCchhhhhccchhh
Confidence            45789999999999999999999999999999 887653        2 59999999887665

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

Probab=98.76  E-value=4.3e-09  Score=69.58  Aligned_cols=31  Identities=35%  Similarity=0.903  Sum_probs=21.8

Q ss_pred             ccccccCCCC----cEEccCCCccCHHHHHHhhhhh
Q 024938           43 CNICLDSAQD----PVVTLCGHLYCWPCIYKWLHVQ   74 (260)
Q Consensus        43 C~ICld~~~~----Pvvt~CGH~fC~~Ci~~wl~~~   74 (260)
                      |+||.+ +.+    |++|+|||+||..||.++++..
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC
Confidence            899999 777    9999999999999999999854

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

Probab=98.73  E-value=2.2e-08  Score=93.16  Aligned_cols=47  Identities=34%  Similarity=0.786  Sum_probs=39.9

Q ss_pred             ccccccccCCCCc---EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           41 FECNICLDSAQDP---VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        41 ~~C~ICld~~~~P---vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..|.||+|.+.+.   ++|+|.|.||..||..||...         +..||+||..+..
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---------r~~CPvCK~di~~  279 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---------RTFCPVCKRDIRT  279 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---------CccCCCCCCcCCC
Confidence            7999999999864   568999999999999999864         3269999997643

>smart00184 RING Ring finger

Probab=98.72  E-value=1.1e-08  Score=63.86  Aligned_cols=39  Identities=51%  Similarity=1.334  Sum_probs=34.3

Q ss_pred             ccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           43 CNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        43 C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      |+||++...++++++|||.||..|+.+|++..        .. .||+|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~--------~~-~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSG--------NN-TCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhC--------cC-CCCCC
Confidence            89999999999999999999999999999832        24 79987

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)

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

Probab=98.70  E-value=2.8e-09  Score=97.74  Aligned_cols=59  Identities=27%  Similarity=0.654  Sum_probs=52.1

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .+...+.|-||.++|..|++++|+|.||.-||..+|..+         + .||.|+..+.+..++.++.
T Consensus        19 ~lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~---------p-~CP~C~~~~~Es~Lr~n~i   77 (442)
T KOG0287|consen   19 TLDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYK---------P-QCPTCCVTVTESDLRNNRI   77 (442)
T ss_pred             hhHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccC---------C-CCCceecccchhhhhhhhH
Confidence            456778999999999999999999999999999999976         4 9999999998877766553

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

Probab=98.62  E-value=4.5e-08  Score=90.90  Aligned_cols=53  Identities=32%  Similarity=0.786  Sum_probs=43.4

Q ss_pred             CCCCCcccccccccCC-CC------------cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           35 EKDGSFFECNICLDSA-QD------------PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~-~~------------Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      .-.+++-.|.||+|.+ +.            |..++|||.++..|++.|++.+         . +||+||.++.-+
T Consensus       282 ql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq---------Q-TCPICr~p~ifd  347 (491)
T COG5243         282 QLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ---------Q-TCPICRRPVIFD  347 (491)
T ss_pred             hhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc---------c-CCCcccCccccc
Confidence            3456788999999984 32            4788999999999999999976         3 999999996433

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.60  E-value=2.7e-08  Score=65.88  Aligned_cols=41  Identities=37%  Similarity=1.027  Sum_probs=33.9

Q ss_pred             cccccccCC---CCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccc
Q 024938           42 ECNICLDSA---QDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA   92 (260)
Q Consensus        42 ~C~ICld~~---~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~   92 (260)
                      .|+||.+.+   ..+++|.|||+||..|+.++...         .. .||+|++
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~---------~~-~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGK---------SV-KCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCC---------CC-CCcCCCC
Confidence            499999998   35788999999999999998821         24 9999974

>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=98.56  E-value=4.5e-08  Score=71.87  Aligned_cols=40  Identities=40%  Similarity=1.176  Sum_probs=32.2

Q ss_pred             cccccccCCCCc-------------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcc
Q 024938           42 ECNICLDSAQDP-------------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK   91 (260)
Q Consensus        42 ~C~ICld~~~~P-------------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr   91 (260)
                      .|.||++.+.++             +...|||.|+..||.+|++.+         . +||+||
T Consensus        21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~---------~-~CP~CR   73 (73)
T PF12678_consen   21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN---------N-TCPLCR   73 (73)
T ss_dssp             BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS---------S-B-TTSS
T ss_pred             cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC---------C-cCCCCC
Confidence            499999999432             334799999999999999865         3 999997

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 ....

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

Probab=98.53  E-value=2.8e-08  Score=89.63  Aligned_cols=55  Identities=35%  Similarity=0.681  Sum_probs=47.3

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      .+..-+.|-||.+.+..|+.|+|||.||.-||.+.|..+         + -||+||.+..+..+.
T Consensus        21 ~LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~q---------p-~CP~Cr~~~~esrlr   75 (391)
T COG5432          21 GLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQ---------P-FCPVCREDPCESRLR   75 (391)
T ss_pred             cchhHHHhhhhhheeecceecccccchhHHHHHHHhcCC---------C-CCccccccHHhhhcc
Confidence            345568999999999999999999999999999999876         4 999999987654443

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

Probab=98.42  E-value=6.9e-08  Score=84.88  Aligned_cols=47  Identities=34%  Similarity=0.849  Sum_probs=41.5

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK   91 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr   91 (260)
                      ....+.+.|+||++.+.+|++++|||.||..||..++. .         ...||.||
T Consensus         8 ~~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~-~---------~~~Cp~cr   54 (386)
T KOG2177|consen    8 EVLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWE-G---------PLSCPVCR   54 (386)
T ss_pred             hhccccccChhhHHHhhcCccccccchHhHHHHHHhcC-C---------CcCCcccC
Confidence            35567899999999999998899999999999999987 2         23999999

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

Probab=98.40  E-value=6.3e-08  Score=96.92  Aligned_cols=59  Identities=24%  Similarity=0.693  Sum_probs=53.7

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      .+.+-+.|++|.+.+.+.|++.|||.||..|+.+.+....        + +||.|...+...++.++|
T Consensus       639 ~yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRq--------R-KCP~Cn~aFganDv~~I~  697 (698)
T KOG0978|consen  639 EYKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQ--------R-KCPKCNAAFGANDVHRIH  697 (698)
T ss_pred             HHHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhc--------C-CCCCCCCCCCcccccccC
Confidence            5667899999999999999999999999999999998753        6 999999999999998876

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

Probab=98.40  E-value=8.5e-08  Score=68.25  Aligned_cols=54  Identities=28%  Similarity=0.750  Sum_probs=28.5

Q ss_pred             CCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           38 GSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      ++.+.|++|.+.+.+||. ..|.|.||+.||..-+.           . .||+|..+....+++.|.
T Consensus         5 e~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~-----------~-~CPvC~~Paw~qD~~~Nr   59 (65)
T PF14835_consen    5 EELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG-----------S-ECPVCHTPAWIQDIQINR   59 (65)
T ss_dssp             HHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT-----------T-B-SSS--B-S-SS----H
T ss_pred             HHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC-----------C-CCCCcCChHHHHHHHhhh
Confidence            356789999999999985 68999999999977554           3 799999988777766543

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

Probab=98.28  E-value=4e-07  Score=90.17  Aligned_cols=51  Identities=29%  Similarity=0.667  Sum_probs=44.0

Q ss_pred             CCCcccccccccCCCC-----cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           37 DGSFFECNICLDSAQD-----PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~-----Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ......|.||.|.+..     |..++|||.||..|+++|++.++          .||.||..+...
T Consensus       288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~q----------tCP~CR~~~~~~  343 (543)
T KOG0802|consen  288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQ----------TCPTCRTVLYDY  343 (543)
T ss_pred             hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhC----------cCCcchhhhhcc
Confidence            3457899999999988     78999999999999999999864          999999955433

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

Probab=98.27  E-value=4.9e-07  Score=82.13  Aligned_cols=48  Identities=33%  Similarity=0.743  Sum_probs=39.5

Q ss_pred             CcccccccccCCCC---cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQD---PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~---Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ...+|.||++.+..   =++|+|.|.|+..|+.+|+..-+        . +||+||.++.
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~--------~-~CPvCrt~iP  372 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYS--------N-KCPVCRTAIP  372 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhc--------c-cCCccCCCCC
Confidence            34899999998864   36799999999999999998332        3 9999998764

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

Probab=98.17  E-value=1.7e-06  Score=65.10  Aligned_cols=50  Identities=34%  Similarity=0.755  Sum_probs=35.9

Q ss_pred             cccccccccCCC-----------C-cEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           40 FFECNICLDSAQ-----------D-PVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        40 ~~~C~ICld~~~-----------~-Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +..|.||...+.           + |++. .|+|.|+..||.+|+..++      ... .||+||+....
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~------~~~-~CPmCR~~w~~   83 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS------SKG-QCPMCRQPWKF   83 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc------CCC-CCCCcCCeeee
Confidence            445666665553           2 4443 6999999999999999753      235 99999998653

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.03  E-value=3.8e-06  Score=77.26  Aligned_cols=52  Identities=23%  Similarity=0.598  Sum_probs=38.5

Q ss_pred             cccccccccC-CCCcE----EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           40 FFECNICLDS-AQDPV----VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        40 ~~~C~ICld~-~~~Pv----vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      +..||||... ...|.    +..|||.||..|+.+.+...+        . .||+|+..+...++.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~--------~-~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGS--------G-SCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCC--------C-CCCCCCCccchhhcc
Confidence            4689999974 34442    226999999999999765332        4 899999988766543

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).

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

Probab=97.99  E-value=3.1e-06  Score=80.59  Aligned_cols=50  Identities=36%  Similarity=0.870  Sum_probs=44.3

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....+|.|.||...+..||+++|||.||..||.+-+...         . .||.||..+.
T Consensus        80 ~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~---------~-~cp~Cr~~l~  129 (398)
T KOG4159|consen   80 EIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQE---------T-ECPLCRDELV  129 (398)
T ss_pred             cccchhhhhhhHhhcCCCccccccccccHHHHHHHhccC---------C-CCcccccccc
Confidence            346789999999999999999999999999999977643         4 9999999986

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

Probab=97.97  E-value=2.9e-06  Score=77.14  Aligned_cols=49  Identities=31%  Similarity=0.675  Sum_probs=42.7

Q ss_pred             cccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           40 FFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        40 ~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      .-+|.||+....-||.+.|+|.||+-||+.-...+.        + .|++||.+|..+
T Consensus         7 ~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk--------~-~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDK--------K-TCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCcCccccccchhhhhhhcchhhcCC--------C-CCceecCCCCcc
Confidence            458999999999999999999999999998777653        4 899999999643

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

Probab=97.93  E-value=5.8e-06  Score=77.73  Aligned_cols=57  Identities=33%  Similarity=0.800  Sum_probs=47.2

Q ss_pred             CcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           39 SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      -...|.||.|.-++-.+-+|||+.|..|+..|.+.+       ++. .||.||.+|+-++.+.++
T Consensus       368 TFeLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd-------~gq-~CPFCRcEIKGte~viid  424 (563)
T KOG1785|consen  368 TFELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSD-------EGQ-TCPFCRCEIKGTEPVIID  424 (563)
T ss_pred             hHHHHHHhhccCCCcccccccchHHHHHHHhhcccC-------CCC-CCCceeeEeccccceeee
Confidence            345899999999998888999999999999999755       235 999999999876655443

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

Probab=97.79  E-value=1.8e-06  Score=79.85  Aligned_cols=51  Identities=29%  Similarity=0.704  Sum_probs=43.5

Q ss_pred             CCCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .+...+.|+|||+.+...+.+ .|+|-||..||..-+....        . .||.||+.+.
T Consensus        39 ~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn--------~-ecptcRk~l~   90 (381)
T KOG0311|consen   39 MFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGN--------N-ECPTCRKKLV   90 (381)
T ss_pred             HhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcC--------C-CCchHHhhcc
Confidence            566789999999999988776 4999999999988777653        6 9999999874

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

Probab=97.77  E-value=9.6e-06  Score=69.87  Aligned_cols=47  Identities=34%  Similarity=0.729  Sum_probs=40.4

Q ss_pred             CCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      .-.|.|-||...+..||++.|||.||..|..+-.+..         . .|-+|.+..
T Consensus       194 ~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg---------~-~C~~Cgk~t  240 (259)
T COG5152         194 KIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKG---------D-ECGVCGKAT  240 (259)
T ss_pred             CCceeehhchhhccchhhhhcchhHHHHHHHHHhccC---------C-cceecchhh
Confidence            3468999999999999999999999999998877643         4 899997765

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

Probab=97.70  E-value=4.6e-05  Score=68.60  Aligned_cols=68  Identities=26%  Similarity=0.580  Sum_probs=48.9

Q ss_pred             HhhhcCCCCCCC--CCCCCCCCcccccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           20 LKQKWSPTSAPT--NVPEKDGSFFECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        20 ~~~~wk~~~~~~--~~~~~~~~~~~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      +.++|+.....+  ..........+|++|.+....|.+.. |||.||+.||..-...+-        -+.||.|...+.
T Consensus       217 ~l~sw~~~l~~ap~~sss~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~a--------sf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  217 VLKSWKLDLDRAPKFSSSTGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDA--------SFTCPLCGENVE  287 (298)
T ss_pred             HHHhhcccccCCCCcccccccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchh--------hcccCccCCCCc
Confidence            356776663332  12234557789999999999998765 999999999987665331        239999977664

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

Probab=97.67  E-value=1.7e-05  Score=57.74  Aligned_cols=56  Identities=30%  Similarity=0.622  Sum_probs=27.1

Q ss_pred             cccccccccCCC-C---cEEc----cCCCccCHHHHHHhhhhhcCCcccc--ccCcCCCCccccccc
Q 024938           40 FFECNICLDSAQ-D---PVVT----LCGHLYCWPCIYKWLHVQTSSLDAD--EQQQNCPVCKANISV   96 (260)
Q Consensus        40 ~~~C~ICld~~~-~---Pvvt----~CGH~fC~~Ci~~wl~~~~~s~~~~--~~~~~CPvCr~~v~~   96 (260)
                      +.+|.||..... +   |++.    .|+..|+..||++|+.....+...-  -.. +||.|+.+|+-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G-~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFG-ECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EE-E-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeeccccc-CCcCCCCeeeE
Confidence            568999998765 2   3322    5999999999999998654332111  123 79999998864

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

Probab=97.61  E-value=6.3e-05  Score=69.98  Aligned_cols=49  Identities=39%  Similarity=0.734  Sum_probs=40.9

Q ss_pred             CCcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +...+|-||++..++-+++||-|+ .|..|.+...-.+         . .||+||..+..
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~---------n-~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQT---------N-NCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhh---------c-CCCccccchHh
Confidence            346799999999999999999997 6999997755333         4 89999999853

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

Probab=97.60  E-value=3.8e-05  Score=53.81  Aligned_cols=45  Identities=29%  Similarity=0.636  Sum_probs=31.1

Q ss_pred             CCCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCC
Q 024938           37 DGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV   89 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPv   89 (260)
                      ..-.+.|||.+..+.+||. ..|||.|....|..|+...       ... .||+
T Consensus         8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~-------~~~-~CPv   53 (57)
T PF11789_consen    8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRN-------GSK-RCPV   53 (57)
T ss_dssp             SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTT-------S-E-E-SC
T ss_pred             cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhc-------CCC-CCCC
Confidence            3456899999999999988 5899999999999999433       224 9998

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

Probab=97.59  E-value=1.3e-05  Score=55.30  Aligned_cols=46  Identities=35%  Similarity=0.898  Sum_probs=39.3

Q ss_pred             ccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           41 FECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        41 ~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .+|-||.|...+.|.-.|||. .|+.|-.+.++..        +. .||+||+++.
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~--------~g-~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKAL--------HG-CCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHcc--------CC-cCcchhhHHH
Confidence            689999999999999999996 6999988876632        25 9999999885

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

Probab=97.59  E-value=2.8e-05  Score=73.33  Aligned_cols=59  Identities=37%  Similarity=0.764  Sum_probs=47.5

Q ss_pred             CcccccccccCCCCc-----EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccC
Q 024938           39 SFFECNICLDSAQDP-----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGR  105 (260)
Q Consensus        39 ~~~~C~ICld~~~~P-----vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~  105 (260)
                      ....||||+|...-+     +.+.|||.|-..||.+|+....        +..||.|+.......+.+.|..
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~--------~~~cp~c~~katkr~i~~e~al   66 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKT--------KMQCPLCSGKATKRQIRPEYAL   66 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhh--------hhhCcccCChhHHHHHHHHHHH
Confidence            346899999998765     4568999999999999997332        3399999998888888777653

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

Probab=97.52  E-value=4.3e-05  Score=72.95  Aligned_cols=55  Identities=36%  Similarity=0.834  Sum_probs=47.3

Q ss_pred             CCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP  101 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p  101 (260)
                      .++.+.|+||...+.+|+.+ .|||.||..|+..|+..+         . .||+|+..+.....++
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~---------~-~cp~~~~~~~~~~~~~   73 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNH---------Q-KCPVCRQELTQAEELP   73 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccC---------c-CCcccccccchhhccC
Confidence            56789999999999999994 999999999999999864         4 9999988876655544

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

Probab=97.43  E-value=7.2e-05  Score=71.36  Aligned_cols=47  Identities=30%  Similarity=0.798  Sum_probs=39.5

Q ss_pred             CCCcccccccccCCCCcE----EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           37 DGSFFECNICLDSAQDPV----VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pv----vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ..+.-.|||||+.+.+-+    .+.|.|.|+..|+.+|...            .||+||....
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~------------scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS------------SCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhcccC------------cChhhhhhcC
Confidence            445679999999998754    3579999999999999973            8999998765

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

Probab=97.41  E-value=6.7e-05  Score=72.92  Aligned_cols=58  Identities=28%  Similarity=0.742  Sum_probs=48.1

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ....+...|.+|.|...+++++.|.|.||..||.+++..-.    ..... +||+|-..++.+
T Consensus       531 ~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~----~~~nv-tCP~C~i~LsiD  588 (791)
T KOG1002|consen  531 DENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFM----ENNNV-TCPVCHIGLSID  588 (791)
T ss_pred             ccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhh----cccCC-CCcccccccccc
Confidence            34557789999999999999999999999999999998654    22334 999998887755

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

Probab=97.36  E-value=0.00017  Score=48.86  Aligned_cols=42  Identities=31%  Similarity=0.875  Sum_probs=33.5

Q ss_pred             ccccccc--CCCCcEEccCC-----CccCHHHHHHhhhhhcCCccccccCcCCCCcc
Q 024938           42 ECNICLD--SAQDPVVTLCG-----HLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK   91 (260)
Q Consensus        42 ~C~ICld--~~~~Pvvt~CG-----H~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr   91 (260)
                      .|-||++  ...++.+.+|.     |.++..|+.+|+..+.       .. .||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~-------~~-~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG-------NK-TCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC-------CC-cCCCCC
Confidence            4889997  44567888985     7899999999998763       24 899995

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

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

Probab=97.34  E-value=8.7e-05  Score=71.56  Aligned_cols=50  Identities=24%  Similarity=0.713  Sum_probs=39.0

Q ss_pred             CCCcccccccccCCCC-----------------cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           37 DGSFFECNICLDSAQD-----------------PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~-----------------Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .+...+|+||+....-                 =++++|.|+|+..|+.+|.+.-         +..||+||..+.
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y---------kl~CPvCR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY---------KLICPVCRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh---------cccCCccCCCCC
Confidence            4456799999977631                 1356999999999999999843         349999998764

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

Probab=97.34  E-value=8e-05  Score=67.71  Aligned_cols=47  Identities=36%  Similarity=0.714  Sum_probs=40.4

Q ss_pred             CcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      -.|.|-||...+.+||++.|||.||-.|..+-++..         . .|.+|.+.+.
T Consensus       240 ~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~---------~-~c~vC~~~t~  286 (313)
T KOG1813|consen  240 LPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKG---------E-KCYVCSQQTH  286 (313)
T ss_pred             CCccccccccccccchhhcCCceeehhhhccccccC---------C-cceecccccc
Confidence            457899999999999999999999999988777643         3 8999987764

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

Probab=97.27  E-value=8.3e-05  Score=66.88  Aligned_cols=59  Identities=27%  Similarity=0.537  Sum_probs=45.0

Q ss_pred             CCCCcccccccccCCCCcE----------EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPV----------VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPL  102 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pv----------vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~  102 (260)
                      +..++..|.||-..+..-+          .+.|+|.|+-.||..|.-..+        +.+||.||..+..+.+..+
T Consensus       220 khl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGK--------kqtCPYCKekVdl~rmfsn  288 (328)
T KOG1734|consen  220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGK--------KQTCPYCKEKVDLKRMFSN  288 (328)
T ss_pred             CCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecC--------CCCCchHHHHhhHhhhccC
Confidence            3446679999997765332          468999999999999998764        5599999998875554443

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

Probab=97.21  E-value=6.1e-05  Score=68.65  Aligned_cols=54  Identities=30%  Similarity=0.691  Sum_probs=42.0

Q ss_pred             ccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccc-ccccccccccc
Q 024938           41 FECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA-NISVASLVPLY  103 (260)
Q Consensus        41 ~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~-~v~~~~l~p~~  103 (260)
                      +.|+.|..++.+|+.| .|+|.||..||..-|-..         .+.||.|.. .+..+.+.|.+
T Consensus       275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~ds---------Df~CpnC~rkdvlld~l~pD~  330 (427)
T COG5222         275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDS---------DFKCPNCSRKDVLLDGLTPDI  330 (427)
T ss_pred             ccCcchhhhhhCcccCccccchHHHHHHhhhhhhc---------cccCCCcccccchhhccCccH
Confidence            8999999999999999 599999999998777633         349999954 34444444443

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

Probab=97.14  E-value=0.00025  Score=66.42  Aligned_cols=55  Identities=29%  Similarity=0.792  Sum_probs=42.0

Q ss_pred             CCcccccccccCCCCcE-----E---ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           38 GSFFECNICLDSAQDPV-----V---TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pv-----v---t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ..+..|.||++...+..     .   ..|.|.||..||..|-.....  +..-.+ .||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~--~~~~sk-sCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF--ESKTSK-SCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc--cccccc-CCCcccCccc
Confidence            45789999999988765     2   469999999999999965431  111235 9999998765

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

Probab=97.12  E-value=0.00013  Score=67.18  Aligned_cols=53  Identities=28%  Similarity=0.634  Sum_probs=44.9

Q ss_pred             CCCCCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ........|.+|..++.|+.. +.|-|+||..||.+++...         + .||.|...+...
T Consensus        10 ~~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~---------~-~CP~C~i~ih~t   63 (331)
T KOG2660|consen   10 TELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEES---------K-YCPTCDIVIHKT   63 (331)
T ss_pred             hhcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHh---------c-cCCccceeccCc
Confidence            345678899999999999864 6799999999999999864         5 999999887643

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

Probab=97.11  E-value=0.00038  Score=51.66  Aligned_cols=30  Identities=30%  Similarity=0.872  Sum_probs=26.3

Q ss_pred             cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           57 LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        57 ~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .|.|.|+..||++||..+.          .||++++....
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~----------~CPld~q~w~~   82 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKG----------VCPLDRQTWVL   82 (88)
T ss_pred             ecchHHHHHHHHHHHhhCC----------CCCCCCceeEE
Confidence            5999999999999999864          99999987653

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

Probab=97.11  E-value=0.00013  Score=74.86  Aligned_cols=52  Identities=33%  Similarity=0.846  Sum_probs=40.5

Q ss_pred             CCCCcccccccccCCC--C---c--EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           36 KDGSFFECNICLDSAQ--D---P--VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~--~---P--vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ..++..+|+||...+.  +   |  +--.|.|-|+..|+++|++...       .. .||+||.++.
T Consensus      1465 ~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~-------~s-~CPlCRseit 1523 (1525)
T COG5219        1465 KFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA-------RS-NCPLCRSEIT 1523 (1525)
T ss_pred             hcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC-------CC-CCCccccccc
Confidence            5677889999998765  2   2  2235999999999999999764       23 9999997764

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

Probab=97.09  E-value=0.00011  Score=54.08  Aligned_cols=32  Identities=38%  Similarity=0.912  Sum_probs=26.9

Q ss_pred             cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           57 LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        57 ~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .|.|.|+..||.+|+..++      .+. .||+||+...
T Consensus        50 ~C~h~fh~hCI~~wl~~~t------sq~-~CPmcRq~~~   81 (84)
T KOG1493|consen   50 YCLHAFHAHCILKWLNTPT------SQG-QCPMCRQTWQ   81 (84)
T ss_pred             HHHHHHHHHHHHHHhcCcc------ccc-cCCcchheeE
Confidence            4999999999999999764      235 9999998764

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

Probab=97.00  E-value=0.00083  Score=56.12  Aligned_cols=63  Identities=21%  Similarity=0.572  Sum_probs=43.3

Q ss_pred             CcccccccccCCCCcEEccCC------------Ccc-CHHHHHHhhhhhcCCccc---------------------cccC
Q 024938           39 SFFECNICLDSAQDPVVTLCG------------HLY-CWPCIYKWLHVQTSSLDA---------------------DEQQ   84 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CG------------H~f-C~~Ci~~wl~~~~~s~~~---------------------~~~~   84 (260)
                      ++..||||+|..++.|.|.|.            ..| +..|+.++.+........                     ....
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE   80 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence            356899999999999998643            322 577888877643222111                     1224


Q ss_pred             cCCCCcccccccccccc
Q 024938           85 QNCPVCKANISVASLVP  101 (260)
Q Consensus        85 ~~CPvCr~~v~~~~l~p  101 (260)
                      +.||+||..|..+.++.
T Consensus        81 L~CPLCRG~V~GWtvve   97 (162)
T PF07800_consen   81 LACPLCRGEVKGWTVVE   97 (162)
T ss_pred             ccCccccCceeceEEch
Confidence            69999999998776653

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

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.97  E-value=0.00072  Score=60.25  Aligned_cols=62  Identities=18%  Similarity=0.290  Sum_probs=51.9

Q ss_pred             CcccccccccCCCCc----EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccCCCCCC
Q 024938           39 SFFECNICLDSAQDP----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISS  110 (260)
Q Consensus        39 ~~~~C~ICld~~~~P----vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~~~~~~  110 (260)
                      ..+.||||.+.+.+.    +.-+|||.+|..|+.+.+..+.          .||+|..++..++++.+-..|..-.
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~----------v~pv~d~plkdrdiI~LqrGGTGfa  285 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDM----------VDPVTDKPLKDRDIIGLQRGGTGFA  285 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccc----------cccCCCCcCcccceEeeeccccccc
Confidence            578999999999874    3347999999999999998764          9999999999999998866555443

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

Probab=96.96  E-value=0.00016  Score=65.64  Aligned_cols=42  Identities=36%  Similarity=0.851  Sum_probs=35.7

Q ss_pred             cccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           40 FFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        40 ~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ...|.||+|...|.+.|.|||. -|..|-++.             . .||+||+-+.
T Consensus       300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm-------------~-eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKRM-------------N-ECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcceEEeecCcEEeehhhcccc-------------c-cCchHHHHHH
Confidence            6799999999999999999994 699996542             2 8999998764

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

Probab=96.96  E-value=0.00066  Score=63.30  Aligned_cols=51  Identities=27%  Similarity=0.570  Sum_probs=44.9

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ...++..|+||.-.....|.++|+|.-|..||.+.+.+.         + .|-.||..+..
T Consensus       418 p~sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~---------k-~CFfCktTv~~  468 (489)
T KOG4692|consen  418 PDSEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNC---------K-RCFFCKTTVID  468 (489)
T ss_pred             CCcccccCcceecccchhhccCCCCchHHHHHHHHHhcC---------C-eeeEecceeee
Confidence            346788999999999999999999999999999999865         4 89999988764

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

Probab=96.95  E-value=0.00025  Score=71.71  Aligned_cols=72  Identities=18%  Similarity=0.388  Sum_probs=51.3

Q ss_pred             hhHhhhcCCCCCCCCCCC----CCCCcccccccccCCCCcEE---ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           18 ASLKQKWSPTSAPTNVPE----KDGSFFECNICLDSAQDPVV---TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        18 ~~~~~~wk~~~~~~~~~~----~~~~~~~C~ICld~~~~Pvv---t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      .....+|+..+...+...    .-.....|++|+..+.+..+   ..|+|.||..||..|-....          +||+|
T Consensus        97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aq----------TCPiD  166 (1134)
T KOG0825|consen   97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQ----------TCPVD  166 (1134)
T ss_pred             cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcc----------cCchh
Confidence            344667777776333221    22355689999988776432   46999999999999999753          99999


Q ss_pred             ccccccccc
Q 024938           91 KANISVASL   99 (260)
Q Consensus        91 r~~v~~~~l   99 (260)
                      |..+....+
T Consensus       167 R~EF~~v~V  175 (1134)
T KOG0825|consen  167 RGEFGEVKV  175 (1134)
T ss_pred             hhhhheeee
Confidence            999865433

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

Probab=96.84  E-value=0.00068  Score=63.25  Aligned_cols=47  Identities=34%  Similarity=0.778  Sum_probs=37.5

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .......|.||++...+.+.++|||..|  |..-..+.          . +||+||..+.
T Consensus       301 ~~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~~l----------~-~CPvCR~rI~  347 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSKHL----------P-QCPVCRQRIR  347 (355)
T ss_pred             ccCCCCceEEecCCccceeeecCCcEEE--chHHHhhC----------C-CCchhHHHHH
Confidence            3445679999999999999999999977  66544442          4 8999999874

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

Probab=96.70  E-value=0.0068  Score=53.48  Aligned_cols=52  Identities=23%  Similarity=0.631  Sum_probs=37.9

Q ss_pred             cccccccCCC--CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           42 ECNICLDSAQ--DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        42 ~C~ICld~~~--~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .|..|...+.  |-+.+-|-|+|+|.|+.+|...-....  .-..++||.|..+|-
T Consensus        52 NC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanT--APaGyqCP~Cs~eiF  105 (299)
T KOG3970|consen   52 NCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANT--APAGYQCPCCSQEIF  105 (299)
T ss_pred             CCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcC--CCCcccCCCCCCccC
Confidence            6777877765  457788999999999999987543111  112348999998875

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

Probab=96.56  E-value=0.0013  Score=60.78  Aligned_cols=57  Identities=32%  Similarity=0.726  Sum_probs=47.2

Q ss_pred             CCcccccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .+...|+||+....+|.++. -|-.||++||..++...         + .|||-..+....+++.++.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~---------~-~CPVT~~p~~v~~l~rl~~  355 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNY---------G-HCPVTGYPASVDHLIRLFN  355 (357)
T ss_pred             CccccChhHHhccCCCceEEecceEEeHHHHHHHHHhc---------C-CCCccCCcchHHHHHHHhc
Confidence            35679999999999987765 69999999999999865         4 9999888887777776653

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

Probab=96.42  E-value=0.0017  Score=61.14  Aligned_cols=52  Identities=25%  Similarity=0.816  Sum_probs=36.8

Q ss_pred             ccccccccCCCCcEE----ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           41 FECNICLDSAQDPVV----TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        41 ~~C~ICld~~~~Pvv----t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      -.|.||.|....-.-    -.|||+|+..|+..|+....      -.+ .||.|+-.+....+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~P------s~R-~cpic~ik~~~r~~   60 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDP------SNR-GCPICQIKLQERHV   60 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCC------ccC-CCCceeecccceee
Confidence            479999666543222    24999999999999998654      125 99999955544433

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

Probab=96.24  E-value=0.0013  Score=66.80  Aligned_cols=52  Identities=29%  Similarity=0.733  Sum_probs=44.2

Q ss_pred             ccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccc
Q 024938           41 FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP  101 (260)
Q Consensus        41 ~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p  101 (260)
                      +.|.||++ ...++++.|||.||..|+...+....       .. .||.||..+...++..
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~-------~~-~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSE-------NA-PCPLCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc-cccceeecccchHHHHHHHhcccccc-------CC-CCcHHHHHHHHHHHhh
Confidence            89999999 88889999999999999999888654       23 7999999988766544

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

Probab=96.11  E-value=0.011  Score=56.68  Aligned_cols=39  Identities=21%  Similarity=0.504  Sum_probs=34.3

Q ss_pred             CCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQT   75 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~   75 (260)
                      +++++.|+||...+.+|++++|+|..|..|....+....
T Consensus         1 meeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~~tp   39 (699)
T KOG4367|consen    1 MEEELKCPVCGSFYREPIILPCSHNLCQACARNILVQTP   39 (699)
T ss_pred             CcccccCceehhhccCceEeecccHHHHHHHHhhcccCC
Confidence            357899999999999999999999999999987766544

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.00  E-value=0.0034  Score=43.47  Aligned_cols=48  Identities=25%  Similarity=0.479  Sum_probs=37.6

Q ss_pred             CcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccc
Q 024938           39 SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS   98 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~   98 (260)
                      ....|-.|...-...++++|||..|..|..-+-.           . .||.|...+...+
T Consensus         6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~rY-----------n-gCPfC~~~~~~~~   53 (55)
T PF14447_consen    6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPGERY-----------N-GCPFCGTPFEFDD   53 (55)
T ss_pred             cceeEEEccccccccccccccceeeccccChhhc-----------c-CCCCCCCcccCCC
Confidence            3456777888878889999999999999865443           3 8999998886543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=95.85  E-value=0.012  Score=53.23  Aligned_cols=61  Identities=18%  Similarity=0.417  Sum_probs=47.8

Q ss_pred             CCCCcccccccccCCCCc---E-EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccCCC
Q 024938           36 KDGSFFECNICLDSAQDP---V-VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGG  107 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~P---v-vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~~~  107 (260)
                      .....+.|||....+..-   | +.+|||+|+..+|.+.- ..         . .||+|-.++...+++++.....
T Consensus       109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~---------~-~Cp~c~~~f~~~DiI~Lnp~~e  173 (260)
T PF04641_consen  109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KS---------K-KCPVCGKPFTEEDIIPLNPPEE  173 (260)
T ss_pred             cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-cc---------c-cccccCCccccCCEEEecCCcc
Confidence            356789999999998542   2 24899999999998863 12         3 8999999999999988776443

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

Probab=95.59  E-value=0.0066  Score=47.24  Aligned_cols=27  Identities=30%  Similarity=0.971  Sum_probs=23.8

Q ss_pred             cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccc
Q 024938           57 LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKAN   93 (260)
Q Consensus        57 ~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~   93 (260)
                      -|.|.|+..||.+||+...          .||+|.++
T Consensus        80 ~CNHaFH~hCisrWlktr~----------vCPLdn~e  106 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRN----------VCPLDNKE  106 (114)
T ss_pred             ecchHHHHHHHHHHHhhcC----------cCCCcCcc
Confidence            4999999999999999764          99999765

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

Probab=95.54  E-value=0.0053  Score=54.54  Aligned_cols=51  Identities=35%  Similarity=0.852  Sum_probs=35.8

Q ss_pred             cccccccccCCC-Cc-EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccc
Q 024938           40 FFECNICLDSAQ-DP-VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPL  102 (260)
Q Consensus        40 ~~~C~ICld~~~-~P-vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~  102 (260)
                      ...|+.|.-... ++ .+|.|+|+||-.|...-..           . .||.||+.+....+..+
T Consensus         3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~-----------~-~C~lCkk~ir~i~l~~s   55 (233)
T KOG4739|consen    3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSP-----------D-VCPLCKKSIRIIQLNRS   55 (233)
T ss_pred             eEEeccccccCCCCceeeeechhhhhhhhcccCCc-----------c-ccccccceeeeeecccc
Confidence            357888886654 34 3578999999999754221           3 89999999875544443

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

Probab=95.44  E-value=0.011  Score=48.09  Aligned_cols=52  Identities=27%  Similarity=0.658  Sum_probs=42.2

Q ss_pred             CcccccccccCCCCcEEcc----CCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           39 SFFECNICLDSAQDPVVTL----CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~----CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ...+|+||.|.-.|...+.    ||-..|--|....++..+      -.+ .||+|+.++...
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~------~yp-vCPvCkTSFKss  134 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN------LYP-VCPVCKTSFKSS  134 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc------cCC-CCCccccccccc
Confidence            5689999999999887774    999999999887776543      346 999999888643

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

Probab=95.37  E-value=0.0036  Score=59.43  Aligned_cols=78  Identities=18%  Similarity=0.471  Sum_probs=48.7

Q ss_pred             hhhcCCCCCCCCCCCCCCCcccccccccCCCC---cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCC--cccccc
Q 024938           21 KQKWSPTSAPTNVPEKDGSFFECNICLDSAQD---PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV--CKANIS   95 (260)
Q Consensus        21 ~~~wk~~~~~~~~~~~~~~~~~C~ICld~~~~---Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPv--Cr~~v~   95 (260)
                      ++.....+.++....-....++|.||.+...-   =+.++|+|.||..|++.+.....  .+..-...+||-  |.....
T Consensus       165 ~~~Il~~deea~~~~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i--~eg~v~~l~Cp~~~C~~~a~  242 (445)
T KOG1814|consen  165 KKEILQFDEEATLEKFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQI--QEGQVSCLKCPDPKCGSVAP  242 (445)
T ss_pred             HHHHHhhhHHHHHHHHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhh--hcceeeeecCCCCCCcccCC
Confidence            44444555544444445567999999988653   35689999999999999988653  111112347875  444444


Q ss_pred             ccccc
Q 024938           96 VASLV  100 (260)
Q Consensus        96 ~~~l~  100 (260)
                      ...+.
T Consensus       243 ~g~vK  247 (445)
T KOG1814|consen  243 PGQVK  247 (445)
T ss_pred             chHHH
Confidence            43333

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

Probab=95.04  E-value=0.026  Score=53.53  Aligned_cols=71  Identities=20%  Similarity=0.423  Sum_probs=50.4

Q ss_pred             cCCCCCCCCCCC-----CCCCcccccccccCCCC---cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           24 WSPTSAPTNVPE-----KDGSFFECNICLDSAQD---PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        24 wk~~~~~~~~~~-----~~~~~~~C~ICld~~~~---Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      |....+...+.+     .....|.|||=.+.-.+   |+.+.|||+.|..-|.+......       ..++||.|-....
T Consensus       313 W~~~deLPveIeL~~~~~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~-------~sfKCPYCP~e~~  385 (394)
T KOG2817|consen  313 WNTKDELPVEIELGKEYHFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGS-------QSFKCPYCPVEQL  385 (394)
T ss_pred             ccccccCccceeccccccccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCC-------eeeeCCCCCcccC
Confidence            766655444433     34567999998876653   89999999999999998776432       2369999977665


Q ss_pred             cccccc
Q 024938           96 VASLVP  101 (260)
Q Consensus        96 ~~~l~p  101 (260)
                      ..+.+.
T Consensus       386 ~~~~kq  391 (394)
T KOG2817|consen  386 ASDTKQ  391 (394)
T ss_pred             HHhccc
Confidence            554443

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

Probab=94.66  E-value=0.02  Score=52.25  Aligned_cols=46  Identities=37%  Similarity=0.759  Sum_probs=37.8

Q ss_pred             cccccccccCCC------CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           40 FFECNICLDSAQ------DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        40 ~~~C~ICld~~~------~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      ...|.||-+.+.      -|.++.|||.+|..|+.+.+....        - .||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~--------i-~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSR--------I-LCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCce--------e-eccCCCCcc
Confidence            468999998875      378889999999999988777542        3 899999984

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

Probab=94.58  E-value=0.022  Score=38.45  Aligned_cols=43  Identities=23%  Similarity=0.609  Sum_probs=20.9

Q ss_pred             ccccccCCCCc--EEc--cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           43 CNICLDSAQDP--VVT--LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        43 C~ICld~~~~P--vvt--~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      |++|.+.+..-  ...  +||+..|..|..+.++..        .. .||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~--------~g-~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENE--------GG-RCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS---------S-B-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhcc--------CC-CCCCCCCCC
Confidence            78898887321  223  599999999998877632        25 899999864

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

Probab=94.51  E-value=0.02  Score=54.25  Aligned_cols=48  Identities=21%  Similarity=0.531  Sum_probs=37.3

Q ss_pred             CcccccccccCCCC-c---EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           39 SFFECNICLDSAQD-P---VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        39 ~~~~C~ICld~~~~-P---vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      -.+.|..|-+.+.. +   -.++|.|+|+..|+++++....       .+ .||.||+-.
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~-------~r-sCP~Crklr  415 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNG-------TR-SCPNCRKLR  415 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCC-------CC-CCccHHHHH
Confidence            35789999988753 2   2478999999999999997542       35 999998543

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

Probab=94.32  E-value=0.044  Score=51.32  Aligned_cols=52  Identities=27%  Similarity=0.697  Sum_probs=40.5

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      +..++...|-||.+...-..++||+|..|.-|-.+.-..=.       .+ .|++||..-
T Consensus        56 dtDEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~-------~K-~C~~CrTE~  107 (493)
T COG5236          56 DTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYM-------QK-GCPLCRTET  107 (493)
T ss_pred             ccccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHh-------cc-CCCcccccc
Confidence            34567789999999999888999999999999866433211       24 999998763

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

Probab=93.88  E-value=0.038  Score=51.09  Aligned_cols=47  Identities=30%  Similarity=0.736  Sum_probs=38.1

Q ss_pred             CCCCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           36 KDGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ...+.++||||.+.+..|+. -.=||+-|..|-.+..            . .||.||..+.
T Consensus        44 ~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~------------~-~CP~Cr~~~g   91 (299)
T KOG3002|consen   44 LDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS------------N-KCPTCRLPIG   91 (299)
T ss_pred             cchhhccCchhhccCcccceecCCCcEehhhhhhhhc------------c-cCCccccccc
Confidence            34567899999999999964 4568999999976433            3 8999999986

>PHA03096 p28-like protein; Provisional

Probab=93.74  E-value=0.034  Score=51.07  Aligned_cols=50  Identities=18%  Similarity=0.367  Sum_probs=34.1

Q ss_pred             ccccccccCCCCc--------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           41 FECNICLDSAQDP--------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        41 ~~C~ICld~~~~P--------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      -.|.||++...+-        +...|.|.||..|+..|.....   .....+ .||+|+..+
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~---~~e~~~-~c~~~~~~~  236 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESL---YKETEP-ENRRLNTVI  236 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhh---hcccCc-cccchhhHH
Confidence            6899999887542        2346999999999999998653   112223 555555444

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

Probab=93.64  E-value=0.028  Score=51.58  Aligned_cols=60  Identities=27%  Similarity=0.649  Sum_probs=39.9

Q ss_pred             CCCCcccccccccCCCC-c--EEccCCCccCHHHHHHhhhhhcCC--------------ccccccCcCCCCccccccc
Q 024938           36 KDGSFFECNICLDSAQD-P--VVTLCGHLYCWPCIYKWLHVQTSS--------------LDADEQQQNCPVCKANISV   96 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~-P--vvt~CGH~fC~~Ci~~wl~~~~~s--------------~~~~~~~~~CPvCr~~v~~   96 (260)
                      +....-.|.|||--|.+ |  ++|.|-|.++..|+.++|..--.-              ....... .||+||..|..
T Consensus       111 nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~ea-vcpVcre~i~~  187 (368)
T KOG4445|consen  111 NNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEA-VCPVCRERIKI  187 (368)
T ss_pred             CCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhh-hhhHhhhhccc
Confidence            33455689999977754 3  678999999999998887621000              0001113 79999998863

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

Probab=93.53  E-value=0.021  Score=57.15  Aligned_cols=37  Identities=32%  Similarity=0.657  Sum_probs=29.7

Q ss_pred             CCCCcccccccccCCC----CcEEccCCCccCHHHHHHhhh
Q 024938           36 KDGSFFECNICLDSAQ----DPVVTLCGHLYCWPCIYKWLH   72 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~----~Pvvt~CGH~fC~~Ci~~wl~   72 (260)
                      .+.+.+.|+||+..+.    .||.+-|||..|..|+.....
T Consensus         7 ~w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn   47 (861)
T KOG3161|consen    7 KWVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN   47 (861)
T ss_pred             hhHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence            3445678999987764    689999999999999977554

>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=93.42  E-value=0.027  Score=46.03  Aligned_cols=34  Identities=32%  Similarity=0.784  Sum_probs=27.0

Q ss_pred             cccccccccCCCC--cEE-ccCC------CccCHHHHHHhhhh
Q 024938           40 FFECNICLDSAQD--PVV-TLCG------HLYCWPCIYKWLHV   73 (260)
Q Consensus        40 ~~~C~ICld~~~~--Pvv-t~CG------H~fC~~Ci~~wl~~   73 (260)
                      ..+|.||++...+  .|+ +.||      |.||..|+.+|-..
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~   68 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRE   68 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence            5699999999877  654 4565      67999999999543

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.

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

Probab=93.16  E-value=0.024  Score=60.62  Aligned_cols=48  Identities=35%  Similarity=0.812  Sum_probs=41.8

Q ss_pred             CCCCcccccccccCCC-CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccc
Q 024938           36 KDGSFFECNICLDSAQ-DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKAN   93 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~-~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~   93 (260)
                      +..+.+.|.||++.+. ...+..|||.+|..|+..|+..++          .||.|+..
T Consensus      1149 ~~~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s----------~~~~~ksi 1197 (1394)
T KOG0298|consen 1149 NLSGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASS----------RCPICKSI 1197 (1394)
T ss_pred             HhhcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhc----------cCcchhhh
Confidence            4456789999999998 667889999999999999999875          89999854

>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=92.92  E-value=0.071  Score=48.74  Aligned_cols=46  Identities=24%  Similarity=0.676  Sum_probs=34.9

Q ss_pred             cccccccC-CCCcE----EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           42 ECNICLDS-AQDPV----VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        42 ~C~ICld~-~~~Pv----vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .||+|... +.+|-    +-+|||..|-.|+.+.+...+        . .||.|-..+..
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~--------~-~CpeC~~iLRk   52 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGP--------A-QCPECMVILRK   52 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCC--------C-CCCcccchhhh
Confidence            59999844 45552    237999999999999887653        5 99999777653

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.80  E-value=0.092  Score=47.10  Aligned_cols=40  Identities=28%  Similarity=0.478  Sum_probs=34.4

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhh
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQ   74 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~   74 (260)
                      +.+.+...|..||..+.+||+++=||+||..||.+++-.+
T Consensus        38 DsiK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~ilaq   77 (303)
T KOG3039|consen   38 DSIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYILAQ   77 (303)
T ss_pred             cccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHHHH
Confidence            3455566789999999999999999999999999887755

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

Probab=92.49  E-value=0.028  Score=56.85  Aligned_cols=53  Identities=26%  Similarity=0.723  Sum_probs=42.5

Q ss_pred             CCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +.-.++|+||...+.+|+.+.|-|.||.-|+..-+..+.      ... .|++|+..+..
T Consensus        18 ~~k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~------~~~-~~~lc~~~~eK   70 (684)
T KOG4362|consen   18 MQKILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKK------GPK-QCALCKSDIEK   70 (684)
T ss_pred             HhhhccCCceeEEeeccchhhhhHHHHhhhhhceeeccC------ccc-cchhhhhhhhh
Confidence            345689999999999999999999999999877665443      124 99999977653

>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=92.42  E-value=0.054  Score=41.45  Aligned_cols=33  Identities=27%  Similarity=0.625  Sum_probs=26.7

Q ss_pred             CCCcccccccccCCCCcE--EccCCCccCHHHHHH
Q 024938           37 DGSFFECNICLDSAQDPV--VTLCGHLYCWPCIYK   69 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pv--vt~CGH~fC~~Ci~~   69 (260)
                      +.+...|++|...+...+  +.||||.+|..|+.|
T Consensus        75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r  109 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR  109 (109)
T ss_pred             ECCCCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence            445668999999998764  469999999999854

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 [].

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

Probab=91.83  E-value=0.069  Score=55.03  Aligned_cols=43  Identities=30%  Similarity=0.750  Sum_probs=35.0

Q ss_pred             CcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           39 SFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      ....|..|.-.+.-|+| ..|||.|+..|+.+-            .. .||.|+.+.
T Consensus       839 q~skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~------------~~-~CP~C~~e~  882 (933)
T KOG2114|consen  839 QVSKCSACEGTLDLPFVHFLCGHSYHQHCLEDK------------ED-KCPKCLPEL  882 (933)
T ss_pred             eeeeecccCCccccceeeeecccHHHHHhhccC------------cc-cCCccchhh
Confidence            45699999999999866 799999999999721            24 899998844

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

Probab=91.68  E-value=0.082  Score=48.82  Aligned_cols=44  Identities=20%  Similarity=0.593  Sum_probs=29.2

Q ss_pred             cccccccccCC-CCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           40 FFECNICLDSA-QDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        40 ~~~C~ICld~~-~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      .-.|.-|---. .-.++++|.|.||.+|...  +.         .| .||.|...|.
T Consensus        90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~--~~---------dK-~Cp~C~d~Vq  134 (389)
T KOG2932|consen   90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARS--DS---------DK-ICPLCDDRVQ  134 (389)
T ss_pred             eEeecccCCcceeeecccccchhhhhhhhhc--Cc---------cc-cCcCcccHHH
Confidence            34566665332 3356789999999999642  22         25 8999977664

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

Probab=91.61  E-value=0.15  Score=52.69  Aligned_cols=55  Identities=27%  Similarity=0.681  Sum_probs=41.4

Q ss_pred             CCcccccccccCCC--CcEE--ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           38 GSFFECNICLDSAQ--DPVV--TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        38 ~~~~~C~ICld~~~--~Pvv--t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....+|-||.+.+.  .|+-  ..|-|+|+..||.+|....   ....+..+.||.|..+..
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~---ek~~~~~WrCP~Cqsv~~  247 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSS---EKTGQDGWRCPACQSVSK  247 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHh---hhccCccccCCcccchhc
Confidence            46789999999986  4543  3589999999999999872   233345579999986543

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

Probab=91.55  E-value=0.12  Score=44.21  Aligned_cols=58  Identities=24%  Similarity=0.573  Sum_probs=37.2

Q ss_pred             CCcccccccccCCCCcEE-------ccCCCccCHHHHHHhhhhhcCCcccccc--CcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVV-------TLCGHLYCWPCIYKWLHVQTSSLDADEQ--QQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvv-------t~CGH~fC~~Ci~~wl~~~~~s~~~~~~--~~~CPvCr~~v~~   96 (260)
                      ++.-.|.||..+--+..+       ..||..|+.-|++.||..=-.+...-..  . .||.|..++..
T Consensus       163 d~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFG-eCPYCS~Pial  229 (234)
T KOG3268|consen  163 DELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFG-ECPYCSDPIAL  229 (234)
T ss_pred             hhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeec-cCCCCCCccee
Confidence            344566777655433322       3699999999999999854333222111  3 89999888754

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=91.23  E-value=0.24  Score=41.60  Aligned_cols=50  Identities=20%  Similarity=0.541  Sum_probs=36.5

Q ss_pred             CCcccccccccCCCCcEEccCCC-----ccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGH-----LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH-----~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..+..|=||.+... +...+|..     ..+..|+.+|+..+.       .. .|+.|+.....
T Consensus         6 ~~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~-------~~-~CeiC~~~Y~i   60 (162)
T PHA02825          6 LMDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTSK-------NK-SCKICNGPYNI   60 (162)
T ss_pred             CCCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcCC-------CC-cccccCCeEEE
Confidence            45569999998864 33456654     348999999999653       35 99999888753

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

Probab=91.23  E-value=0.14  Score=34.17  Aligned_cols=40  Identities=25%  Similarity=0.948  Sum_probs=25.7

Q ss_pred             ccccccCCCC--cEEccCCC-----ccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           43 CNICLDSAQD--PVVTLCGH-----LYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        43 C~ICld~~~~--Pvvt~CGH-----~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      |-||++...+  +.+.+|.-     ..+..|+.+|+..+.       .. +|++|
T Consensus         1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~-------~~-~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESG-------NR-KCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT--------S-B-TTT
T ss_pred             CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcC-------CC-cCCCC
Confidence            6788876543  57788764     458899999999753       24 78887

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

Probab=90.87  E-value=0.19  Score=34.10  Aligned_cols=46  Identities=24%  Similarity=0.694  Sum_probs=25.0

Q ss_pred             ccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccc
Q 024938           41 FECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA   92 (260)
Q Consensus        41 ~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~   92 (260)
                      +.|||....+..|+. ..|.|.-|.+ +..|++....     ...+.||+|.+
T Consensus         3 L~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~-----~~~W~CPiC~~   49 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQR-----TPKWKCPICNK   49 (50)
T ss_dssp             SB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHH-----S---B-TTT--
T ss_pred             eeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhc-----cCCeECcCCcC
Confidence            689999999999987 5799998876 4466664421     12368999976

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

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

Probab=90.38  E-value=0.35  Score=31.74  Aligned_cols=40  Identities=20%  Similarity=0.556  Sum_probs=24.8

Q ss_pred             ccccccCCCCcEEcc---CCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           43 CNICLDSAQDPVVTL---CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        43 C~ICld~~~~Pvvt~---CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      |.+|.+.+...+.-+   |+-.++..|+..++...+       .. .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~-------~~-~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS-------NP-KCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S-------S--B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC-------CC-CCcCC
Confidence            788999998887754   999999999999998653       23 69987

; PDB: 3NW0_A 2CT0_A.

>PHA02862 5L protein; Provisional

Probab=90.06  E-value=0.23  Score=41.11  Aligned_cols=47  Identities=23%  Similarity=0.692  Sum_probs=35.1

Q ss_pred             ccccccccCCCCcEEccCCC-----ccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           41 FECNICLDSAQDPVVTLCGH-----LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        41 ~~C~ICld~~~~Pvvt~CGH-----~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..|=||.+.-.+. +-+|..     ..|..|+.+|+....       .. .|+.|+.+...
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~-------k~-~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSK-------KK-ECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCC-------Cc-CccCCCCeEEE
Confidence            4799999887655 466654     358999999997542       34 99999988753

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

Probab=89.41  E-value=0.27  Score=46.62  Aligned_cols=42  Identities=21%  Similarity=0.773  Sum_probs=29.8

Q ss_pred             CCCccCHHHHHHhhhhhcCCcccc---ccCcCCCCcccccccccc
Q 024938           58 CGHLYCWPCIYKWLHVQTSSLDAD---EQQQNCPVCKANISVASL   99 (260)
Q Consensus        58 CGH~fC~~Ci~~wl~~~~~s~~~~---~~~~~CPvCr~~v~~~~l   99 (260)
                      |.-..|..|+-+|+..+.+...++   .++..||.||+.+...|+
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV  355 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDV  355 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeee
Confidence            445668999999999776444442   223499999999876543

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

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

Probab=89.11  E-value=0.29  Score=45.37  Aligned_cols=59  Identities=20%  Similarity=0.392  Sum_probs=43.8

Q ss_pred             CCCCcccccccccCCCC---cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccc
Q 024938           36 KDGSFFECNICLDSAQD---PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP  101 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~---Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p  101 (260)
                      .....|.||+=.+...+   |+.+.|||..-..-+.+..+...       ..++||.|-......++..
T Consensus       332 hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~-------~~FKCPYCP~~~~~~~~~r  393 (396)
T COG5109         332 HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGV-------LSFKCPYCPEMSKYENILR  393 (396)
T ss_pred             cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCc-------EEeeCCCCCcchhhhhhhc
Confidence            55678999998877653   89999999999988877655432       3469999977665555443

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

Probab=88.44  E-value=0.27  Score=53.69  Aligned_cols=59  Identities=22%  Similarity=0.427  Sum_probs=38.6

Q ss_pred             CCcccccccccCC-C-C-cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSA-Q-D-PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~-~-~-Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +.+..|-||.... . . .+.+.|+|.|+..|..+.|+..=-....--....||+|+..+..
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            4566899998553 2 2 46789999999999987776431000000001389999999864

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=87.93  E-value=0.35  Score=45.35  Aligned_cols=51  Identities=18%  Similarity=0.432  Sum_probs=33.2

Q ss_pred             cccccccccCCCC--cEE--ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           40 FFECNICLDSAQD--PVV--TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        40 ~~~C~ICld~~~~--Pvv--t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      +..||.|.+.+..  --.  .+||...|.-|+...-+.=        .. .||.||.....+++
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~l--------ng-rcpacrr~y~denv   68 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNL--------NG-RCPACRRKYDDENV   68 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhc--------cC-CChHhhhhccccce
Confidence            3459999998753  222  3688777777765443321        25 89999998765543

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

Probab=87.85  E-value=0.35  Score=44.24  Aligned_cols=56  Identities=23%  Similarity=0.643  Sum_probs=40.7

Q ss_pred             CCcccccccccCCCCcEEccC----CCccCHHHHHHhhhhhcCCccc--cccCcCCCCccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLC----GHLYCWPCIYKWLHVQTSSLDA--DEQQQNCPVCKANI   94 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~C----GH~fC~~Ci~~wl~~~~~s~~~--~~~~~~CPvCr~~v   94 (260)
                      ...+.|-+|.+.++|-....|    .|.||++|-.+.++.+..+.+-  .-.. +||+-...+
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGd-kCPLvgS~v  327 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGD-KCPLVGSNV  327 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCC-cCcccCCcc
Confidence            345899999999999876666    6999999999999987654322  1123 677665544

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

Probab=87.50  E-value=0.33  Score=46.45  Aligned_cols=55  Identities=25%  Similarity=0.671  Sum_probs=37.0

Q ss_pred             CcccccccccCCCCc----EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCC--cccccccc
Q 024938           39 SFFECNICLDSAQDP----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV--CKANISVA   97 (260)
Q Consensus        39 ~~~~C~ICld~~~~P----vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPv--Cr~~v~~~   97 (260)
                      ...+|.||......+    .+..|+|.||..|+++.+..+.   ..+... .||.  |...+...
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~---~~~~~~-~C~~~~C~~~l~~~  205 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKL---LSGTVI-RCPHDGCESRLTLE  205 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhh---ccCCCc-cCCCCCCCccCCHH
Confidence            467999999444332    2567999999999999998652   122234 7764  66666543

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

Probab=86.93  E-value=0.6  Score=45.38  Aligned_cols=65  Identities=25%  Similarity=0.544  Sum_probs=44.7

Q ss_pred             CCcccccccccCCCC-cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCC--Cccccccccccccccc
Q 024938           38 GSFFECNICLDSAQD-PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCP--VCKANISVASLVPLYG  104 (260)
Q Consensus        38 ~~~~~C~ICld~~~~-Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CP--vCr~~v~~~~l~p~~~  104 (260)
                      .....|.||.+.... .+.+.|||.||..|+..++..+-.......  .+||  -|++.+..+.+..+..
T Consensus        68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~--i~cp~~~C~a~v~~~~i~~~~s  135 (444)
T KOG1815|consen   68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAK--IKCPAHGCPALVGEDTVEKLVS  135 (444)
T ss_pred             CccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeecccccc--ccCCCCCccccCCCceeeeecC
Confidence            456899999999885 566789999999999998986642221111  2565  4777776555444433

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

Probab=82.68  E-value=0.52  Score=41.33  Aligned_cols=39  Identities=28%  Similarity=0.739  Sum_probs=30.8

Q ss_pred             ccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           43 CNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        43 C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      |-+|.+.-..-+.+||.|+ +|..|-.. +            + .||+|+....
T Consensus       161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~-~------------~-~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGEREATVLLLPCRHLCLCGICDES-L------------R-ICPICRSPKT  200 (207)
T ss_pred             ceecCcCCceEEeecccceEeccccccc-C------------c-cCCCCcChhh
Confidence            9999988888677899995 79999543 2            3 8999988664

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

Probab=82.66  E-value=0.63  Score=42.58  Aligned_cols=43  Identities=30%  Similarity=0.666  Sum_probs=33.9

Q ss_pred             cccccccccCCC----CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccc
Q 024938           40 FFECNICLDSAQ----DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA   92 (260)
Q Consensus        40 ~~~C~ICld~~~----~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~   92 (260)
                      ...||||.+.+.    .+.+++|||.-+..|+......         . +.||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~---------~-y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE---------G-YTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc---------C-CCCCcccc
Confidence            445999998764    4678899999998888776653         2 49999988

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.50  E-value=0.78  Score=42.22  Aligned_cols=42  Identities=19%  Similarity=0.614  Sum_probs=29.7

Q ss_pred             CCCccCHHHHHHhhhhhcCCcccc---ccCcCCCCcccccccccc
Q 024938           58 CGHLYCWPCIYKWLHVQTSSLDAD---EQQQNCPVCKANISVASL   99 (260)
Q Consensus        58 CGH~fC~~Ci~~wl~~~~~s~~~~---~~~~~CPvCr~~v~~~~l   99 (260)
                      |....|..|+.+|+....+...+.   +++.+||.||+.+...++
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv  369 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDV  369 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeee
Confidence            566778999999998665333331   333499999999876554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	260
1jm7_A	112	Solution Structure Of The Brca1/bard1 Ring-domain H		2e-04

>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain Heterodimer Length = 112

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 32 NVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
          NV        EC ICL+  ++PV T C H++C  C+ K L+ +            CP+CK
Sbjct: 13 NVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGP-------SQCPLCK 65
Query: 92 ANISVASL 99
           +I+  SL
Sbjct: 66 NDITKRSL 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	260
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	7e-19
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	3e-18
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-18
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	1e-17
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-17
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-16
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	2e-13
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-12
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-12
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	5e-12
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-11
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	3e-11
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	4e-11
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-11
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-10
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	2e-10
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-09
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	2e-09
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	2e-09
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	2e-09
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-09
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	3e-09
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	3e-09
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-07
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	1e-08
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	2e-08
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-08
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	3e-08
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	4e-08
2ect_A	78	Ring finger protein 126; metal binding protein, st	6e-08
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	8e-08
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-07
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	2e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-07
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-07
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-07
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-07
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-06
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	1e-06
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	1e-06
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	5e-06
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	7e-06
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-05
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-05
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	3e-05
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	3e-05
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	4e-05
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	6e-05
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	7e-05
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	9e-05
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-04
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	3e-04
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	3e-04
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	5e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	6e-04

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 78.4 bits (193), Expect = 7e-19
 Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 10/73 (13%)

Query: 32  NVPEKDGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
              E     F C IC++  +D  +   C  L C+ CI +WL          EQ+  CP C
Sbjct: 14  QSVESIAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLT---------EQRAQCPHC 64

Query: 91  KANISVASLVPLY 103
           +A + +  LV   
Sbjct: 65  RAPLQLRELVNCR 77

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

 Score = 76.0 bits (187), Expect = 3e-18
 Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 10/80 (12%)

Query: 27  TSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQN 86
           +S  +       +  EC ICL +   PV   C H++C+ C+                 + 
Sbjct: 2   SSGSSGNTAPSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGAS----------WLGKR 51

Query: 87  CPVCKANISVASLVPLYGRG 106
           C +C+  I    L      G
Sbjct: 52  CALCRQEIPEDFLDSGPSSG 71

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

 Score = 75.2 bits (185), Expect = 4e-18
 Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 17/73 (23%)

Query: 38  GSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
           G+   C IC+D   +        V T CGH++C  C+   L          +    CP C
Sbjct: 1   GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----------KNANTCPTC 50

Query: 91  KANISVASLVPLY 103
           +  I+     P+Y
Sbjct: 51  RKKINHKRYHPIY 63

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

 Score = 74.1 bits (182), Expect = 1e-17
 Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 10/68 (14%)

Query: 27 TSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQN 86
          +S  +   E++   F C IC  + Q+PVVT C H +C  C  +                 
Sbjct: 2  SSGSSGGSEEEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHF----------RATPR 51

Query: 87 CPVCKANI 94
          C +C    
Sbjct: 52 CYICDQPT 59

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389

 Score = 79.8 bits (196), Expect = 2e-17
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 35  EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI 94
           E   +F  C IC ++ +D  +  CGHL C  C+  W            + Q CP C+  I
Sbjct: 327 EMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQE---------SEGQGCPFCRCEI 377

Query: 95  SVASLVPLY 103
                + + 
Sbjct: 378 KGTEPIVVD 386

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 70.3 bits (172), Expect = 3e-16
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 17/76 (22%)

Query: 35  EKDGSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNC 87
            +      C IC+D   +        V T CGH++C  C+   L          +    C
Sbjct: 5   LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----------KNANTC 54

Query: 88  PVCKANISVASLVPLY 103
           P C+  I+     P+Y
Sbjct: 55  PTCRKKINHKRYHPIY 70

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

 Score = 62.5 bits (152), Expect = 2e-13
 Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 9/55 (16%)

Query: 41 FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
          ++C  C      P  T CGH +C  C+   L               C  C+ +I 
Sbjct: 16 YKCEKCHLVLCSPKQTECGHRFCESCMAALLS---------SSSPKCTACQESIV 61

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 63.9 bits (155), Expect = 5e-13
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 14  TEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHV 73
             ++   K +       +++ +   +  +C IC +   + V   C H +C  CI +W+  
Sbjct: 38  QTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWM-- 95

Query: 74  QTSSLDADEQQQNCPVCKANIS 95
                   +++  CP+C+ +I 
Sbjct: 96  --------KRKIECPICRKDIK 109

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

 Score = 61.5 bits (149), Expect = 7e-13
 Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 17/76 (22%)

Query: 27 TSAPTNVPEKDGSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLD 79
          +S  +    +      C IC+D   +        V T CGH++C  C+   L        
Sbjct: 2  SSGSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL-------- 53

Query: 80 ADEQQQNCPVCKANIS 95
            +    CP C+  I+
Sbjct: 54 --KNANTCPTCRKKIN 67

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

 Score = 60.5 bits (147), Expect = 1e-12
 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 11/55 (20%)

Query: 42 ECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
           C ICL+   +  + L C H +C+ CI +W+           Q   CP+CK  + 
Sbjct: 7  RCPICLEDPSNYSMALPCLHAFCYVCITRWI----------RQNPTCPLCKVPVE 51

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124

 Score = 61.9 bits (150), Expect = 2e-12
 Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 15 EEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQ 74
          E  ASLK + +  S       K    F+C  C +    P+ T+C H  C  C+ +     
Sbjct: 27 EVLASLKDRPASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSF--- 83

Query: 75 TSSLDADEQQQNCPVCKANIS 95
                  Q  +CP C+ ++ 
Sbjct: 84 ------RAQVFSCPACRYDLG 98

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112

 Score = 60.1 bits (146), Expect = 5e-12
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 7/61 (11%)

Query: 41  FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV 100
            EC ICL+  ++PV T C H++C  C+ K L+ +       +    CP+CK +I+  SL 
Sbjct: 22  LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQK-------KGPSQCPLCKNDITKRSLQ 74

Query: 101 P 101
            
Sbjct: 75  E 75

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116

 Score = 58.8 bits (142), Expect = 2e-11
 Identities = 23/81 (28%), Positives = 27/81 (33%), Gaps = 9/81 (11%)

Query: 21  KQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDA 80
           K   S      + P        C IC     DPV T C HL+C  CI + L V  S    
Sbjct: 4   KIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGS---- 59

Query: 81  DEQQQNCPVCKANISVASLVP 101
                 CP C+       L  
Sbjct: 60  -----YCPSCRYPCFPTDLES 75

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118

 Score = 58.3 bits (141), Expect = 3e-11
 Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 9/61 (14%)

Query: 41  FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV 100
           +EC ICL + ++ V T CGH +C  CI K +          +    CPV    +    L 
Sbjct: 19  YECPICLMALREAVQTPCGHRFCKACIIKSIR---------DAGHKCPVDNEILLENQLF 69

Query: 101 P 101
           P
Sbjct: 70  P 70

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

 Score = 56.6 bits (137), Expect = 4e-11
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 11/62 (17%)

Query: 34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKAN 93
           ++     EC IC+D     ++  C H +C  CI KW           ++ +NCP+C+  
Sbjct: 9  VKQLTDEEECCICMDGRA-DLILPCAHSFCQKCIDKWS----------DRHRNCPICRLQ 57

Query: 94 IS 95
          ++
Sbjct: 58 MT 59

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 57.1 bits (138), Expect = 5e-11
 Identities = 19/86 (22%), Positives = 30/86 (34%), Gaps = 14/86 (16%)

Query: 17  DASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPV-VTLCGHLYCWPCIYKWLHVQT 75
           D+  + +W P  A     +       C IC +     + +  C H YC  CI K+L    
Sbjct: 2   DSLAESRWPPGLAVMKTIDDL---LRCGICFEYFNIAMIIPQCSHNYCSLCIRKFL---- 54

Query: 76  SSLDADEQQQNCPVCKANISVASLVP 101
                   +  CP C   ++   L  
Sbjct: 55  ------SYKTQCPTCCVTVTEPDLKN 74

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

 Score = 56.8 bits (137), Expect = 1e-10
 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 9/61 (14%)

Query: 41  FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV 100
            +C IC++   +PV   C H  C PC    +         ++    CP C+  +S  +  
Sbjct: 16  CQCGICMEILVEPVTLPCNHTLCKPCFQSTV---------EKASLCCPFCRRRVSSWTRY 66

Query: 101 P 101
            
Sbjct: 67  H 67

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 41  FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV 100
             C ICL+  ++PV   C H +C  CI        ++    + + NCPVC+      +L 
Sbjct: 20  VTCPICLELLKEPVSADCNHSFCRACITLNYESNRNT----DGKGNCPVCRVPYPFGNLK 75

Query: 101 P 101
           P
Sbjct: 76  P 76

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 52.7 bits (127), Expect = 1e-09
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 43  CNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP 101
           C ICL+   +P+   CGH  C  CI        +S+     + +CPVC  + S   L  
Sbjct: 15  CPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSM---GGKSSCPVCGISYSFEHLQA 70

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 7/50 (14%)

Query: 41 FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
            C++CL+  ++PV+  CGH +C  CI +W           E+   CPVC
Sbjct: 16 ASCSVCLEYLKEPVIIECGHNFCKACITRWWEDL-------ERDFPCPVC 58

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 52.3 bits (126), Expect = 2e-09
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 13/67 (19%)

Query: 43  CNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA---------N 93
           C ICL+    P+   CGH +C  C+             D+ + +CPVC+          N
Sbjct: 22  CPICLELLTQPLSLDCGHSFCQACLTANH----KKSMLDKGESSCPVCRISYQPENIRPN 77

Query: 94  ISVASLV 100
             VA++V
Sbjct: 78  RHVANIV 84

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 19/52 (36%), Positives = 22/52 (42%), Gaps = 7/52 (13%)

Query: 41 FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA 92
            C ICLD  Q PV   CGH +C  CI       T   +       CP+CK 
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCI-------TQIGETSCGFFKCPLCKT 65

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

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 9/55 (16%)

Query: 41  FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
           F C  C +    PV T C H  C  C+ +             Q  +CP C+ ++ 
Sbjct: 79  FMCVCCQELVYQPVTTECFHNVCKDCLQRSF---------KAQVFSCPACRHDLG 124

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141

 Score = 53.6 bits (128), Expect = 3e-09
 Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 9/51 (17%)

Query: 41 FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
          + C+ C +  + P    CGH YC  C+   L             QNC  C 
Sbjct: 32 YLCSACRNVLRRPFQAQCGHRYCSFCLASILS---------SGPQNCAACV 73

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170

 Score = 53.9 bits (129), Expect = 3e-09
 Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 9/61 (14%)

Query: 41  FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV 100
           +EC ICL + ++ V T CGH +C  CI K +          +    CPV    +    L 
Sbjct: 19  YECPICLMALREAVQTPCGHRFCKACIIKSIR---------DAGHKCPVDNEILLENQLF 69

Query: 101 P 101
           P
Sbjct: 70  P 70

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

 Score = 51.3 bits (123), Expect = 4e-09
 Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 11/56 (19%)

Query: 41 FECNICLDSAQDPV-VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
            C+IC     D   +T C H +C  CI +                 CP C   + 
Sbjct: 16 ILCSICKGYLIDATTITECLHTFCKSCIVRHF----------YYSNRCPKCNIVVH 61

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 52.5 bits (125), Expect = 5e-09
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 17/62 (27%)

Query: 41 FECNICLDSAQD-------PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKAN 93
            C IC+D   +        V T CGH++C  C+   L          +    CP C+  
Sbjct: 8  VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL----------KNANTCPTCRKK 57

Query: 94 IS 95
          I+
Sbjct: 58 IN 59

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 47.5 bits (112), Expect = 3e-07
 Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 17/89 (19%)

Query: 22  QKWSPTSAPTNVPEKDGSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQ 74
            +        +          C IC+D   +        V T CGH++C  C+   L   
Sbjct: 54  CRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-- 111

Query: 75  TSSLDADEQQQNCPVCKANISVASLVPLY 103
                       CP C+  I+     P+Y
Sbjct: 112 --------NANTCPTCRKKINHKRYHPIY 132

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 19/72 (26%), Positives = 26/72 (36%), Gaps = 13/72 (18%)

Query: 25 SPTSAPTNVPEKDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQ 83
            +     +P++      C IC D   D VV   CG+ YC  CI   L         +  
Sbjct: 4  GSSGEDDPIPDE----LLCLICKDIMTDAVVIPCCGNSYCDECIRTAL--------LESD 51

Query: 84 QQNCPVCKANIS 95
          +  CP C  N  
Sbjct: 52 EHTCPTCHQNDV 63

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 18/50 (36%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 41 FECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
            C ICLD  Q PV   CGH +C  CI       T   +       CP+C
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCI-------TQIGETSCGFFKCPLC 63

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 117

 Score = 50.3 bits (120), Expect = 2e-08
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 16/79 (20%)

Query: 24  WSPTSAPTNVPEKDGSFFECNICLDSAQDPV-VTLCGHLYCWPCIYKWLHVQTSSLDADE 82
           W+ + A  +  EK      C+ C +  ++PV +  C H++C  C+   +           
Sbjct: 9   WAHSRAALDRLEKL---LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG-------- 57

Query: 83  QQQNCPVCKANISVASLVP 101
               CPVC     +  L  
Sbjct: 58  ----CPVCYTPAWIQDLKI 72

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Length = 92

 Score = 49.4 bits (118), Expect = 3e-08
 Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 10/63 (15%)

Query: 41  FECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA-NISVAS 98
             C IC D   D VV   CG+ YC  CI   L         +  +  CP C   ++S  +
Sbjct: 14  LLCLICKDIMTDAVVIPCCGNSYCDECIRTAL--------LESDEHTCPTCHQNDVSPDA 65

Query: 99  LVP 101
           L+ 
Sbjct: 66  LIA 68

>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 Length = 61

 Score = 48.1 bits (115), Expect = 4e-08
 Identities = 10/67 (14%), Positives = 25/67 (37%), Gaps = 11/67 (16%)

Query: 38  GSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV 96
           GS   C I     + PV++     ++    + +++          +   N P+    +S+
Sbjct: 1   GSHMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYV----------KDTGNDPITNEPLSI 50

Query: 97  ASLVPLY 103
             +V + 
Sbjct: 51  EEIVEIV 57

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78

 Score = 48.2 bits (115), Expect = 6e-08
 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 13/71 (18%)

Query: 27 TSAPTNVPEKDGSFFECNICLD--SAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQ 83
          +S  +   E  GS  EC +C +  +  + V  L C HL+   CI  WL    S       
Sbjct: 2  SSGSSGTEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDS------- 54

Query: 84 QQNCPVCKANI 94
             CPVC+ ++
Sbjct: 55 ---CPVCRKSL 62

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

 Score = 51.4 bits (122), Expect = 8e-08
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 9/81 (11%)

Query: 26  PTSAPTNVPEKDGSFFECNIC----LDSAQDPVVTL----CGHLYCWPCIYKWLH-VQTS 76
             S    + E+D     CNIC    LD  + P+V+     C       C+ +W   +   
Sbjct: 294 DWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDG 353

Query: 77  SLDADEQQQNCPVCKANISVA 97
               +     CP CKA +S +
Sbjct: 354 KTFLEVSFGQCPFCKAKLSTS 374

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

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 11/77 (14%)

Query: 27 TSAPTNVPEKDGSFFECNICL----DSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADE 82
          +S  +   +      EC IC+    +    P +  CGH  C  C+ K L    + +    
Sbjct: 2  SSGSSGNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVR--- 58

Query: 83 QQQNCPVCKANISVASL 99
              CP C     + SL
Sbjct: 59 ----CPFCSKITRITSL 71

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

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 13/64 (20%)

Query: 35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI 94
          E++  F  C  C   A+ P +  C H  C  C+             +     CP+C+A  
Sbjct: 1  EEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCL-------------EASGMQCPICQAPW 47

Query: 95 SVAS 98
           + +
Sbjct: 48 PLGA 51

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 11/56 (19%)

Query: 41 FECNICLDSAQDPV-VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
            C +C     D   +  C H +C  CI ++L          E  + CP+C   + 
Sbjct: 16 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYL----------ETSKYCPICDVQVH 61

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 10/56 (17%)

Query: 41  FECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
             C ICLD  ++ + T  C H +C  CI   L             + CP C+  + 
Sbjct: 55  LMCPICLDMLKNTMTTKECLHRFCADCIITAL---------RSGNKECPTCRKKLV 101

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 13/63 (20%)

Query: 35 EKDGSFFECNICLDS--AQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
          ++      C +CL+    +D +    C H +   C+ KWL          E ++ CP+C 
Sbjct: 10 KELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWL----------EVRKVCPLCN 59

Query: 92 ANI 94
            +
Sbjct: 60 MPV 62

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

 Score = 46.6 bits (111), Expect = 3e-07
 Identities = 18/72 (25%), Positives = 22/72 (30%), Gaps = 13/72 (18%)

Query: 26 PTSAPTNVPEKDGSFFECNICLD--SAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADE 82
          P    T      G    C IC       D    L C H +  PC+  WL    +      
Sbjct: 26 PEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGT------ 79

Query: 83 QQQNCPVCKANI 94
              CPVC+   
Sbjct: 80 ----CPVCRCMF 87

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 13/67 (19%)

Query: 35 EKDGSFFECNICLDS--AQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
           ++ +  +C ICL      + V  L C HL+   C+ +WL               CP+C+
Sbjct: 9  TEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK----------CPICR 58

Query: 92 ANISVAS 98
           +I    
Sbjct: 59 VDIEAQL 65

>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 Length = 281

 Score = 47.6 bits (113), Expect = 1e-06
 Identities = 15/100 (15%), Positives = 35/100 (35%), Gaps = 13/100 (13%)

Query: 2   EQNLFEPETGYATEEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHL 61
           +Q   E +      +   L  +        ++P+    +    I  +  ++P +T  G  
Sbjct: 174 QQACIEAKHDKYMADMDELFSQVDEKRKKRDIPD----YLCGKISFELMREPCITPSGIT 229

Query: 62  YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP 101
           Y    I + L  +    +        PV ++ ++   L+P
Sbjct: 230 YDRKDIEEHLQ-RVGHFN--------PVTRSPLTQEQLIP 260

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 14/58 (24%)

Query: 42 ECNICLD---SAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
           C ICL+   +++     L CGHL    C  + L          ++   CP+C    S
Sbjct: 7  GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEML----------KEGYRCPLCSGPSS 54

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

 Score = 42.7 bits (101), Expect = 5e-06
 Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 13/64 (20%)

Query: 35 EKDGSFFECNICLD--SAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
                  C +C+    ++  +  L C H +   C+ KWL    +          CP+C+
Sbjct: 18 NHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRT----------CPICR 67

Query: 92 ANIS 95
          A+  
Sbjct: 68 ADSG 71

>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} Length = 267

 Score = 45.3 bits (106), Expect = 7e-06
 Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 11/64 (17%)

Query: 41  FECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV--CKANISVA 97
             C I     + P++   C H++    I  +L   T+         +CP   C   +S+ 
Sbjct: 182 LTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTR--------DCPQAACSQVVSMR 233

Query: 98  SLVP 101
             V 
Sbjct: 234 DFVR 237

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 13/54 (24%), Positives = 16/54 (29%), Gaps = 9/54 (16%)

Query: 42 ECNICLDSA-QDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI 94
           CNIC     Q      CG     PC+ K+             +  CP C    
Sbjct: 17 ICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSN--------AEPRCPHCNDYW 62

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 14/59 (23%)

Query: 42 ECNICLDSAQDP----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV 96
          EC +CL   +D      +  CGH +   C+  WL   ++          CP+C+  + V
Sbjct: 7  ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHST----------CPLCRLTVVV 55

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

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 5/54 (9%)

Query: 41 FECNICLD---SAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
            C +CL      Q   +  C  ++C  C+ +++ +     +  E   +CP   
Sbjct: 6  SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIK--EGLETAISCPDAA 57

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2 Length = 78

 Score = 40.2 bits (95), Expect = 3e-05
 Identities = 21/73 (28%), Positives = 28/73 (38%), Gaps = 13/73 (17%)

Query: 29  APTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCP 88
                PE    +F C I L+  +DPV+   G  Y    I KWL         D   + CP
Sbjct: 1   GSPEFPE----YFRCPISLELMKDPVIVSTGQTYERSSIQKWL---------DAGHKTCP 47

Query: 89  VCKANISVASLVP 101
             +  +  A L P
Sbjct: 48  KSQETLLHAGLTP 60

>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 Length = 100

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 11/72 (15%), Positives = 21/72 (29%), Gaps = 14/72 (19%)

Query: 30  PTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV 89
            ++ P+     F   +      DPV    G +     I + L                P 
Sbjct: 23  YSDAPD----EFRDPLMDTLMTDPVRLPSGTIMDRSIILRHL----------LNSPTDPF 68

Query: 90  CKANISVASLVP 101
            +  ++ + L P
Sbjct: 69  NRQTLTESMLEP 80

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 94

 Score = 39.9 bits (93), Expect = 6e-05
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 8/65 (12%)

Query: 41  FECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV---CKANISV 96
           F C I  +  + PV   +CGH Y    I + +     S    +++  CP       +I  
Sbjct: 8   FTCPITKEEMKKPVKNKVCGHTYEEDAIVRMI----ESRQKRKKKAYCPQIGCSHTDIRK 63

Query: 97  ASLVP 101
           + L+ 
Sbjct: 64  SDLIQ 68

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus} Length = 85

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 11/71 (15%), Positives = 21/71 (29%), Gaps = 14/71 (19%)

Query: 31  TNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
           ++ P+     F   +      DPV    G +     I + L                P  
Sbjct: 9   SDAPD----EFRDPLMDTLMTDPVRLPSGTVMDRSIILRHL----------LNSPTDPFN 54

Query: 91  KANISVASLVP 101
           +  ++ + L P
Sbjct: 55  RQMLTESMLEP 65

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C Length = 179

 Score = 41.1 bits (96), Expect = 9e-05
 Identities = 13/87 (14%), Positives = 28/87 (32%), Gaps = 13/87 (14%)

Query: 15  EEDASLKQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQ 74
            +   L  +         +P+    +    I  +  ++P +T  G  Y    I + L   
Sbjct: 85  MDMDELFSQVDEKRKKREIPD----YLCGKISFELMREPCITPSGITYDRKDIEEHL--- 137

Query: 75  TSSLDADEQQQNCPVCKANISVASLVP 101
                        PV ++ ++   L+P
Sbjct: 138 ------QRVGHFDPVTRSPLTQDQLIP 158

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

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 14/59 (23%)

Query: 43 CNICLDSAQD----PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA 97
          C  C    +      V   C H +   C+  W+          +Q   CP+C+ +  V 
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWV----------KQNNRCPLCQQDWVVQ 77

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B* Length = 63

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 15/65 (23%)

Query: 42  ECNICLDSAQDPVVTL--CGHLY-CWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
            C++C    +D  +     GHL  C+ C  +            +   +CP+CK  I    
Sbjct: 9   PCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLK----------KAGASCPICKKEIQ--L 56

Query: 99  LVPLY 103
           ++ ++
Sbjct: 57  VIKVF 61

>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 Length = 93

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 9/79 (11%)

Query: 27  TSAPTNVPEKDGSFFECNICLDSAQDPVVTLC----GHLYCWPCIYKWLHVQTSSLDADE 82
           +S  +  P  +     C IC +  +D     C     H +C+PC  + +  Q ++ +   
Sbjct: 2   SSGSSGSPMANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATGEVY- 60

Query: 83  QQQNCPVCKANISVASLVP 101
               CP  +    V S VP
Sbjct: 61  ----CPSGEKCPLVGSNVP 75

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A Length = 64

 Score = 36.7 bits (85), Expect = 5e-04
 Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 15/65 (23%)

Query: 42  ECNICLDSAQDPVV--TLCGHLY-CWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
            C IC    ++  +     GHL  C+ C          +    ++ + CPVC+  I    
Sbjct: 10  PCVICQGRPKNGCIVHGKTGHLMACFTC----------AKKLKKRNKPCPVCRQPIQ--M 57

Query: 99  LVPLY 103
           +V  Y
Sbjct: 58  IVLTY 62

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 5e-04
 Identities = 50/303 (16%), Positives = 82/303 (27%), Gaps = 74/303 (24%)

Query: 5   LFEPETGYATEEDASLKQKWSPTSAPTNVPE--KDGSFFECNICLDSAQDPVVTLCGHLY 62
           L         +E  SL  K+     P ++P      +    +I  +S +D          
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCR-PQDLPREVLTTNPRRLSIIAESIRD---------- 339

Query: 63  CWPCIYK-WLHVQTS-----------SLDADEQQQNCPVC-----KANISVASLVPLYGR 105
                +  W HV               L+  E ++           A+I    L  ++  
Sbjct: 340 -GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF- 397

Query: 106 GGISSASDSKKPNLGEVVPSRPHPSALNTSVTSSSTS----------TRHQTQQLH---- 151
                  D  K ++  VV      S +      S+ S                 LH    
Sbjct: 398 -------DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIV 450

Query: 152 ------SDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISF------FNPLMGML 199
                   F        +  QYF  H G H  L +       T+ F      F  L   +
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHH--LKNIEHPERMTL-FRMVFLDFRFLEQKI 507

Query: 200 GGMTLERIFGGSTTSLFT----YPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVL 255
              +      GS  +       Y  +  +  N+P+  R    +   L ++   L C    
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFY--KPYICDNDPKYERLVNAILDFLPKIEENLICSKYT 565

Query: 256 CLL 258
            LL
Sbjct: 566 DLL 568

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

 Score = 37.0 bits (85), Expect = 6e-04
 Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 13/66 (19%)

Query: 34 PEKDGSFFECNICLD----SAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV 89
          P+      EC +C++       +     CG+  C  C ++    +            CP 
Sbjct: 5  PDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGL---------CPA 55

Query: 90 CKANIS 95
          C+    
Sbjct: 56 CRKPYP 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	260
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.54
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.5
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.48
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.47
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.46
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.46
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.46
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.46
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.45
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.45
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.45
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.44
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.44
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.43
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.42
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.42
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.41
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.41
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.4
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.38
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.38
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.37
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.36
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.35
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.34
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.34
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.33
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.32
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.32
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.31
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.3
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.3
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.29
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.28
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.27
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.27
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.27
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.26
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.25
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.25
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.25
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.24
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.24
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.24
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.23
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.2
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.18
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.17
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.17
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.15
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.15
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.09
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.09
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.03
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.03
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.99
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.95
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.93
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.9
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.89
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.8
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.8
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.75
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.69
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.68
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.57
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.38
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.16
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.11
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.78
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	96.59
3nw0_A	238	Non-structural maintenance of chromosomes element	96.56
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.28
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	93.47
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	90.85
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	89.15
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	88.72
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	85.55
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	82.97

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

Probab=99.54  E-value=1.2e-14  Score=104.66  Aligned_cols=63  Identities=19%  Similarity=0.433  Sum_probs=53.7

Q ss_pred             CCCCCCCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           32 NVPEKDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        32 ~~~~~~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ...+..++.+.|+||++.+.+|+.+ +|||.||..||.+|+..+         . .||+||..+...++..+..
T Consensus         7 ~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~~~~~~   70 (72)
T 2djb_A            7 GNLSELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYS---------N-RCPKCNIVVHQTQPLSGPS   70 (72)
T ss_dssp             CCCCCCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHC---------S-SCTTTCCCCCSSCSCCCCS
T ss_pred             hhHhhcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcC---------C-cCCCcCcccCcccccccCC
Confidence            3445677889999999999999987 999999999999999764         4 9999999998877766543

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

Probab=99.50  E-value=1.5e-14  Score=105.40  Aligned_cols=61  Identities=31%  Similarity=0.625  Sum_probs=52.8

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      +...+.+.|+||++.+.+|++++|||.||..||.+|+...        .. .||+||..+...++.+++.
T Consensus         3 ~~~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~--------~~-~CP~C~~~~~~~~l~~n~~   63 (78)
T 1t1h_A            3 PEFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAG--------HK-TCPKSQETLLHAGLTPNYV   63 (78)
T ss_dssp             CCCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTT--------CC-BCTTTCCBCSSCCCEECTT
T ss_pred             cCCcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHC--------cC-CCCCCcCCCChhhCccCHH
Confidence            3456789999999999999999999999999999999752        24 8999999998877777654

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

Probab=99.48  E-value=1.1e-13  Score=101.53  Aligned_cols=70  Identities=30%  Similarity=0.600  Sum_probs=56.3

Q ss_pred             CCCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccCC
Q 024938           33 VPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRG  106 (260)
Q Consensus        33 ~~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~~  106 (260)
                      ..+...+.+.|+||++.+.+|++++|||.||..||.+|+....   ...... .||+||..+..+++.+++...
T Consensus        12 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~---~~~~~~-~CP~Cr~~~~~~~~~~n~~l~   81 (85)
T 2ecw_A           12 VLEMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNR---NTDGKG-NCPVCRVPYPFGNLKPNLHVA   81 (85)
T ss_dssp             CCCCCCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSB---CTTSCB-CCTTTCCCCCTTCCEECSCCC
T ss_pred             HHHhCccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhcc---CCCCCC-CCCCCCCcCCHHhCCcCHHHH
Confidence            3455677899999999999999999999999999999998632   011234 999999999888777776543

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

Probab=99.47  E-value=2.8e-14  Score=102.39  Aligned_cols=57  Identities=26%  Similarity=0.639  Sum_probs=49.0

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP  101 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p  101 (260)
                      +...+.+.|+||++.+.+|+.++|||.||..||.+|+...         . .||+||..+...+++.
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~~~   66 (71)
T 2d8t_A           10 APSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLG---------K-RCALCRQEIPEDFLDS   66 (71)
T ss_dssp             CSSSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCS---------S-BCSSSCCBCCHHHHSC
T ss_pred             ccCCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCC---------C-cCcCcCchhCHhhccC
Confidence            3455678999999999999999999999999999999854         4 9999999998765543

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

Probab=99.46  E-value=8.5e-14  Score=100.78  Aligned_cols=55  Identities=33%  Similarity=0.593  Sum_probs=47.2

Q ss_pred             CCCCCCCcccccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           33 VPEKDGSFFECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        33 ~~~~~~~~~~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ..+...+.+.|+||++.+.+|++++ |||.||..||.+|+....       .. .||+||+.+.
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~-------~~-~CP~Cr~~~~   63 (74)
T 2yur_A            8 EDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESD-------EH-TCPTCHQNDV   63 (74)
T ss_dssp             CCCCSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSS-------SS-CCSSSCCSSC
T ss_pred             ccccCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcC-------CC-cCCCCCCcCC
Confidence            3456778899999999999999999 999999999999998541       23 8999999754

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

Probab=99.46  E-value=6.2e-14  Score=104.65  Aligned_cols=60  Identities=17%  Similarity=0.143  Sum_probs=53.5

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ....+.+.|+||++.+.+||+++|||+||..||.+|+...         . .||+|+..+...+++++..
T Consensus         9 ~~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~---------~-~cP~~~~~l~~~~l~pn~~   68 (85)
T 2kr4_A            9 SDAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNS---------P-TDPFNRQMLTESMLEPVPE   68 (85)
T ss_dssp             TTCCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHC---------S-BCTTTCCBCCGGGCEECHH
T ss_pred             hcCchheECcccCchhcCCeECCCCCEECHHHHHHHHhcC---------C-CCCCCcCCCChHhcchHHH
Confidence            3456789999999999999999999999999999999853         4 9999999999888888754

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

Probab=99.46  E-value=2.1e-14  Score=102.38  Aligned_cols=58  Identities=31%  Similarity=0.801  Sum_probs=51.4

Q ss_pred             CCCCcccccccccCCCCc-------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~P-------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      ...+.+.|+||++.+.+|       +.++|||.||..||.+|+..+         . .||+||..+..+++.++|
T Consensus         6 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~~~~~   70 (71)
T 3ng2_A            6 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---------N-TCPTCRKKINHKRYHPIY   70 (71)
T ss_dssp             CCTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC---------S-BCTTTCCBCCCCSCCCCC
T ss_pred             CCCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC---------C-CCCCCCCccChhheeecc
Confidence            345678999999999887       889999999999999999865         4 999999999988888876

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

Probab=99.46  E-value=4.6e-14  Score=99.72  Aligned_cols=57  Identities=23%  Similarity=0.543  Sum_probs=48.5

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      .+...+.+.|+||++.+.+|+.++|||.||..||.+|+...        .. .||+||+.+..+++
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~--------~~-~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A            9 VKTVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSS--------SP-KCTACQESIVKDKV   65 (66)
T ss_dssp             CCSCCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTS--------SC-CCTTTCCCCCTTTC
T ss_pred             hhcCCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhC--------cC-CCCCCCcCCChhhc
Confidence            34567789999999999999999999999999999999632        24 89999999876643

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

Probab=99.45  E-value=6.5e-14  Score=105.07  Aligned_cols=64  Identities=31%  Similarity=0.506  Sum_probs=51.8

Q ss_pred             CCCCCCCcccccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc-cccccccccc
Q 024938           33 VPEKDGSFFECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI-SVASLVPLYG  104 (260)
Q Consensus        33 ~~~~~~~~~~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v-~~~~l~p~~~  104 (260)
                      ..+...+.+.|+||++.+.+|++++ |||.||..||.+|+....       .. .||+||..+ ....+.+++.
T Consensus         6 ~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~-------~~-~CP~Cr~~~~~~~~~~~n~~   71 (92)
T 3ztg_A            6 EDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESD-------EH-TCPTCHQNDVSPDALIANKF   71 (92)
T ss_dssp             SCCCCCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCT-------TC-CCTTTCCSSCCTTSCEECHH
T ss_pred             ccccCCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcC-------CC-cCcCCCCcCCCccccCcCHH
Confidence            3446678899999999999999999 999999999999997532       24 999999997 4555555543

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

Probab=99.45  E-value=9.1e-14  Score=99.65  Aligned_cols=59  Identities=32%  Similarity=0.647  Sum_probs=49.2

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      .+...+.+.|+||++.+.+|++++|||.||..||.+|+....      ... .||+||..+..+++
T Consensus        14 ~~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~------~~~-~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           14 VNKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSC------GFF-KCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSC------SCC-CCSSSCCCCCCCCC
T ss_pred             HHhCccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCC------CCC-CCCCCCCcCCcccC
Confidence            345677899999999999999999999999999999997321      224 89999999876654

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

Probab=99.45  E-value=3.1e-14  Score=103.55  Aligned_cols=70  Identities=24%  Similarity=0.463  Sum_probs=55.7

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccCC
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRG  106 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~~  106 (260)
                      .+...+.+.|+||++.+.+|++++|||.||..||.+|+.....  ...... .||+||..+...++.+++...
T Consensus         6 ~~~~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~--~~~~~~-~CP~Cr~~~~~~~l~~n~~l~   75 (79)
T 2egp_A            6 SGNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVT--SMGGKS-SCPVCGISYSFEHLQANQHLA   75 (79)
T ss_dssp             SCCCCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSS--SCCCCC-CCSSSCCCCCSSGGGTCSSSC
T ss_pred             HhhcccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhccc--CCCCCC-cCCCCCCcCCHhhCCcCHHHH
Confidence            3456778999999999999999999999999999999985310  011234 999999999888877776543

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

Probab=99.44  E-value=1.6e-13  Score=100.57  Aligned_cols=69  Identities=22%  Similarity=0.474  Sum_probs=55.2

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccCC
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRG  106 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~~  106 (260)
                      .+...+.+.|+||++.+.+|+.++|||.||..||.+|+..+.   ...... .||+||..+...++.+++...
T Consensus        13 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~---~~~~~~-~CP~Cr~~~~~~~~~~n~~l~   81 (85)
T 2ecv_A           13 LVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSM---LDKGES-SCPVCRISYQPENIRPNRHVA   81 (85)
T ss_dssp             CCCCCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHH---HTTSCC-CCTTTCCSSCSSSCCCSCCCC
T ss_pred             HHHccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhh---cCCCCC-cCCCCCCccCHHhcCccHHHH
Confidence            345677899999999999999999999999999999998631   011234 999999999887777766543

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.44  E-value=6.5e-14  Score=107.77  Aligned_cols=60  Identities=17%  Similarity=0.164  Sum_probs=53.6

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ....+.+.||||++.+.+||+++|||+||..||.+|+...         . .||+|+..+...+++++..
T Consensus        24 ~~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~---------~-~cP~~~~~l~~~~L~pn~~   83 (100)
T 2kre_A           24 SDAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNS---------P-TDPFNRQTLTESMLEPVPE   83 (100)
T ss_dssp             SSCSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSC---------S-BCSSSCCBCCTTSSEECHH
T ss_pred             ccCcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcC---------C-CCCCCCCCCChhhceECHH
Confidence            3556789999999999999999999999999999999843         4 9999999999888888764

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.43  E-value=1.2e-13  Score=105.82  Aligned_cols=60  Identities=18%  Similarity=0.115  Sum_probs=53.7

Q ss_pred             CCCCCcccccccccCCCCcEEccCC-CccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCG-HLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CG-H~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ....+.+.|+||++.+.+||+++|| |.||..||.+|+...         . .||+|+..+...+++++..
T Consensus        17 ~~~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~---------~-~cP~~~~~l~~~~L~pn~~   77 (98)
T 1wgm_A           17 ADACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSD---------Q-TDPFNRSPLTMDQIRPNTE   77 (98)
T ss_dssp             CSCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTS---------C-BCTTTCSBCCTTTSEECHH
T ss_pred             hcCcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhC---------C-CCCCCCCCCChhhceEcHH
Confidence            3556789999999999999999999 999999999999853         4 8999999999888888764

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

Probab=99.42  E-value=4.9e-15  Score=117.50  Aligned_cols=58  Identities=24%  Similarity=0.580  Sum_probs=48.2

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc-cccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV-ASLVPL  102 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~-~~l~p~  102 (260)
                      ...+.+.|+||++.+.+|+.++|||.||..||.+|+..+.        . .||+||..+.. ..+.++
T Consensus        48 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~~~~~n  106 (124)
T 3fl2_A           48 KVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQV--------F-SCPACRYDLGRSYAMQVN  106 (124)
T ss_dssp             HHHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTC--------C-BCTTTCCBCCTTCCCCCC
T ss_pred             hCccCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCc--------C-CCCCCCccCCCCCCCCCC
Confidence            3356789999999999999999999999999999998432        4 89999999976 444443

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

Probab=99.42  E-value=1.8e-13  Score=100.43  Aligned_cols=51  Identities=31%  Similarity=0.751  Sum_probs=45.6

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      +...+.+.|+||++.+.+|++++|||.||..||.+|+...         . .||+||..+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~---------~-~CP~Cr~~~~   60 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRAT---------P-RCYICDQPTG   60 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHC---------S-BCSSSCCBCC
T ss_pred             ccCCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCC---------C-cCCCcCcccc
Confidence            4456678999999999999999999999999999999854         4 9999999986

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

Probab=99.41  E-value=5.8e-14  Score=97.83  Aligned_cols=55  Identities=33%  Similarity=0.857  Sum_probs=49.4

Q ss_pred             CcccccccccCCCCc-------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           39 SFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        39 ~~~~C~ICld~~~~P-------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      +.+.|+||++.+.+|       +.++|||.||..||.+|+..+         . .||+||..+...++.++|
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~~~~~   63 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---------N-TCPTCRKKINHKRYHPIY   63 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHC---------S-BCTTTCCBCTTTCEEECC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcC---------C-CCCCCCccCCccceeeee
Confidence            467999999999887       789999999999999999864         4 999999999998888876

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

Probab=99.41  E-value=1e-13  Score=106.21  Aligned_cols=60  Identities=32%  Similarity=0.781  Sum_probs=52.4

Q ss_pred             CCCCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .+.+.+.|+||++.+.+|+. ++|||.||..||.+|+....        . .||+||..+...++++++.
T Consensus        18 ~l~~~~~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~l~~~~~   78 (100)
T 3lrq_A           18 SIAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQR--------A-QCPHCRAPLQLRELVNCRW   78 (100)
T ss_dssp             HHHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHTC--------S-BCTTTCCBCCGGGCEECTT
T ss_pred             cCCCCCCCccCCccccCccccCCCCChhhHHHHHHHHHHCc--------C-CCCCCCCcCCHHHhHhhHH
Confidence            44578899999999999999 99999999999999998652        3 8999999998888777654

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

Probab=99.40  E-value=7e-13  Score=98.10  Aligned_cols=60  Identities=30%  Similarity=0.670  Sum_probs=49.8

Q ss_pred             CCCCCCCcccccccccCCCC----cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           33 VPEKDGSFFECNICLDSAQD----PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        33 ~~~~~~~~~~C~ICld~~~~----Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      ..+...+.+.|+||++.+.+    |++++|||.||..||.+|+..+.      ... .||+||..+...++
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~------~~~-~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A            8 NLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSI------NGV-RCPFCSKITRITSL   71 (88)
T ss_dssp             SCCCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCS------SCB-CCTTTCCCBCCSST
T ss_pred             ChhhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCC------CCc-CCCCCCCcccchhH
Confidence            34566788999999999998    99999999999999999998641      124 99999999876543

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

Probab=99.38  E-value=6.8e-13  Score=92.68  Aligned_cols=51  Identities=35%  Similarity=0.687  Sum_probs=43.1

Q ss_pred             CCCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           33 VPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        33 ~~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      ..+...+.+.|+||++.+.+|++++|||.||..||.+|++...      ... .||+|
T Consensus        13 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~------~~~-~CP~C   63 (63)
T 2ysj_A           13 FVNKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSC------GFF-KCPLC   63 (63)
T ss_dssp             CCCCCCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCS------SCC-CCSCC
T ss_pred             HHHhCccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCC------CCC-cCcCC
Confidence            3456778899999999999999999999999999999998521      124 89998

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

Probab=99.38  E-value=3.4e-13  Score=98.04  Aligned_cols=58  Identities=29%  Similarity=0.654  Sum_probs=47.5

Q ss_pred             CCCCCCcccccccccCCCCc---EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDP---VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP  101 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~P---vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p  101 (260)
                      .+...+...|+||++.+.++   ++++|||.||..||.+|+..+         . .||+||+.+...++.+
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A            9 EEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH---------D-SCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             CTTSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTT---------C-SCTTTCCCCCCSCSCC
T ss_pred             cccCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcC---------C-cCcCcCCccCCcccCC
Confidence            34556788999999999765   567999999999999999754         4 9999999987765544

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

Probab=99.37  E-value=2.7e-13  Score=95.76  Aligned_cols=53  Identities=30%  Similarity=0.751  Sum_probs=45.8

Q ss_pred             CCCCCCcccccccccCCCCc-------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~P-------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+...+.+.|+||++.+.++       ++++|||.||..||.+|+..+         . .||+||..+..
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~   68 (69)
T 2ea6_A            9 GLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---------N-TCPTCRKKINH   68 (69)
T ss_dssp             CCCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHC---------S-SCTTTCCCCCC
T ss_pred             ccCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcC---------C-CCCCCCCccCc
Confidence            34566789999999999887       889999999999999999864         4 99999998753

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

Probab=99.36  E-value=3e-13  Score=95.19  Aligned_cols=57  Identities=23%  Similarity=0.516  Sum_probs=48.0

Q ss_pred             Cccccccccc-CCCCc----EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           39 SFFECNICLD-SAQDP----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        39 ~~~~C~ICld-~~~~P----vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      +++.|+||++ .+.+|    ++++|||.||..||.+|+....        . .||+||+.+...++.+++.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~~~~~~~   63 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGA--------G-NCPECGTPLRKSNFRVQLF   63 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTS--------S-SCTTTCCCCSSCCCEEECC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCC--------C-cCCCCCCccccccceeecc
Confidence            4578999999 88888    5789999999999999986432        4 8999999999888877654

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

Probab=99.35  E-value=9.8e-14  Score=105.66  Aligned_cols=59  Identities=25%  Similarity=0.604  Sum_probs=50.7

Q ss_pred             CCCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ...+.+.|+||++.+.+|+++ +|||.||..||.+|+..+         . .||+||..+...++.+++.
T Consensus        18 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~l~~n~~   77 (99)
T 2y43_A           18 TIDDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYK---------T-QCPTCCVTVTEPDLKNNRI   77 (99)
T ss_dssp             HHHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTC---------C-BCTTTCCBCCGGGCEECHH
T ss_pred             hCCCCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCC---------C-CCCCCCCcCChhhCCcCHH
Confidence            345678999999999999998 899999999999999854         4 9999999998777776653

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

Probab=99.34  E-value=3.7e-13  Score=95.86  Aligned_cols=55  Identities=33%  Similarity=0.785  Sum_probs=46.8

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      .+...+...|+||++.+.+ ++++|||.||..||.+|+...         . .||+||..+...+.
T Consensus         9 ~~~~~~~~~C~IC~~~~~~-~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A            9 VKQLTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSDRH---------R-NCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCCCCCSSSCCSCCS-EEETTTEEECHHHHHHSSCCC---------S-SCHHHHHCTTCCCC
T ss_pred             hhcCCCCCCCeeCCcCccC-cccCCCCcccHHHHHHHHHCc---------C-cCCCcCCcccCCCc
Confidence            3456678899999999999 999999999999999999843         4 99999999875543

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

Probab=99.34  E-value=3.1e-14  Score=117.14  Aligned_cols=58  Identities=26%  Similarity=0.574  Sum_probs=48.9

Q ss_pred             CCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc-cccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA-SLVPLY  103 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~-~l~p~~  103 (260)
                      ..+.+.|+||++.+.+|++++|||.||..||.+|+....        . .||+||..+... .+.+++
T Consensus        75 l~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~~l~~n~  133 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQV--------F-SCPACRHDLGQNYIMIPNE  133 (150)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTC--------C-BCTTTCCBCCTTCCCCBCH
T ss_pred             CccCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCC--------C-cCCCCCccCCCCCCCCCCH
Confidence            446789999999999999999999999999999998532        4 899999999876 454443

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

Probab=99.33  E-value=1e-12  Score=103.32  Aligned_cols=60  Identities=33%  Similarity=0.609  Sum_probs=52.3

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPL  102 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~  102 (260)
                      .+...+.+.|+||++.+.+|+.++|||.||..||.+|+..+.        . .||+||..+...++.++
T Consensus        12 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~~~~~   71 (118)
T 3hct_A           12 DPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAG--------H-KCPVDNEILLENQLFPD   71 (118)
T ss_dssp             SSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHC--------S-BCTTTCCBCCGGGCEEC
T ss_pred             ccCCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCC--------C-CCCCCCCCcCHHhcccC
Confidence            356778899999999999999999999999999999998753        4 89999999987766554

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

Probab=99.32  E-value=2.1e-12  Score=91.65  Aligned_cols=52  Identities=29%  Similarity=0.753  Sum_probs=43.5

Q ss_pred             CCCCCcccccccccCCC---CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           35 EKDGSFFECNICLDSAQ---DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~---~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +.......|+||++.+.   .++.++|||.||..||.+|+..+         . .||+||..+..
T Consensus         9 ~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~   63 (69)
T 2kiz_A            9 TEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITN---------K-KCPICRVDIEA   63 (69)
T ss_dssp             CSTTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHC---------S-BCTTTCSBSCS
T ss_pred             CcCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcC---------C-CCcCcCccccC
Confidence            44556789999999885   45779999999999999999865         4 89999998864

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

Probab=99.32  E-value=4.7e-13  Score=108.14  Aligned_cols=49  Identities=29%  Similarity=0.813  Sum_probs=43.9

Q ss_pred             CCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+++.|+||++.+.+|++++|||.||..||.+|+..+         . .||+||..+..
T Consensus        51 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~   99 (138)
T 4ayc_A           51 ENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRK---------I-ECPICRKDIKS   99 (138)
T ss_dssp             HHHSBCTTTCSBCSSEEEETTSCEEEHHHHHHHTTTC---------S-BCTTTCCBCCC
T ss_pred             cccCCCcccCcccCCceECCCCCCccHHHHHHHHHcC---------C-cCCCCCCcCCC
Confidence            3467899999999999999999999999999999854         4 89999999864

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

Probab=99.31  E-value=1.8e-12  Score=88.62  Aligned_cols=51  Identities=33%  Similarity=0.834  Sum_probs=42.2

Q ss_pred             CCCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCc
Q 024938           33 VPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC   90 (260)
Q Consensus        33 ~~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvC   90 (260)
                      ..+...+.+.|+||++.+.+|++++|||.||..||.+|+....      ... .||+|
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~------~~~-~CP~C   58 (58)
T 2ecj_A            8 ALENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLE------RDF-PCPVC   58 (58)
T ss_dssp             CSSCSCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSC------CSC-CCSCC
T ss_pred             HhhccccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcC------CCC-CCCCC
Confidence            3455677899999999999999999999999999999976311      124 89998

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

Probab=99.30  E-value=1.8e-12  Score=98.35  Aligned_cols=64  Identities=25%  Similarity=0.493  Sum_probs=51.8

Q ss_pred             CCCcccccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCC--cccc-ccccccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV--CKAN-ISVASLVPLYG  104 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPv--Cr~~-v~~~~l~p~~~  104 (260)
                      ..+.+.||||++.+.+||+++ |||+||..||.+|+....   +..... .||+  |+.. +...+++++..
T Consensus         4 ~~~~~~CPI~~~~~~dPV~~~~cGh~f~r~cI~~~l~~~~---~~~~~~-~CP~tgc~~~~l~~~~L~pn~~   71 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQ---KRKKKA-YCPQIGCSHTDIRKSDLIQDEA   71 (94)
T ss_dssp             CSSCCBCTTTCSBCSSEEEESSSCCEEEHHHHHHHHHHHH---TTTCCB-CCCSTTCCCCCBCGGGEEECHH
T ss_pred             CCcEeECcCcCchhcCCEEcCCCCCeecHHHHHHHHHHcc---CcCCCC-CCCcCcCcccccCHhhCcCCHH
Confidence            456799999999999999996 999999999999998641   001124 8999  9887 88888888764

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.30  E-value=1.6e-12  Score=114.84  Aligned_cols=60  Identities=18%  Similarity=0.275  Sum_probs=53.0

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ...+.+.|+||++.+.+||+++|||+||+.||.+|+....        . .||+|+..+...+++|+..
T Consensus       204 ~~~~~~~c~i~~~~~~dPv~~~~gh~f~~~~i~~~~~~~~--------~-~cP~~~~~~~~~~l~~n~~  263 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVG--------H-FNPVTRSPLTQEQLIPNLA  263 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTC--------S-SCTTTCCCCCGGGCEECHH
T ss_pred             CCCcccCCcCcCCHhcCCeECCCCCEECHHHHHHHHHHCC--------C-CCcCCCCCCchhcCcccHH
Confidence            4557899999999999999999999999999999998542        3 6999999999888888764

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

Probab=99.29  E-value=9.9e-13  Score=101.67  Aligned_cols=60  Identities=35%  Similarity=0.786  Sum_probs=50.0

Q ss_pred             CCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .+.+.|+||++.+.+|+.++|||.||..||.+|+..+.      ... .||+||..+...++.++..
T Consensus        19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~------~~~-~CP~Cr~~~~~~~~~~~~~   78 (112)
T 1jm7_A           19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKK------GPS-QCPLCKNDITKRSLQESTR   78 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSS------SSC-CCTTTSCCCCTTTCBCCCS
T ss_pred             cCCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCC------CCC-CCcCCCCcCCHhhcCccHH
Confidence            45679999999999999999999999999999998542      124 8999999998776665543

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

Probab=99.28  E-value=1.3e-12  Score=100.92  Aligned_cols=52  Identities=23%  Similarity=0.639  Sum_probs=46.0

Q ss_pred             CCCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ...+.+.|+||++.+.+|+.+ +|||.||..||.+|+...         . .||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~---------~-~CP~Cr~~~~~~   63 (108)
T 2ckl_A           11 ELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETS---------K-YCPICDVQVHKT   63 (108)
T ss_dssp             HHGGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSC---------S-BCTTTCCBSCSS
T ss_pred             ccCCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhC---------C-cCcCCCcccccc
Confidence            345788999999999999997 999999999999999854         4 999999998764

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

Probab=99.27  E-value=4.4e-12  Score=91.22  Aligned_cols=53  Identities=25%  Similarity=0.652  Sum_probs=43.8

Q ss_pred             CCCCCCcccccccccCCCCcE---EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDPV---VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pv---vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+...+...|+||++.+.++.   +++|||.||..||.+|+..+         . .||+||..+..
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~---------~-~CP~Cr~~~~~   64 (74)
T 2ep4_A            9 VKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR---------K-VCPLCNMPVLQ   64 (74)
T ss_dssp             CCCCCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC---------S-BCTTTCCBCSS
T ss_pred             cccCCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC---------C-cCCCcCccccc
Confidence            345566789999999997664   45999999999999999865         4 89999998854

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

Probab=99.27  E-value=9.9e-13  Score=102.67  Aligned_cols=53  Identities=28%  Similarity=0.666  Sum_probs=46.3

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ....+.+.|+||++.+.+|++++|||.||..||.+|+....        . .||+||..+..
T Consensus        10 ~~~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~   62 (115)
T 3l11_A           10 IPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKAS--------L-CCPFCRRRVSS   62 (115)
T ss_dssp             CCCHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTT--------S-BCTTTCCBCHH
T ss_pred             cCCCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCc--------C-CCCCCCcccCc
Confidence            45567899999999999999999999999999999997532        4 99999999864

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

Probab=99.27  E-value=1.5e-12  Score=102.80  Aligned_cols=58  Identities=31%  Similarity=0.758  Sum_probs=51.7

Q ss_pred             CCcccccccccCCCCc-------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccC
Q 024938           38 GSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGR  105 (260)
Q Consensus        38 ~~~~~C~ICld~~~~P-------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~  105 (260)
                      .+.+.|+||++.+.+|       +.++|||.||+.||.+|++.+         . .||+||+.+...++.+++..
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~l~~l~i~   69 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---------N-TCPTCRKKINHKRYHPIYIG   69 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTC---------S-BCTTTCCBCTTTCEEECBCS
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhC---------C-CCCCCCCcCccccccccccC
Confidence            4678999999999988       899999999999999999854         4 99999999998888887654

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

Probab=99.26  E-value=1.2e-12  Score=102.37  Aligned_cols=57  Identities=33%  Similarity=0.640  Sum_probs=49.1

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP  101 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p  101 (260)
                      ...+.+.|+||++.+.+|+.++|||.||..||.+|+....        . .||+||..+...++.+
T Consensus        19 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           19 HFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMG--------S-YCPSCRYPCFPTDLES   75 (116)
T ss_dssp             HHHHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTC--------S-BCTTTCCBCCGGGCBC
T ss_pred             hccCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCc--------C-cCCCCCCCCCHhhccc
Confidence            3456789999999999999999999999999999998632        4 8999999998766543

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

Probab=99.25  E-value=4.1e-12  Score=86.09  Aligned_cols=48  Identities=29%  Similarity=0.783  Sum_probs=41.3

Q ss_pred             CCcccccccccCCCC---cEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           38 GSFFECNICLDSAQD---PVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        38 ~~~~~C~ICld~~~~---Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ++...|+||++.+.+   ++.++ |||.||..||.+|++.+         . .||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~---------~-~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH---------S-TCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC---------C-SCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcC---------C-cCcCCCCEeE
Confidence            466799999999987   67787 99999999999999854         4 9999998763

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

Probab=99.25  E-value=3.5e-12  Score=86.32  Aligned_cols=47  Identities=32%  Similarity=0.654  Sum_probs=41.0

Q ss_pred             CcccccccccCCCC----cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQD----PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~----Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      +...|+||++.+.+    +++++|||.||..||.+|+...         . .||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG---------Y-RCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT---------C-CCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC---------C-cCCCCCCcCC
Confidence            46789999999865    7789999999999999999865         3 9999998774

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=99.25  E-value=1.8e-12  Score=107.49  Aligned_cols=52  Identities=31%  Similarity=0.672  Sum_probs=45.1

Q ss_pred             CCCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ...+.+.|+||++.+.+|+.+ +|||.||..||.+|+....        . .||+||..+..
T Consensus        50 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~  102 (165)
T 2ckl_B           50 SLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGN--------K-ECPTCRKKLVS  102 (165)
T ss_dssp             CCHHHHBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHHTTC--------C-BCTTTCCBCCS
T ss_pred             hCCCCCCCcccChHhhCcCEeCCCCChhHHHHHHHHHHhCc--------C-CCCCCCCcCCC
Confidence            455678999999999999987 9999999999999998532        4 89999999853

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

Probab=99.24  E-value=3.4e-12  Score=92.23  Aligned_cols=50  Identities=26%  Similarity=0.692  Sum_probs=43.1

Q ss_pred             CCCcccccccccCCCCc---EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           37 DGSFFECNICLDSAQDP---VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~P---vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..+...|+||++.+.++   +.++|||.||..||.+|+..+         . .||+||+.+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~---------~-~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN---------R-TCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHC---------S-SCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcC---------C-cCcCcCCcCCC
Confidence            44667999999999877   678999999999999999865         4 99999998764

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

Probab=99.24  E-value=4.9e-12  Score=106.96  Aligned_cols=61  Identities=18%  Similarity=0.267  Sum_probs=54.1

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ....+.+.||||++.+.+||+++|||+||..||.+|+....        . .||+|+..+...+++|+..
T Consensus       101 ~~ip~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~--------~-tcP~t~~~l~~~~L~pN~~  161 (179)
T 2f42_A          101 REIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVG--------H-FDPVTRSPLTQDQLIPNLA  161 (179)
T ss_dssp             CCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTC--------S-BCTTTCCBCCGGGCEECHH
T ss_pred             cCCcHhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCC--------C-CCCCCcCCCChhhCcchHH
Confidence            35578999999999999999999999999999999998632        4 7999999999888988864

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

Probab=99.24  E-value=5.4e-12  Score=94.89  Aligned_cols=51  Identities=27%  Similarity=0.665  Sum_probs=43.4

Q ss_pred             CCCCcccccccccCCCC---cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           36 KDGSFFECNICLDSAQD---PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~---Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ...+...|+||++.+.+   ++.++|||.||..||.+|+..+         . .||+||..+..
T Consensus        36 ~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~---------~-~CP~Cr~~~~~   89 (91)
T 2l0b_A           36 AVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS---------G-TCPVCRCMFPP   89 (91)
T ss_dssp             SSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTT---------C-BCTTTCCBSSC
T ss_pred             ccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcC---------C-cCcCcCccCCC
Confidence            34567899999999876   7779999999999999999854         4 99999998753

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

Probab=99.23  E-value=1e-11  Score=87.75  Aligned_cols=47  Identities=30%  Similarity=0.897  Sum_probs=41.7

Q ss_pred             CcccccccccCCCCc-EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQDP-VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~P-vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....|+||++.+.+| +.++|||.||..|+.+|+...         . .||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQN---------P-TCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHS---------C-STTTTCCCCC
T ss_pred             CCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCc---------C-cCcCCChhhH
Confidence            456899999999997 778999999999999999854         4 9999999885

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.20  E-value=3.1e-12  Score=100.37  Aligned_cols=55  Identities=24%  Similarity=0.608  Sum_probs=48.2

Q ss_pred             CCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      +.+.+.|+||++.+.+|+++ +|||.||..||.+|+.           . .||+||..+...++.+++
T Consensus        19 l~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~-----------~-~CP~Cr~~~~~~~~~~n~   74 (117)
T 1jm7_B           19 LEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG-----------T-GCPVCYTPAWIQDLKINR   74 (117)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT-----------T-BCSSSCCBCSCSSCCCCH
T ss_pred             chhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhc-----------C-CCcCCCCcCccccccccH
Confidence            34678999999999999999 9999999999999996           2 899999999776666655

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

Probab=99.18  E-value=3.3e-12  Score=87.67  Aligned_cols=47  Identities=28%  Similarity=0.643  Sum_probs=40.7

Q ss_pred             CCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..+.+.|+||++.+.+|++++|||.||..||.+|.            . .||+||+.+..
T Consensus         3 e~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~------------~-~CP~Cr~~~~~   49 (56)
T 1bor_A            3 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG------------M-QCPICQAPWPL   49 (56)
T ss_dssp             SCCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSSS------------S-SCSSCCSSSSC
T ss_pred             cccCCCceEeCCccCCeEEcCCCCcccHHHHccCC------------C-CCCcCCcEeec
Confidence            34678999999999999999999999999997742            3 89999998864

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

Probab=99.17  E-value=1.7e-11  Score=101.91  Aligned_cols=60  Identities=33%  Similarity=0.609  Sum_probs=52.1

Q ss_pred             CCCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccc
Q 024938           34 PEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPL  102 (260)
Q Consensus        34 ~~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~  102 (260)
                      .+.+.+.+.|+||++.+.+|+.++|||.||..||.+|+..+.        . .||+||..+...++.++
T Consensus        12 ~~~~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~--------~-~CP~Cr~~~~~~~~~~~   71 (170)
T 3hcs_A           12 DPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAG--------H-KCPVDNEILLENQLFPD   71 (170)
T ss_dssp             SSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHC--------S-BCTTTCCBCCGGGCEEC
T ss_pred             ccCCCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCC--------C-CCCCCccCcchhhhhhh
Confidence            346778999999999999999999999999999999998653        4 89999999987665543

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

Probab=99.17  E-value=3.8e-12  Score=103.56  Aligned_cols=52  Identities=29%  Similarity=0.604  Sum_probs=45.9

Q ss_pred             CCCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           35 EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      +..++.+.|+||++.+.+|+.++|||.||..||.+|+....        . .||+||..+.
T Consensus        26 ~~l~~~~~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~--------~-~CP~Cr~~~~   77 (141)
T 3knv_A           26 TKLEAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGP--------Q-NCAACVHEGI   77 (141)
T ss_dssp             GGCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHGGGSC--------E-ECHHHHHTTC
T ss_pred             ccCCcCcCCCCCChhhcCcEECCCCCccCHHHHHHHHhcCC--------C-CCCCCCCccc
Confidence            46678899999999999999999999999999999997542        4 8999999764

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

Probab=99.15  E-value=8.5e-12  Score=98.47  Aligned_cols=58  Identities=31%  Similarity=0.764  Sum_probs=51.4

Q ss_pred             CCCcccccccccCCCCc-------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           37 DGSFFECNICLDSAQDP-------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~P-------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .++...|+||++.+.++       +.++|||.||..||.+|++..         + .||+||..+..+++.++|.
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---------~-~CP~Cr~~~~~~~~~~~~~  133 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---------N-TCPTCRKKINHKRYHPIYI  133 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHC---------S-BCTTTCCBCCGGGEEEECC
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcC---------C-CCCCCCCcCChhcceeeeC
Confidence            34678999999999876       889999999999999999865         4 9999999999999988873

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

Probab=99.15  E-value=2.8e-11  Score=88.91  Aligned_cols=56  Identities=20%  Similarity=0.472  Sum_probs=43.9

Q ss_pred             CCCCCcccccccccCCC--CcEEcc--CCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccc
Q 024938           35 EKDGSFFECNICLDSAQ--DPVVTL--CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASL   99 (260)
Q Consensus        35 ~~~~~~~~C~ICld~~~--~Pvvt~--CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l   99 (260)
                      ...++++.|+||++.+.  ++++++  |||.||..|+.+++...        .. .||+||+.+....+
T Consensus         6 ~~~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~--------~~-~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            6 DAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDE--------NG-LCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSS--------CS-BCTTTCCBCSSCSS
T ss_pred             cccccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcC--------CC-CCCCCCCccCCCch
Confidence            34567899999999884  455555  99999999999987532        24 99999999976544

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

Probab=99.12  E-value=2.8e-11  Score=94.06  Aligned_cols=52  Identities=23%  Similarity=0.510  Sum_probs=40.7

Q ss_pred             cccccccccCCCCcE------------------EccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           40 FFECNICLDSAQDPV------------------VTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        40 ~~~C~ICld~~~~Pv------------------vt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +..|+||++.+.+++                  .++|||.||..||.+|+....    ..... .||+||..+..
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~----~~~~~-~CP~CR~~~~~   94 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN----KDGSL-QCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC----CSSCC-BCTTTCCBSSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHccc----CCCCC-cCCCCCCccCC
Confidence            459999999997654                  688999999999999996421    01224 99999998854

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

Probab=99.09  E-value=7.8e-11  Score=86.74  Aligned_cols=50  Identities=28%  Similarity=0.633  Sum_probs=40.5

Q ss_pred             CcccccccccCCCC--------------cEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccc
Q 024938           39 SFFECNICLDSAQD--------------PVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS   98 (260)
Q Consensus        39 ~~~~C~ICld~~~~--------------Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~   98 (260)
                      +...|+||++.+.+              ++++ .|||.||..||.+|+..+         . +||+||+.+...+
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~---------~-~CP~CR~~~~~~~   78 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN---------N-RCPLCQQDWVVQR   78 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC---------C-BCTTTCCBCCEEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC---------C-CCCCcCCCcchhh
Confidence            45679999988866              4555 499999999999999865         3 9999999986554

>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=99.09  E-value=6e-11  Score=83.19  Aligned_cols=55  Identities=15%  Similarity=0.310  Sum_probs=50.1

Q ss_pred             cccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           40 FFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        40 ~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      .+.|+||++.+.+||++ +|||.|++.||.+|+..+         . +||+++..+..++++++..
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~yer~~I~~~l~~~---------~-~cP~t~~~L~~~~Lip~~~   58 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDT---------G-NDPITNEPLSIEEIVEIVP   58 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHH---------S-BCTTTCCBCCGGGCEECCC
T ss_pred             eEEecCCCCCCCCCEEeCCCCcEEcHHHHHHHHHhC---------C-CCcCCcCCCChhhcEECcc
Confidence            47899999999999999 999999999999999865         4 7999999999999998864

>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=99.03  E-value=1.4e-10  Score=103.04  Aligned_cols=61  Identities=21%  Similarity=0.417  Sum_probs=52.2

Q ss_pred             CCCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCC--ccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPV--CKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPv--Cr~~v~~~~l~p~~~  104 (260)
                      .....+.||||++.+.+||.. .|||.||..||.+|+....       .. .||+  |+..+...+++++..
T Consensus       177 ~~~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~-------~~-~CPvtGCr~~l~~~dL~pN~~  240 (267)
T 3htk_C          177 GGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYT-------TR-DCPQAACSQVVSMRDFVRDPI  240 (267)
T ss_dssp             SSBCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCS-------CE-ECSGGGCSCEECGGGEEECHH
T ss_pred             CCceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCC-------CC-CCCcccccCcCchhhCCcCHH
Confidence            456789999999999999984 9999999999999997431       23 8999  999999888888754

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=99.03  E-value=1.3e-10  Score=108.87  Aligned_cols=53  Identities=32%  Similarity=0.868  Sum_probs=45.7

Q ss_pred             CcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           39 SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      ....|+||++.+.+|+.++|||.||+.|+..|+....        . .||+||..+.....+
T Consensus       331 ~~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~--------~-~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          331 TFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEG--------Q-GCPFCRCEIKGTEPI  383 (389)
T ss_dssp             SSSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTC--------S-BCTTTCCBCCEEEEC
T ss_pred             CCCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCC--------C-CCCCCCCccCCceeE
Confidence            4479999999999999999999999999999998422        4 999999999765543

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

Probab=98.99  E-value=1.2e-10  Score=84.24  Aligned_cols=46  Identities=33%  Similarity=0.655  Sum_probs=41.0

Q ss_pred             CCCcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..+...|+||++.+.+++.++|||. ||..|+.+|    .          .||+||..+..
T Consensus        21 ~~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~----------~CP~Cr~~i~~   67 (74)
T 4ic3_A           21 LQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----D----------KCPMCYTVITF   67 (74)
T ss_dssp             HHHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----S----------BCTTTCCBCSE
T ss_pred             CccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----c----------cCCCcCcCccC
Confidence            3456799999999999999999999 999999988    1          89999999864

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=98.95  E-value=3e-10  Score=80.04  Aligned_cols=54  Identities=30%  Similarity=0.688  Sum_probs=44.6

Q ss_pred             CCcccccccccCCCCcEEc--cCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           38 GSFFECNICLDSAQDPVVT--LCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt--~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      ++...|.||++...+++.+  +|||. +|+.|+.+|...+         . .||+||+.+.  .++.+|
T Consensus         6 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~---------~-~CPiCR~~i~--~~i~i~   62 (64)
T 2vje_A            6 NAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRN---------K-PCPVCRQPIQ--MIVLTY   62 (64)
T ss_dssp             GGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTT---------C-CCTTTCCCCC--EEEEEE
T ss_pred             CCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcC---------C-cCCCcCcchh--ceEeee
Confidence            3566899999999999987  99999 8999999999743         4 8999999985  344443

>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=98.93  E-value=5.5e-10  Score=86.65  Aligned_cols=47  Identities=28%  Similarity=0.704  Sum_probs=39.3

Q ss_pred             cccccccccCCCCc------------------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           40 FFECNICLDSAQDP------------------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        40 ~~~C~ICld~~~~P------------------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ...|+||++.+.++                  +.++|+|.||..||.+|+..+         . .||+||+.+..
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~---------~-~CP~Cr~~~~~  101 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR---------Q-VCPLDNREWEF  101 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTC---------S-BCSSSCSBCCE
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcC---------C-cCcCCCCccee
Confidence            45799999998765                  347899999999999999864         3 99999998653

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.90  E-value=5.3e-10  Score=78.51  Aligned_cols=47  Identities=28%  Similarity=0.726  Sum_probs=41.4

Q ss_pred             CcccccccccCCCCcEEc--cCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQDPVVT--LCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt--~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....|.||++...+++++  +|||. ||+.|+.+|....         . .||+||+.+.
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~---------~-~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAG---------A-SCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTT---------C-BCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhC---------C-cCCCcCchhh
Confidence            456899999999999887  99998 9999999998743         4 8999999985

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

Probab=98.89  E-value=4.5e-10  Score=81.27  Aligned_cols=45  Identities=33%  Similarity=0.705  Sum_probs=39.1

Q ss_pred             CCcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+...|+||++.+.+|+.++|||. ||..|+.++             . .||+||..+..
T Consensus        23 ~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~~-------------~-~CP~Cr~~i~~   68 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV-------------D-KCPMCYTVITF   68 (75)
T ss_dssp             HHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHHC-------------S-BCTTTCCBCCC
T ss_pred             CCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhCC-------------C-CCccCCceecC
Confidence            456789999999999999999999 999999542             3 89999998864

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

Probab=98.80  E-value=4.3e-09  Score=75.04  Aligned_cols=46  Identities=24%  Similarity=0.659  Sum_probs=39.7

Q ss_pred             CCCcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ..+...|.||++...+++.++|||. ||+.|+.+ +            + .||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~-~------------~-~CP~CR~~i~~   58 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKY-F------------Q-QCPMCRQFVQE   58 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHH-C------------S-SCTTTCCCCCC
T ss_pred             CCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhc-C------------C-CCCCCCcchhc
Confidence            3456899999999999999999999 99999973 1            3 89999998864

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

Probab=98.80  E-value=8.3e-09  Score=76.02  Aligned_cols=51  Identities=25%  Similarity=0.658  Sum_probs=41.9

Q ss_pred             CCcccccccccCCC--CcEEccCC-----CccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQ--DPVVTLCG-----HLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~--~Pvvt~CG-----H~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+...|.||++.+.  ++++++|.     |.||..||.+|+..+.       .. .||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~-------~~-~CplCr~~~~~   70 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSD-------TR-CCELCKYEFIM   70 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHC-------CS-BCSSSCCBCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCC-------CC-CCCCCCCeeec
Confidence            34568999998774  67889996     9999999999998753       23 89999998864

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.75  E-value=2.1e-09  Score=78.87  Aligned_cols=45  Identities=24%  Similarity=0.717  Sum_probs=39.7

Q ss_pred             CCcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+...|+||++...+++.++|||. ||..|+.+|.              .||+||..+..
T Consensus        16 ~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~~--------------~CP~Cr~~i~~   61 (79)
T 2yho_A           16 KEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQ--------------SCPVCRSRVEH   61 (79)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTCS--------------BCTTTCCBCCE
T ss_pred             CCCCEeEEeCcccCcEEEECCCCHHHHHHHHHhcC--------------cCCCCCchhhC
Confidence            345689999999999999999999 9999998652              89999999865

>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=98.69  E-value=2.2e-09  Score=84.78  Aligned_cols=47  Identities=30%  Similarity=0.746  Sum_probs=0.4

Q ss_pred             cccccccccCCCCc-----------------EE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           40 FFECNICLDSAQDP-----------------VV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        40 ~~~C~ICld~~~~P-----------------vv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ...|+||++.+.++                 ++ ++|+|.||..||.+|+..+         . .||+||+.+..
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~---------~-~CP~Cr~~~~~  112 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR---------Q-VCPLDNREWEF  112 (117)
T ss_dssp             C--------------------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcC---------C-cCCCCCCeeee
Confidence            35899999998763                 22 4899999999999999865         3 99999998643

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

Probab=98.68  E-value=4.1e-09  Score=79.26  Aligned_cols=61  Identities=16%  Similarity=0.469  Sum_probs=45.2

Q ss_pred             CCcccccccccCCCCcEEc---cCCCccCHHHHHHhhhhhcCCccccc-cCcCCCC--cccc--cccccccc
Q 024938           38 GSFFECNICLDSAQDPVVT---LCGHLYCWPCIYKWLHVQTSSLDADE-QQQNCPV--CKAN--ISVASLVP  101 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt---~CGH~fC~~Ci~~wl~~~~~s~~~~~-~~~~CPv--Cr~~--v~~~~l~p  101 (260)
                      ++.+.|+||++.+.+++.+   +|||.||..||..++..+-   .++. ....||.  |+..  +....+..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i---~~g~~~~i~CP~~~C~~~~~~~~~~i~~   71 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLI---KEGLETAISCPDAACPKQGHLQENEIEC   71 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHH---HHCSCCCEECSCTTCSSCCEECHHHHHH
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHh---hcCCcccccCccccCCCCCccCHHHHHH
Confidence            3578999999999887553   6999999999999998642   1111 2348999  9998  76554443

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.57  E-value=1.4e-08  Score=93.81  Aligned_cols=45  Identities=31%  Similarity=0.756  Sum_probs=40.5

Q ss_pred             CCcccccccccCCCCcEEccCCCc-cCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHL-YCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~-fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      .+...|+||++.+.+|+.++|||. ||..|+.+|    .          .||+||..+..
T Consensus       293 ~~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~----------~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----R----------KCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----S----------BCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----C----------cCCCCCCCccC
Confidence            456899999999999999999999 999999887    1          89999999864

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

Probab=98.38  E-value=5.2e-07  Score=65.44  Aligned_cols=49  Identities=24%  Similarity=0.577  Sum_probs=39.6

Q ss_pred             CcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....|.||.+.+..-..- .|+|.|+..||++|++...       .. +||+|+....
T Consensus        14 ~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~-------~~-~CP~Cr~~w~   63 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNA-------EP-RCPHCNDYWP   63 (74)
T ss_dssp             SSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCS-------SC-CCTTTCSCCC
T ss_pred             CCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcC-------CC-CCCCCcCcCC
Confidence            456999999999865543 7999999999999998642       24 8999998764

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.16  E-value=1.6e-06  Score=60.20  Aligned_cols=50  Identities=20%  Similarity=0.537  Sum_probs=40.2

Q ss_pred             CCcccccccccCCCCcEEccCC--C---ccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCG--H---LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CG--H---~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ++...|.||++...++.+++|.  +   .|+..||.+|+..+.       .. .||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~-------~~-~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISR-------NT-ACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHT-------CS-BCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCC-------CC-ccCCCCCeee
Confidence            3556899999887778788865  4   899999999998652       24 9999998774

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

Probab=98.11  E-value=1.2e-06  Score=80.49  Aligned_cols=60  Identities=28%  Similarity=0.588  Sum_probs=42.6

Q ss_pred             CCCCcccccccccCCCC----cEE----ccCCCccCHHHHHHhhhhhcCCcccc--ccCcCCCCccccccc
Q 024938           36 KDGSFFECNICLDSAQD----PVV----TLCGHLYCWPCIYKWLHVQTSSLDAD--EQQQNCPVCKANISV   96 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~----Pvv----t~CGH~fC~~Ci~~wl~~~~~s~~~~--~~~~~CPvCr~~v~~   96 (260)
                      ..++..+|+||++.+.+    |..    ..|||.|+..||++|+.....+...-  -.. .||.||+.+..
T Consensus       304 ~ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G-~CPyCr~pIs~  373 (381)
T 3k1l_B          304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFG-QCPFCKAKLST  373 (381)
T ss_dssp             CCCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEE-ECTTTCCEEEG
T ss_pred             cccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCC-CCCCCCCcCCc
Confidence            34567799999998876    322    37999999999999998653211110  113 79999998864

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.78  E-value=1.4e-05  Score=60.92  Aligned_cols=48  Identities=19%  Similarity=0.492  Sum_probs=38.1

Q ss_pred             cccccccCCC-CcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccc
Q 024938           42 ECNICLDSAQ-DPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS   98 (260)
Q Consensus        42 ~C~ICld~~~-~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~   98 (260)
                      .|++|.-.+. -.++++|.|.||.+|+..|.+.+.        + .||.|+..+..-+
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~--------k-~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGD--------K-MCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTC--------C-BCTTTCCBCSEEE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccC--------C-CCcCcCCeeeeeE
Confidence            5788876654 367889999999999999987543        5 9999999987543

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=96.59  E-value=0.0014  Score=67.26  Aligned_cols=59  Identities=14%  Similarity=0.087  Sum_probs=53.4

Q ss_pred             CCCCcccccccccCCCCcEEccCC-CccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCG-HLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CG-H~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ...++|.|||-++.+.|||+++.| ++|-+.+|.+|+...         . +||+-|.++...+++|+..
T Consensus       887 ~iP~~F~cPIs~~lM~DPVilpsG~~TydR~~I~~wl~~~---------~-tdP~Tr~~L~~~~liPN~~  946 (968)
T 3m62_A          887 DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSD---------S-TDPFNRMPLKLEDVTPNEE  946 (968)
T ss_dssp             CSCGGGBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTC---------C-BCTTTCCBCCGGGCEECHH
T ss_pred             CCcHHhCCcchhhHHhCCeEcCCCCEEECHHHHHHHHhcC---------C-CCCCCCCCCCcccccccHH
Confidence            556899999999999999999998 599999999999854         4 9999999999999999875

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=96.56  E-value=0.002  Score=56.32  Aligned_cols=49  Identities=24%  Similarity=0.567  Sum_probs=39.6

Q ss_pred             CcccccccccCCCCcEEcc-CCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           39 SFFECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~-CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ....|.||.+.+...+.-+ |+|.|+..|+.+|++...       .. .||.|+....
T Consensus       179 ~i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~-------~~-~CP~C~~~W~  228 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNA-------EP-RCPHCNDYWP  228 (238)
T ss_dssp             TCCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCS-------SC-BCTTTCCBCC
T ss_pred             CCCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCC-------CC-CCCCCCCCCC
Confidence            3568999999998776654 999999999999997542       24 9999988653

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.28  E-value=0.0016  Score=48.76  Aligned_cols=31  Identities=32%  Similarity=0.633  Sum_probs=27.1

Q ss_pred             CcccccccccC-CCCcEE--ccCCCccCHHHHHH
Q 024938           39 SFFECNICLDS-AQDPVV--TLCGHLYCWPCIYK   69 (260)
Q Consensus        39 ~~~~C~ICld~-~~~Pvv--t~CGH~fC~~Ci~~   69 (260)
                      ++..|+||.+. +.+++.  +.|+|.||..|+..
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~   35 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKA   35 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHH
Confidence            45789999975 678888  89999999999987

>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=93.47  E-value=0.11  Score=37.81  Aligned_cols=39  Identities=26%  Similarity=0.706  Sum_probs=31.8

Q ss_pred             CCCcccccccccCCCCcEEccC----CCccCHHHHHHhhhhhc
Q 024938           37 DGSFFECNICLDSAQDPVVTLC----GHLYCWPCIYKWLHVQT   75 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~C----GH~fC~~Ci~~wl~~~~   75 (260)
                      ....+.|.+|.+.+++-....|    +|.||++|-...++.+.
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q~   54 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQG   54 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHH
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhcC
Confidence            3567899999999998654444    69999999999998764

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=89.15  E-value=0.24  Score=45.81  Aligned_cols=59  Identities=27%  Similarity=0.553  Sum_probs=42.6

Q ss_pred             CCCCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      ...-.+.|||-...+..|+. ..|.|+-|++- ..|+....     ....+.||+|.+.+...+|.
T Consensus       245 s~~vSL~CPlS~~ri~~PvRg~~C~HlQCFDl-~sfL~~~~-----~~~~W~CPIC~k~~~~~dL~  304 (371)
T 3i2d_A          245 STIMSLQCPISYTRMKYPSKSINCKHLQCFDA-LWFLHSQL-----QIPTWQCPVCQIDIALENLA  304 (371)
T ss_dssp             EEEEESBCTTTSSBCSSEEEETTCCSSCCEEH-HHHHHHHH-----HSCCCBCTTTCCBCCGGGEE
T ss_pred             eeEEeecCCCccccccccCcCCcCCCcceECH-HHHHHHhh-----cCCceeCCCCCcccCHHHee
Confidence            33456899999999999987 57999988875 34555331     12357999999998765543

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=88.72  E-value=0.35  Score=44.55  Aligned_cols=59  Identities=22%  Similarity=0.443  Sum_probs=43.2

Q ss_pred             CCCCcccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      ...-.+.|||-...+..|+. ..|.|.-|++-. .|+....     ....+.||+|.+.+..++|.
T Consensus       211 ~~~vSL~CPlS~~ri~~P~Rg~~C~HlqCFDl~-sfL~~~~-----~~~~W~CPiC~k~~~~~dL~  270 (360)
T 4fo9_A          211 SLRVSLMCPLGKMRLTIPCRAVTCTHLQCFDAA-LYLQMNE-----KKPTWICPVCDKKAAYESLI  270 (360)
T ss_dssp             CEEEESBCTTTCSBCSSEEEETTCCCCCCEEHH-HHHHHHH-----HSCCCBCTTTCSBCCGGGEE
T ss_pred             eeEEeeeCCCccceeccCCcCCCCCCCccCCHH-HHHHHHh-----hCCCeECCCCCcccCHHHeE
Confidence            34456899999999999986 579999888743 4555332     12357999999998866654

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=85.55  E-value=3.4  Score=30.50  Aligned_cols=50  Identities=34%  Similarity=0.557  Sum_probs=34.7

Q ss_pred             CcccccccccCCC-----CcEEc--cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           39 SFFECNICLDSAQ-----DPVVT--LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        39 ~~~~C~ICld~~~-----~Pvvt--~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ....|.||-|.+-     ++.+.  .|+-..|.+|+.-=.+.        +.+ .||.|+......
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErke--------G~q-~CpqCktrYkr~   71 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERRE--------GTQ-NCPQCKTRYKRL   71 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHT--------SCS-SCTTTCCCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhc--------cCc-cccccCCccccc
Confidence            4579999999863     23232  58888999998543332        224 999999988644

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=82.97  E-value=1.5  Score=30.33  Aligned_cols=47  Identities=21%  Similarity=0.588  Sum_probs=32.4

Q ss_pred             CcccccccccCCCCcEEc--cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccc
Q 024938           39 SFFECNICLDSAQDPVVT--LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKAN   93 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt--~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~   93 (260)
                      ....|.||.+.- + +++  .|...||..|+...+..-.      ...+.|+.|++.
T Consensus        11 ~~~~C~vC~~~~-~-ll~Cd~C~~~~H~~Cl~P~l~~~P------~g~W~C~~C~~~   59 (66)
T 2lri_C           11 PGARCGVCGDGT-D-VLRCTHCAAAFHWRCHFPAGTSRP------GTGLRCRSCSGD   59 (66)
T ss_dssp             TTCCCTTTSCCT-T-CEECSSSCCEECHHHHCTTTCCCC------SSSCCCTTTTTC
T ss_pred             CCCCcCCCCCCC-e-EEECCCCCCceecccCCCccCcCC------CCCEECccccCC
Confidence            445799998642 2 222  5889999999987765332      335799999754

---

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	260
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	8e-14
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-13
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-13
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	9e-12
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-11
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	9e-10
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	1e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-07
d2c2la2	80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	8e-07
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-06
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-06
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	9e-06
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	2e-05
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	4e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	5e-05
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	0.001

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 8e-14
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
              EC ICL+  ++PV T C H++C  C+ K L+ +       +    CP+CK +I+  S
Sbjct: 20  KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQK-------KGPSQCPLCKNDITKRS 72

Query: 99  LVP 101
           L  
Sbjct: 73  LQE 75

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 2e-13
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 9/68 (13%)

Query: 35  EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI 94
           E   +F  C IC ++ +D  +  CGHL C  C+  W            + Q CP C+  I
Sbjct: 18  EMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQE---------SEGQGCPFCRCEI 68

Query: 95  SVASLVPL 102
                + +
Sbjct: 69  KGTEPIVV 76

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.9 bits (150), Expect = 2e-13
 Identities = 23/81 (28%), Positives = 27/81 (33%), Gaps = 9/81 (11%)

Query: 21  KQKWSPTSAPTNVPEKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDA 80
           K   S      + P        C IC     DPV T C HL+C  CI + L V  S    
Sbjct: 4   KIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY--- 60

Query: 81  DEQQQNCPVCKANISVASLVP 101
                 CP C+       L  
Sbjct: 61  ------CPSCRYPCFPTDLES 75

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.8 bits (137), Expect = 9e-12
 Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 13/67 (19%)

Query: 35  EKDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI 94
           E++  F  C  C   A+ P +  C H  C  C+                   CP+C+A  
Sbjct: 1   EEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS-------------GMQCPICQAPW 47

Query: 95  SVASLVP 101
            + +  P
Sbjct: 48  PLGADTP 54

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 56.1 bits (135), Expect = 2e-11
 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 11/55 (20%)

Query: 42 ECNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
           C ICL+   +  + L C H +C+ CI +W+           Q   CP+CK  + 
Sbjct: 7  RCPICLEDPSNYSMALPCLHAFCYVCITRWI----------RQNPTCPLCKVPVE 51

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 51.0 bits (122), Expect = 9e-10
 Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 14/59 (23%)

Query: 42 ECNICLDSAQDP----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV 96
          EC +CL   +D      +  CGH +   C+  WL               CP+C+  + V
Sbjct: 7  ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWL----------GSHSTCPLCRLTVVV 55

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

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]

 Score = 48.5 bits (115), Expect = 1e-08
 Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 9/63 (14%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
            +F C I L+  +DPV+   G  Y    I KWL         D   + CP  +  +  A 
Sbjct: 7   EYFRCPISLELMKDPVIVSTGQTYERSSIQKWL---------DAGHKTCPKSQETLLHAG 57

Query: 99  LVP 101
           L P
Sbjct: 58  LTP 60

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 43.7 bits (102), Expect = 4e-07
 Identities = 9/66 (13%), Positives = 17/66 (25%), Gaps = 13/66 (19%)

Query: 36 KDGSFFECNICLDSAQDPVVTL-----CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVC 90
          +D     C IC +   +                  C+  WL +         +   C +C
Sbjct: 2  EDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTIS--------RNTACQIC 53

Query: 91 KANISV 96
              + 
Sbjct: 54 GVVYNT 59

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

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]

 Score = 43.7 bits (102), Expect = 8e-07
 Identities = 8/62 (12%), Positives = 19/62 (30%)

Query: 39  SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
            +    I  +  ++P +T  G  Y    I + L                     N+++  
Sbjct: 6   DYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKE 65

Query: 99  LV 100
           ++
Sbjct: 66  VI 67

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 11/63 (17%), Positives = 20/63 (31%), Gaps = 13/63 (20%)

Query: 40  FFECNICLDS-AQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS 98
              C+ C +   +   +  C H++C  C+   +               CPVC     +  
Sbjct: 22  LLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG------------CPVCYTPAWIQD 69

Query: 99  LVP 101
           L  
Sbjct: 70  LKI 72

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 4e-06
 Identities = 12/59 (20%), Positives = 17/59 (28%), Gaps = 14/59 (23%)

Query: 42 ECNICLDSAQDP-----VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
           C  C  +         +V +CGH  C  C+                  NCP C   + 
Sbjct: 5  GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF---------VRGAGNCPECGTPLR 54

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 9e-06
 Identities = 10/58 (17%), Positives = 19/58 (32%), Gaps = 13/58 (22%)

Query: 42 ECNICLD----SAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS 95
          EC +C++       +     CG+  C  C ++    +            CP C+    
Sbjct: 2  ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENG---------LCPACRKPYP 50

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.0 bits (90), Expect = 2e-05
 Identities = 8/62 (12%), Positives = 22/62 (35%), Gaps = 11/62 (17%)

Query: 43  CNICLDSAQDPVVTL-CGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVP 101
           C I     + PV++     ++    + +++              N P+    +S+  +V 
Sbjct: 3   CAISGKVPRRPVLSPKSRTIFEKSLLEQYVK----------DTGNDPITNEPLSIEEIVE 52

Query: 102 LY 103
           + 
Sbjct: 53  IV 54

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 4e-05
 Identities = 9/51 (17%), Positives = 16/51 (31%), Gaps = 10/51 (19%)

Query: 42 ECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKA 92
                         +C H + + CI +WL          + +Q CP+   
Sbjct: 41 NQASATSEECTVAWGVCNHAFHFHCISRWL----------KTRQVCPLDNR 81

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 5/54 (9%)

Query: 41 FECNICLD---SAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK 91
            C +CL      Q   +  C  ++C  C+ +++ +     +  E   +CP   
Sbjct: 6  SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIK--EGLETAISCPDAA 57

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (81), Expect = 0.001
 Identities = 10/61 (16%), Positives = 19/61 (31%), Gaps = 5/61 (8%)

Query: 54  VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGRGGISSASD 113
            +T C H +   C+              +    CP CK      +    +G+  +  +  
Sbjct: 57  RLTKCSHAFHLLCLLAMYCNGNK-----DGSLQCPSCKTIYGEKTGTQPWGKMEVFRSGP 111

Query: 114 S 114
           S
Sbjct: 112 S 112

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	260
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.49
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.48
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.48
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.47
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.43
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.3
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.3
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.29
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.29
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.28
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.27
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.24
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.05
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.93
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.82
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.28
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	93.85
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	80.61

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=5.4e-15  Score=109.18  Aligned_cols=55  Identities=35%  Similarity=0.657  Sum_probs=48.0

Q ss_pred             CCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      ..+.+.|+||++.+.+|++++|||.||+.||.+|++.+.        + +||+||.++...++.
T Consensus        20 ~~~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~--------~-~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          20 FVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMG--------S-YCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTC--------S-BCTTTCCBCCGGGCB
T ss_pred             hccCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCC--------C-cCcccCCCCChhhcc
Confidence            345689999999999999999999999999999998653        5 899999998876654

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.48  E-value=1.2e-14  Score=104.88  Aligned_cols=61  Identities=31%  Similarity=0.608  Sum_probs=53.8

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccccC
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYGR  105 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~~  105 (260)
                      ...++|.|+||++.+.+||+++|||+||..||.+|+....        . .||.|+..+...+++++...
T Consensus         4 eiP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~~~~~--------~-~cP~~~~~l~~~~l~pN~~L   64 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGH--------K-TCPKSQETLLHAGLTPNYVL   64 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTC--------C-BCTTTCCBCSSCCCEECTTT
T ss_pred             CCCccCCCcCcCchhhCceEccCCCcchHHHHHHHHHHCC--------C-CCCcccccCCcccccchHHH
Confidence            4568899999999999999999999999999999998542        4 89999999998888887653

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.48  E-value=8.6e-15  Score=99.53  Aligned_cols=53  Identities=15%  Similarity=0.332  Sum_probs=48.3

Q ss_pred             ccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           41 FECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        41 ~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      +.|+||++.+.+||++ .|||.||+.||.+|+..+         . +||+||..+..++++++.
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~---------~-~CP~c~~~l~~~dLipik   54 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDT---------G-NDPITNEPLSIEEIVEIV   54 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHH---------S-BCTTTCCBCCGGGCEECC
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhc---------c-CCCccCCcCCHHhceeCC
Confidence            4799999999999987 599999999999999976         4 899999999999998865

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=1.3e-14  Score=105.26  Aligned_cols=60  Identities=18%  Similarity=0.275  Sum_probs=53.0

Q ss_pred             CCCCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ...+++.|+||++.+.+||+++|||+||..||.+|+....        . .||+|+..+...++.+++.
T Consensus         3 eiP~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~--------~-~cP~c~~~l~~~~l~pN~~   62 (80)
T d2c2la2           3 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVG--------H-FNPVTRSPLTQEQLIPNLA   62 (80)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTC--------S-SCTTTCCCCCGGGCEECHH
T ss_pred             CCCccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCC--------c-cCCCccccccccccccHHH
Confidence            3457899999999999999999999999999999997542        4 8999999999888888764

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=4e-14  Score=102.70  Aligned_cols=50  Identities=34%  Similarity=0.905  Sum_probs=43.8

Q ss_pred             cccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccc
Q 024938           40 FFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS   98 (260)
Q Consensus        40 ~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~   98 (260)
                      ...|+||++.+.+|++++|||.||..||.+|+..+.        + .||+||..+...+
T Consensus        23 ~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~wl~~~~--------~-~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEG--------Q-GCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBCCEECSSSCCEECHHHHHHHHHTTC--------C-SCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCCCeEEeCCCCeeeHHHHHHHHHHCc--------C-cCCCCCcCccCCc
Confidence            347999999999999999999999999999997542        4 8999999997654

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.9e-14  Score=109.15  Aligned_cols=60  Identities=35%  Similarity=0.786  Sum_probs=50.2

Q ss_pred             CCcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ++.+.|+||++.+.+|+.++|||.||..||.+|+....      ... .||+||..+...++.+++.
T Consensus        19 ~~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~------~~~-~CP~Cr~~~~~~~l~~n~~   78 (103)
T d1jm7a_          19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKK------GPS-QCPLCKNDITKRSLQESTR   78 (103)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSS------SSC-CCTTTSCCCCTTTCBCCCS
T ss_pred             ccCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCC------CCC-cCcCCCCcCChhhCCcCHH
Confidence            45689999999999999999999999999999997542      123 8999999998777766543

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.30  E-value=5.6e-13  Score=93.71  Aligned_cols=46  Identities=30%  Similarity=0.915  Sum_probs=40.0

Q ss_pred             cccccccccCCCCcEE-ccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           40 FFECNICLDSAQDPVV-TLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        40 ~~~C~ICld~~~~Pvv-t~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ...|+||++.+.++++ ++|||.||..||.+|++.+         . +||+||..+.
T Consensus         5 ~d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~---------~-~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQN---------P-TCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHS---------C-STTTTCCCCC
T ss_pred             CCCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHhC---------C-cCCCCCcchH
Confidence            3479999999988755 7999999999999999865         4 9999999874

>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=99.30  E-value=1.1e-12  Score=98.68  Aligned_cols=59  Identities=19%  Similarity=0.132  Sum_probs=51.9

Q ss_pred             CCCCcccccccccCCCCcEEccCCC-ccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccccccc
Q 024938           36 KDGSFFECNICLDSAQDPVVTLCGH-LYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLYG  104 (260)
Q Consensus        36 ~~~~~~~C~ICld~~~~Pvvt~CGH-~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~~  104 (260)
                      ...++|.||||++++.+||+++||| .||+.||.+|+..+         . .||+|+..+..++++++..
T Consensus        18 ~~P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~---------~-~~P~~~~~l~~~~L~pN~~   77 (98)
T d1wgma_          18 DACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSD---------Q-TDPFNRSPLTMDQIRPNTE   77 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTS---------C-BCTTTCSBCCTTTSEECHH
T ss_pred             CCcHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhc---------C-CcccccccccchhhcchHH
Confidence            4456899999999999999998775 89999999999854         4 8999999999999988765

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=2e-13  Score=92.73  Aligned_cols=47  Identities=28%  Similarity=0.672  Sum_probs=40.9

Q ss_pred             CcccccccccCCCCcEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccc
Q 024938           39 SFFECNICLDSAQDPVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVAS   98 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~   98 (260)
                      +.+.|+||++.+.+|++++|||.||..||.+|.            . +||+||..+....
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~~~------------~-~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG------------M-QCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSSS------------S-SCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCCCEEecCCCHHhHHHHHcCC------------C-cCcCCCCcccCCC
Confidence            457999999999999999999999999997652            3 8999999987543

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=2.7e-13  Score=101.59  Aligned_cols=55  Identities=24%  Similarity=0.608  Sum_probs=47.0

Q ss_pred             CCCcccccccccCCCCcEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccccccccc
Q 024938           37 DGSFFECNICLDSAQDPVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLVPLY  103 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~p~~  103 (260)
                      +.+.+.|+||++.+.+||.+ +|||.||..||.+|+.           . .||+||..+...++.++.
T Consensus        19 l~~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~-----------~-~CP~Cr~~~~~~~l~~n~   74 (97)
T d1jm7b_          19 LEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG-----------T-GCPVCYTPAWIQDLKINR   74 (97)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT-----------T-BCSSSCCBCSCSSCCCCH
T ss_pred             hhhcCCCccCCchhhcCceeCCCCCchhHHHHHHHHh-----------c-cccccCCcCchhhCcccH
Confidence            34568999999999999875 8999999999999995           3 799999998877776654

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=5.5e-13  Score=93.04  Aligned_cols=53  Identities=23%  Similarity=0.531  Sum_probs=41.9

Q ss_pred             CcccccccccCCCC-----cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccccccc
Q 024938           39 SFFECNICLDSAQD-----PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVASLV  100 (260)
Q Consensus        39 ~~~~C~ICld~~~~-----Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~~l~  100 (260)
                      ++..|+||++.+..     .++++|||.||..||.+|+...+        . .||+||+.+...++.
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~--------~-~CP~CR~~i~~~~~~   59 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGA--------G-NCPECGTPLRKSNFR   59 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTS--------S-SCTTTCCCCSSCCCE
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCc--------C-CCCCCCcCccccccc
Confidence            45799999986532     25679999999999999997542        4 899999998766543

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.27  E-value=1.1e-12  Score=88.65  Aligned_cols=48  Identities=29%  Similarity=0.770  Sum_probs=39.6

Q ss_pred             CCCcccccccccCCCC---cEEc-cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccc
Q 024938           37 DGSFFECNICLDSAQD---PVVT-LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANI   94 (260)
Q Consensus        37 ~~~~~~C~ICld~~~~---Pvvt-~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v   94 (260)
                      +++..+|+||++.+.+   .+.+ .|||.||..||.+|++.+         . .||+||+.+
T Consensus         2 ~ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~---------~-~CP~CR~~i   53 (55)
T d1iyma_           2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH---------S-TCPLCRLTV   53 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC---------C-SCSSSCCCS
T ss_pred             CCCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhC---------C-cCCCCCCEe
Confidence            3566789999999975   3444 699999999999999865         4 999999876

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=1.1e-12  Score=87.62  Aligned_cols=47  Identities=21%  Similarity=0.530  Sum_probs=38.7

Q ss_pred             ccccccccCCCC----cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           41 FECNICLDSAQD----PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        41 ~~C~ICld~~~~----Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ++|+||++.+.+    ++.++|||.||..||.+|+..++        . +||+||+++.+
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~--------~-~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDEN--------G-LCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSC--------C-BCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcC--------C-CCCccCCcCCC
Confidence            479999998853    34468999999999999998643        4 89999998864

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.05  E-value=1.5e-10  Score=88.40  Aligned_cols=52  Identities=23%  Similarity=0.504  Sum_probs=39.0

Q ss_pred             cccccccccCCCCc------------------EEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           40 FFECNICLDSAQDP------------------VVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        40 ~~~C~ICld~~~~P------------------vvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      +..|+||++.+.++                  ++++|||.||..||..|+..+.    ..... +||+||+.+..
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~----~~~~~-~CP~CR~~~~~   94 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN----KDGSL-QCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC----CSSCC-BCTTTCCBSSS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcC----cCCCC-ccccccchhcc
Confidence            45799999887532                  4578999999999999998642    11123 89999987743

>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=98.93  E-value=2.5e-10  Score=83.73  Aligned_cols=47  Identities=28%  Similarity=0.705  Sum_probs=37.3

Q ss_pred             ccccccccCCCC------------------cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcccccccc
Q 024938           41 FECNICLDSAQD------------------PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISVA   97 (260)
Q Consensus        41 ~~C~ICld~~~~------------------Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~~   97 (260)
                      ..|+||++.+.+                  .+.++|||.||..||.+|++.+         . +||+||+.....
T Consensus        22 d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~---------~-~CP~CR~~~~~~   86 (88)
T d3dplr1          22 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR---------Q-VCPLDNREWEFQ   86 (88)
T ss_dssp             CCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTC---------S-BCSSSCSBCCEE
T ss_pred             CcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHC---------C-cCCCCCCccccc
Confidence            358888776643                  2457899999999999999865         4 999999987643

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=98.82  E-value=1.2e-09  Score=74.38  Aligned_cols=50  Identities=18%  Similarity=0.476  Sum_probs=41.0

Q ss_pred             CCcccccccccCCCCcEEccC-----CCccCHHHHHHhhhhhcCCccccccCcCCCCcccccc
Q 024938           38 GSFFECNICLDSAQDPVVTLC-----GHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANIS   95 (260)
Q Consensus        38 ~~~~~C~ICld~~~~Pvvt~C-----GH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~   95 (260)
                      ++...|.||++.+.++.+.+|     +|.||..||.+|+..+.       .. +||+||+.+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~-------~~-~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISR-------NT-ACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHT-------CS-BCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCC-------CC-CCcccCCeee
Confidence            456789999999888877665     49999999999997653       24 8999999875

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.28  E-value=1.3e-07  Score=69.13  Aligned_cols=51  Identities=18%  Similarity=0.538  Sum_probs=36.3

Q ss_pred             CcccccccccCCCC---cEEccCCCccCHHHHHHhhhhhcCCccccccCcCCCCcc
Q 024938           39 SFFECNICLDSAQD---PVVTLCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCK   91 (260)
Q Consensus        39 ~~~~C~ICld~~~~---Pvvt~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr   91 (260)
                      ....|+||++.+..   ++.+.|||.||..||..|+..+-.  +......+||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~--~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIK--EGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHH--HCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHh--cCCccccCCcCCC
Confidence            45799999998753   445689999999999999986521  0111223799854

>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=93.85  E-value=0.032  Score=37.93  Aligned_cols=37  Identities=27%  Similarity=0.721  Sum_probs=30.5

Q ss_pred             CcccccccccCCCCcEEccC----CCccCHHHHHHhhhhhc
Q 024938           39 SFFECNICLDSAQDPVVTLC----GHLYCWPCIYKWLHVQT   75 (260)
Q Consensus        39 ~~~~C~ICld~~~~Pvvt~C----GH~fC~~Ci~~wl~~~~   75 (260)
                      ..+.|.+|.+.++|-....|    +|.||.+|-...++.+.
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~q~   47 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQG   47 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHhcC
Confidence            45899999999998654444    69999999999998775

>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=80.61  E-value=2.7  Score=29.02  Aligned_cols=49  Identities=35%  Similarity=0.576  Sum_probs=34.3

Q ss_pred             CcccccccccCCC-----CcEEc--cCCCccCHHHHHHhhhhhcCCccccccCcCCCCccccccc
Q 024938           39 SFFECNICLDSAQ-----DPVVT--LCGHLYCWPCIYKWLHVQTSSLDADEQQQNCPVCKANISV   96 (260)
Q Consensus        39 ~~~~C~ICld~~~-----~Pvvt--~CGH~fC~~Ci~~wl~~~~~s~~~~~~~~~CPvCr~~v~~   96 (260)
                      ....|.||-|.+-     ++.+.  .|+--.|.+|..==.+.        +.+ .||.|+.....
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErke--------G~q-~CpqCkt~Ykr   70 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERRE--------GTQ-NCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHT--------SCS-SCTTTCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhc--------cCc-cCcccCChhhh
Confidence            4579999999874     23332  58888999998533332        235 99999988754