Citrus Sinensis ID: 043965

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340--
Protein Sequence
MGDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSESSSVGTAAHIDET
Secondary Structure (PSIPRED)
cccccccEEEcccccEEEccccccccccccccccEEcccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHcccccccccccccHHHcccccccccccccHHHHHHHccccccccccccccccHHHHHHHHHHccccccccccccHHHHHcccEEEEcccccccccccccccccEEEEcccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEccEEEccccccccEccccccccEEEccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccHHcccccHHHHHHHHHHccccccccccccHHHHHccccEEEcccccccccHHHccccHHHcccccccccccccEcHHHHHccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MGDAMVGYWCYICSQmvnprmeagikcpfcesgiveqmsssiagdsindgihvRSDRALSLWASILLRMMtglspsrpriaahehfnnanprveeAEQEREFESLLTRRMRRNSSASLSRMLQDIRFgitsrsdgpealRERSGslilvnpmneealiiqdhnttsslgeylvgpgLDLLLQHLlendpnrygcpaanKAVLKAlptvtidknlqcAVCLEefeigneakempckhkfhgecimpwlevrsscpvcrfqvpsddfkiqgngsgnrdeslgnedaqnnlrlgngedrvgngrrywipipwpfdslfsmsgsqeggtsnsesssvgtaahidet
Flexible Loop (DISEMBL)
MGDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILLRMMTGLSPSRPRIAAHEHFnnanprveeaeqEREFESLLTRRMRRNSSASLSRMLQDIrfgitsrsdgpeaLRERSGSLILVNPMNEEALIIQDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPsddfkiqgngsgnrdeslgnedaqnnlrlgngedrvgngRRYWIPIPWPFDSLFSMSGSQEggtsnsesssvgtaahidet
Low Complexity Region (SEG)
MGDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVeeaeqerefeSLLTRRMRRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYlvgpgldlllqhllENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSESSSVGTAAHIDET
Disordered region (IsUnstruct)
****MVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILLRMMTG*************************************************************************LILVNPMNEEALIIQDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS**********************************VGNGRRYWIPIPWPFDSLF***************************
Disordered Region (DISOPRED)
***AMVG*WCYICSQMVNPRMEAGIKCPFCESGIVEQMS*********************************************************************************MLQD**********************ILVNPMNEE***IQDHNTTSSLGEYLVGPGLDLLLQH*****************VLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV**********************************************************************************
Disordered Region (DISEMBL)
MGDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILLRMMTGLSPSRPRIAAHEHFNNAN************ESLLTRRMRRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSM*************************
Disordered Region (DISPRO)
****MVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSS******************LSLWASILLRMMTGLSP**P******************************************MLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV**********************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSESSSVGTAAHIDET
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	342	2.2.26 [Sep-21-2011]
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.771	0.804	0.309	3e-36
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.421	0.426	0.480	9e-36
Q9D0C1	305	E3 ubiquitin-protein liga	yes	no	0.754	0.845	0.284	7e-22
Q9Y4L5	304	E3 ubiquitin-protein liga	yes	no	0.687	0.773	0.286	4e-20
Q91YL2	313	RING finger protein 126 O	no	no	0.672	0.734	0.290	8e-19
Q6IRP0	312	RING finger protein 126-B	N/A	no	0.707	0.775	0.269	1e-17
Q9BV68	326	RING finger protein 126 O	no	no	0.701	0.736	0.285	3e-17
Q0II22	313	RING finger protein 126 O	no	no	0.672	0.734	0.279	4e-17
Q7T0Q3	312	RING finger protein 126-A	N/A	no	0.707	0.775	0.265	3e-16
Q7ZW78	156	E3 ubiquitin-protein liga	no	no	0.204	0.448	0.506	5e-16

>sp|Q8LPN7|RNG1L_ARATH E3 ubiquitin-protein ligase RING1-like OS=Arabidopsis thaliana GN=At3g19950 PE=2 SV=1

 Score =  152 bits (385), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 99/320 (30%), Positives = 151/320 (47%), Gaps = 56/320 (17%)

Query: 8   YWCYICSQMVNPRMEAGIK--CPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLW--A 63
           ++CY C+Q V   + +     CP C  G +E+        S+N   +  SD    +    
Sbjct: 21  FFCYQCNQTVTISISSSADPFCPICNQGFLEEYEDPNPNQSLNFNPN-SSDSFFPMADPF 79

Query: 64  SILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLSRMLQ 123
           S LL ++ G S + P                      +F SL    M+  + ++      
Sbjct: 80  STLLPLIFGSSAAAPS-------------------GMDFMSLFGPSMQPQARSTQQNPQS 120

Query: 124 DIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNT------TSSLGEYLVGPGL 177
           D     T   +  + LR  SG+            +I++H +        + G+Y  GPGL
Sbjct: 121 DAFDPFTFLQNHLQTLRS-SGTHF--------EFVIENHPSDPGNRMPGNFGDYFFGPGL 171

Query: 178 DLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNL------QCAVCLEEFEIGNEAKE 231
           + L+Q L ENDPNRYG P A+K+ + ALPTV + K++      QCAVC++EFE G++ K+
Sbjct: 172 EQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCMDEFEDGSDVKQ 231

Query: 232 MPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQNNLRLG 291
           MPCKH FH +C++PWLE+ +SCPVCRF++P+DD   +     NR +             G
Sbjct: 232 MPCKHVFHQDCLLPWLELHNSCPVCRFELPTDDPDYE-----NRSQGSQGSGDGQGSVEG 286

Query: 292 NGEDRVGNGRRYWIPIPWPF 311
                     R+ I +PWPF
Sbjct: 287 Q------QTPRFSIQLPWPF 300

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|P0CH30|RING1_GOSHI E3 ubiquitin-protein ligase RING1 OS=Gossypium hirsutum GN=RING1 PE=2 SV=1

 Score =  150 bits (380), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 73/152 (48%), Positives = 106/152 (69%), Gaps = 8/152 (5%)

Query: 166 SSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDK-NL-----QCAVC 219
           +++G+Y +GPGL+ L+Q L ENDPNRYG P A+K+ ++ALP V I K NL     QCAVC
Sbjct: 168 ANIGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFNQCAVC 227

Query: 220 LEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESL 279
           +++FE G EAK+MPCKH +H +C++PWLE+ +SCPVCR ++P+DD   +    G +  S 
Sbjct: 228 MDDFEEGTEAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELPTDDPDYERRVRGAQGTSG 287

Query: 280 GNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPF 311
           GN D  N+ +  +G++R    R + I +PWPF
Sbjct: 288 GN-DGDNSGQRSDGDNRTVE-RSFRISLPWPF 317

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.

Gossypium hirsutum (taxid: 3635)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9D0C1|RN115_MOUSE E3 ubiquitin-protein ligase RNF115 OS=Mus musculus GN=Rnf115 PE=1 SV=1

 Score =  104 bits (260), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 137/299 (45%), Gaps = 41/299 (13%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS--SSIAGDSINDGIHVRSDRALSLWASI 65
           ++C+ C   VNP++   I CP C+SG +E+++  SS  G   +   +  +     LW  +
Sbjct: 20  FFCHFCKGEVNPKLPEYI-CPRCDSGFIEEVTDDSSFLGGGGSRTDNSTATHFAELWDHL 78

Query: 66  LLRMMTGLSPSRPRIAAH--EHFNNANPRVEEAEQE-----REFESLLTRRMRRNSSASL 118
              M   L   RP ++++  +  N AN R  +   +     R     +TRR R   S   
Sbjct: 79  DHTMF--LQDFRPFLSSNPLDQDNRANERGHQTHTDFWGPSRPPRLPMTRRYRSRGSTRP 136

Query: 119 SR------MLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYL 172
            R      ++Q I  G  + S  P +    S S +L                 S+ G+Y 
Sbjct: 137 DRSPAIEGIIQQIFAGFFANSAIPGSPHPFSWSGML----------------HSNPGDYA 180

Query: 173 VG-PGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTI-----DKNLQCAVCLEEFEIG 226
            G  GLD ++  LL    N  G P A+K  + +LPTVT+     +  L+C VC E++ + 
Sbjct: 181 WGQTGLDAIVTQLLGQLENT-GPPPADKEKITSLPTVTVTQEQVNTGLECPVCKEDYTVE 239

Query: 227 NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQ 285
            + +++PC H FH  CI+PWLE+  +CPVCR  +  +D   Q   S     +  + D+Q
Sbjct: 240 EKVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSLNGEDSTRQTQSSEASASNRFSNDSQ 298

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9Y4L5|RN115_HUMAN E3 ubiquitin-protein ligase RNF115 OS=Homo sapiens GN=RNF115 PE=1 SV=2

 Score = 99.0 bits (245), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 80/279 (28%), Positives = 128/279 (45%), Gaps = 44/279 (15%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS--SSIAGDSINDGIHVRSDRALSLWASI 65
           ++C+ C   V+P++   I CP CESG +E+++  SS  G   +   +  +     LW  +
Sbjct: 20  FFCHFCKGEVSPKLPEYI-CPRCESGFIEEVTDDSSFLGGGGSRIDNTTTTHFAELWGHL 78

Query: 66  LLRMMTGLSPSRPRIAAH--EHFNNANPRVEEAEQEREFESLLTRRM------------R 111
              M       RP +++   +  N AN R  +   +  F      R+            R
Sbjct: 79  DHTMF--FQDFRPFLSSSPLDQDNRANERGHQTHTD--FWGARPPRLPLGRRYRSRGSSR 134

Query: 112 RNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEY 171
            + S ++  +LQ I  G  + S  P +    S S +L                 S+ G+Y
Sbjct: 135 PDRSPAIEGILQHIFAGFFANSAIPGSPHPFSWSGML----------------HSNPGDY 178

Query: 172 LVG-PGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTI-----DKNLQCAVCLEEFEI 225
             G  GLD ++  LL    N  G P A+K  + +LPTVT+     D  L+C VC E++ +
Sbjct: 179 AWGQTGLDAIVTQLLGQLENT-GPPPADKEKITSLPTVTVTQEQVDMGLECPVCKEDYTV 237

Query: 226 GNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
             E +++PC H FH  CI+PWLE+  +CPVCR  +  +D
Sbjct: 238 EEEVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSLNGED 276

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q91YL2|RN126_MOUSE RING finger protein 126 OS=Mus musculus GN=Rnf126 PE=1 SV=1

 Score = 94.7 bits (234), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 121/282 (42%), Gaps = 52/282 (18%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQM-----------SSSIAGDSINDGIHVRSD 56
           Y+C+ CS  + PR+   I CP CESG +E++           + S A    N       D
Sbjct: 11  YFCHCCSVEIVPRLPDYI-CPRCESGFIEELPEETRNTENGSAPSTAPTDQNRQPFENVD 69

Query: 57  RALSLWASILLRMMTGLSPSRPRIAAHEHFNNANP-RVEEAEQEREFES----------- 104
           + L        +   G+      I        A+  R  E+ +ERE +S           
Sbjct: 70  QHLFTLPQGYSQFAFGIFDDSFEIPTFPPGAQADDGRDPESRREREHQSRHRYGARQPRA 129

Query: 105 -LLTRRM--RRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQD 161
            L  RR   R     +L  ++Q +  GI S +  P +L      ++  NPM+        
Sbjct: 130 RLTARRATGRHEGVPTLEGIIQQLVNGIISPAAVP-SLGLGPWGVLHSNPMD-------- 180

Query: 162 HNTTSSLGEYLVGP-GLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKN-----LQ 215
                    Y  G  GLD ++  LL N     G P A+K  ++ALPTV + +      L+
Sbjct: 181 ---------YAWGANGLDTIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGLE 230

Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           C VC E++ +G   +++PC H FH  CI+PWLE   SCPVCR
Sbjct: 231 CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 272

Mus musculus (taxid: 10090)

>sp|Q6IRP0|R126B_XENLA RING finger protein 126-B OS=Xenopus laevis GN=rnf126-b PE=2 SV=1

 Score = 90.9 bits (224), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 118/267 (44%), Gaps = 25/267 (9%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILL 67
           Y+C+ C+  + PR+     CP C+SG +E++  +      N   +  +D+    + +I  
Sbjct: 11  YFCHSCTAEITPRLPE-YTCPRCDSGFIEELPETSRNSESNSSNNSGTDQNRPSFENIES 69

Query: 68  RMMTGLSPSRPRIAAHEHFNNANPRVE--------EAEQEREFESLLTRRMRRNSSASLS 119
              T      P       F   N  ++          E+ R+ ES    + R+   A   
Sbjct: 70  AQFT-----LPSGYGQVTFGIFNEGLDFPMFGTSGPVEETRDGESRREHQSRQRYGARQP 124

Query: 120 RMLQDIRFGITSRSDGPEALRERSGSLI--LVNPMNEEALIIQDHNTT-SSLGEYLVGP- 175
           R     R G   R++G   L      L+  ++ P     L +       S+  +Y  G  
Sbjct: 125 RARMSTRRG-AGRNEGVPTLEGIIQQLVNGIIAPTAMSNLGVGPWGVLHSNPMDYAWGAN 183

Query: 176 GLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDK-----NLQCAVCLEEFEIGNEAK 230
           GLD ++  LL N     G P A+   ++ALPT+ I +      L+C VC E++ +G   +
Sbjct: 184 GLDTIITQLL-NQFENTGPPPADTDKIQALPTIQITEEHVGFGLECPVCKEDYTVGESVR 242

Query: 231 EMPCKHKFHGECIMPWLEVRSSCPVCR 257
           ++PC H FH +CI+PWLE   +CPVCR
Sbjct: 243 QLPCNHLFHNDCIIPWLEQHDTCPVCR 269

Xenopus laevis (taxid: 8355)

>sp|Q9BV68|RN126_HUMAN RING finger protein 126 OS=Homo sapiens GN=RNF126 PE=1 SV=1

 Score = 89.4 bits (220), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/270 (28%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS----SSIAGDSINDGIHVRSDRALSLWA 63
           Y+C+ CS  + PR+   I CP CESG +E++     S+  G + +     +S   L    
Sbjct: 11  YFCHCCSVEIVPRLPDYI-CPRCESGFIEELPEETRSTENGSAPSTAPTDQSRPPLEHVD 69

Query: 64  SILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLSRMLQ 123
             L  +  G       I          P   +A+  R+ ES    R  R+  +      +
Sbjct: 70  QHLFTLPQGYGQFAFGIFDDSFEIPTFPPGAQADDGRDPES----RRERDHPSRHRYGAR 125

Query: 124 DIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHNTTSSLGEYLV---------- 173
             R  +T+R     A     G   L   + +    I    T  SLG + V          
Sbjct: 126 QPRARLTTR----RATGRHEGVPTLEGIIQQLVNGIITPATIPSLGPWGVLHSNPMDYAW 181

Query: 174 -GPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDK-----NLQCAVCLEEFEIGN 227
              GLD ++  LL N     G P A+K  ++ALPTV + +      L+C VC +++ +G 
Sbjct: 182 GANGLDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECPVCKDDYALGE 240

Query: 228 EAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
             +++PC H FH  CI+PWLE   SCPVCR
Sbjct: 241 RVRQLPCNHLFHDGCIVPWLEQHDSCPVCR 270

Homo sapiens (taxid: 9606)

>sp|Q0II22|RN126_BOVIN RING finger protein 126 OS=Bos taurus GN=RNF126 PE=2 SV=1

 Score = 89.4 bits (220), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 79/283 (27%), Positives = 118/283 (41%), Gaps = 53/283 (18%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS------------SSIAGDSINDGIHVRS 55
           Y+C+ CS  + PR+   I CP CESG +E++             S+ + D          
Sbjct: 11  YFCHCCSVEIVPRLPDYI-CPRCESGFIEELPEETRSAENGSAPSTASADQSRQQPFENV 69

Query: 56  DRALSLWASILLRMMTGLSPSRPRIAAHEHFNNAN-PRVEEAEQEREFES---------- 104
           D+ L            G+      I        A+  R  E+ +ERE  S          
Sbjct: 70  DQPLFTLPQGYGHFAFGIFDDSFEIPTFPPGAQADDSRDPESRREREQHSRHRYGARQPR 129

Query: 105 --LLTRRM--RRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQ 160
             L  RR   R     +L  ++Q +  GI + +  P  L      ++  NPM+       
Sbjct: 130 ARLTARRATGRHEGVPTLEGIIQQLVNGIITPATIPN-LGLGPWGVLHSNPMD------- 181

Query: 161 DHNTTSSLGEYLVGP-GLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDK-----NL 214
                     Y  G  GLD ++  LL N     G P A+K  ++ALPTV + +      L
Sbjct: 182 ----------YAWGANGLDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGL 230

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           +C VC +++ +G   +++PC H FH  CI+PWLE   SCPVCR
Sbjct: 231 ECPVCKDDYGLGEHVRQLPCNHLFHDGCIVPWLEQHDSCPVCR 273

Bos taurus (taxid: 9913)

>sp|Q7T0Q3|R126A_XENLA RING finger protein 126-A OS=Xenopus laevis GN=rnf126-a PE=2 SV=1

 Score = 86.3 bits (212), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/267 (26%), Positives = 118/267 (44%), Gaps = 25/267 (9%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILL 67
           Y+C+ C+  + PR+     CP C+SG +E++  +      N   + R+D+    + ++  
Sbjct: 11  YFCHSCTAEITPRLPE-YTCPRCDSGFIEELPETSRNSENNSSNNSRTDQNRPSFENLES 69

Query: 68  RMMTGLSPSRPRIAAHEHFNNANPRVE--------EAEQEREFESLLTRRMRRNSSASLS 119
              T      P       F   N  ++          E+ R+ ES    + R+   A   
Sbjct: 70  AQFT-----LPSGYGQVTFGIFNEGLDFPIFGTSGPVEETRDGESRREHQSRQRYGARQP 124

Query: 120 RMLQDIRFGITSRSDGPEALRERSGSLI--LVNPMNEEALIIQDHNTT-SSLGEYLVGP- 175
           R     R     R++G   L      L+  ++ P     L +       S+  +Y  G  
Sbjct: 125 RARLSTRRA-AGRNEGVPTLEGIIQQLVNGIIAPTAMSNLGVGPWGVLHSNPMDYAWGAN 183

Query: 176 GLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDK-----NLQCAVCLEEFEIGNEAK 230
           GLD ++  LL N     G P A+   ++ALPT+ I +      L+C VC E++ +G   +
Sbjct: 184 GLDTIITQLL-NQFENTGPPPADNEKIQALPTIQITEEHVGSGLECPVCKEDYTVGECVR 242

Query: 231 EMPCKHKFHGECIMPWLEVRSSCPVCR 257
           ++PC H FH +CI+PWLE   +CPVCR
Sbjct: 243 QLPCNHLFHNDCIIPWLEQHDTCPVCR 269

Xenopus laevis (taxid: 8355)

>sp|Q7ZW78|RN181_DANRE E3 ubiquitin-protein ligase RNF181 OS=Danio rerio GN=rnf181 PE=2 SV=2

 Score = 85.5 bits (210), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 51/75 (68%), Gaps = 5/75 (6%)

Query: 195 PAANKAVLKALPTVTI-----DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV 249
           P A KAV+++LP V I     DK ++C VCL EFE     +EMPCKH FH  CI+PWL  
Sbjct: 53  PPAAKAVVQSLPVVIISPEQADKGVKCPVCLLEFEEQESVREMPCKHLFHTGCILPWLNK 112

Query: 250 RSSCPVCRFQVPSDD 264
            +SCP+CR ++P+D+
Sbjct: 113 TNSCPLCRLELPTDN 127

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

Danio rerio (taxid: 7955)

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	342
255568972	348	zinc finger protein, putative [Ricinus c	0.979	0.962	0.512	8e-85
224125900	344	predicted protein [Populus trichocarpa]	0.944	0.938	0.504	7e-81
356567978	344	PREDICTED: E3 ubiquitin-protein ligase R	0.859	0.854	0.459	5e-70
224073116	356	predicted protein [Populus trichocarpa]	0.888	0.853	0.468	2e-69
225435816	368	PREDICTED: uncharacterized protein LOC10	0.923	0.858	0.451	6e-65
297746512	349	unnamed protein product [Vitis vinifera]	0.836	0.819	0.449	3e-64
357462645	352	RING finger protein [Medicago truncatula	0.926	0.900	0.446	1e-63
449463838	362	PREDICTED: E3 ubiquitin-protein ligase R	0.921	0.870	0.42	5e-63
15241188	396	RING/U-box domain-containing protein [Ar	0.853	0.737	0.435	9e-63
297793133	395	zinc finger family protein [Arabidopsis	0.862	0.746	0.437	3e-62

>gi|255568972|ref|XP_002525456.1| zinc finger protein, putative [Ricinus communis] gi|223535269|gb|EEF36946.1| zinc finger protein, putative [Ricinus communis]

 Score =  320 bits (819), Expect = 8e-85,   Method: Compositional matrix adjust.
 Identities = 182/355 (51%), Positives = 234/355 (65%), Gaps = 20/355 (5%)

Query: 1   MGDAMVG-YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRAL 59
           MGD MV  YWC++CS+MV P MEA IKCP CE+G VE++ S+   D  N+GI   S+RA 
Sbjct: 1   MGDEMVDRYWCHMCSRMVTPVMEAEIKCPLCENGFVEEIGST--RDLNNNGIDFVSERAF 58

Query: 60  SLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLS 119
           S+WA ILL +M GL P R RI A EH ++ N + E  E EREFESL  RR RRN ++ LS
Sbjct: 59  SMWAPILLGLMGGLGPVRARITAQEHDSSNNAQEEREELEREFESLFRRR-RRNPASILS 117

Query: 120 RMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQD-----------HNTTSSL 168
            +     F     S         + ++ILVNP N+EALI+Q             N  SS 
Sbjct: 118 MLQGSENFENNGES---NGNNNNNNNVILVNPFNQEALILQGSFDASQPENPIRNMRSSF 174

Query: 169 GEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNE 228
            +YL+GPGLDLLLQHL ENDPNRYG   A K  +KA+PT+ +++N +C+VCLEEFEIG E
Sbjct: 175 RDYLIGPGLDLLLQHLAENDPNRYGTLPAQKKAVKAMPTIAVEQNAECSVCLEEFEIGGE 234

Query: 229 AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNG-SGNRDESLGNEDAQNN 287
           AKEMPCKHKFH  CI+PWLE+ SSCPVCRFQ+P D+ KI+ N    N   ++ N  A+ N
Sbjct: 235 AKEMPCKHKFHSACILPWLELHSSCPVCRFQMPCDNSKIEANSLRSNDGRTIENNAARMN 294

Query: 288 LRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSESSSVGTAAHIDET 342
              G+  ++  NGRR+W+P+PWPFD LFS+S SQ  G S S ++  G+++H DET
Sbjct: 295 DSWGDVGEQTDNGRRFWVPVPWPFDGLFSLSASQSDGNSTS-ATLTGSSSHTDET 348

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125900|ref|XP_002319703.1| predicted protein [Populus trichocarpa] gi|222858079|gb|EEE95626.1| predicted protein [Populus trichocarpa]

 Score =  306 bits (785), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 183/363 (50%), Positives = 235/363 (64%), Gaps = 40/363 (11%)

Query: 1   MGDAMVG-YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRAL 59
           M D MV  YWC++CSQMVNP  EA IKCPFCESG +E+M S    +  N+   + S+ A 
Sbjct: 1   MEDEMVDQYWCHMCSQMVNPVTEAEIKCPFCESGFLEEMGS--VREVNNNIFDLGSEHAF 58

Query: 60  SLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLS 119
           SLW + LL +M GL  S  R  A EH ++ + + E+   E +FESLL RR R  S++S+ 
Sbjct: 59  SLWDTFLLDLMGGLGTSGSRRIAQEHISSTSSQDED--DELDFESLLRRRGRL-STSSVQ 115

Query: 120 RMLQDIRFGITSRSDGPEALRERSGS------LILVNPMNEEALIIQD-----------H 162
           R+LQD+      RS+ PE  RE SG       +ILVNP NEEA+I+              
Sbjct: 116 RLLQDLHL----RSENPENDRESSGGSSSSSSVILVNPFNEEAIILHSPDNMNQPENPSQ 171

Query: 163 NTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEE 222
           N + S  +YL+GP +DLLL HL E+ PNRYG P A K  +KA+PTV+I +NLQC+VCLEE
Sbjct: 172 NVSISFQDYLIGPDVDLLLHHLAESGPNRYGTPPAEKEAVKAMPTVSITQNLQCSVCLEE 231

Query: 223 FEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNE 282
           F+IG EAKEMPCKHKFHGECI+PWLE+ SSCPVCRF +PSDD     + S + +E   + 
Sbjct: 232 FDIGCEAKEMPCKHKFHGECIVPWLELHSSCPVCRFLMPSDDSTTGVSQSRSDEERTESN 291

Query: 283 DAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSESSSV---GTAAHI 339
           DA+           + NGRRYW+PIPWPFD LF +SGSQ GG+S+S  SS    G+A++ 
Sbjct: 292 DAR----------IINNGRRYWVPIPWPFDGLFPLSGSQNGGSSSSAPSSTTMRGSASYS 341

Query: 340 DET 342
           DET
Sbjct: 342 DET 344

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567978|ref|XP_003552191.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Glycine max]

 Score =  271 bits (692), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 159/346 (45%), Positives = 211/346 (60%), Gaps = 52/346 (15%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQM-----SSSIAGDSINDGIHVRSDRALSLW 62
           YWC++CSQMVNP M+  I+CPFC+SG VE+M     SSSI   S +D     SDRALSLW
Sbjct: 5   YWCHMCSQMVNPIMDMEIRCPFCQSGFVEEMGNTPSSSSIPNTSESD---FESDRALSLW 61

Query: 63  ASILLRMMTGLSPSRPRIAAHEHFNNANPRV--------EEAEQEREFESLLTRRMRRNS 114
           A ILL MM   +P  PR       +N N            E E ++EFES+L RR  RNS
Sbjct: 62  APILLGMMG--NPRHPRRLRQIANDNGNRDYVDGVADHGRETEYDQEFESILRRR--RNS 117

Query: 115 SASLSRMLQDIRFGITSRS---------DGPEALRERSGSLILVNPMNEEALIIQ----- 160
            A++ ++LQ IR G+ S S         D           +IL+NP+N+  +I+Q     
Sbjct: 118 -ATILQLLQGIRTGLASESYENTDGHDHDREREREREREHMILINPLNQ-TIIVQGSYES 175

Query: 161 ------DHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNL 214
                 +H++  SLG+Y  GPG D+LLQHL ENDPNRYG P A K  ++ALPTV I++N 
Sbjct: 176 NRDQSDNHSSVGSLGDYFTGPGFDILLQHLAENDPNRYGTPPAQKEAIEALPTVIINENS 235

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGN 274
           QC+VCL++FE+G+EAKEMPCKH+FH  CI+PWLE+ SSCPVCR Q+P D+ K   + S +
Sbjct: 236 QCSVCLDDFEVGSEAKEMPCKHRFHSGCILPWLELHSSCPVCRLQLPLDESKQDSDLSRD 295

Query: 275 -----RDESLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLF 315
                 DES+ +++ +   R G G +  G GRR+    PWPF+ LF
Sbjct: 296 SRSQREDESIEHDNDEE--RDGEGRNASG-GRRF--SFPWPFNGLF 336

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073116|ref|XP_002303979.1| predicted protein [Populus trichocarpa] gi|222841411|gb|EEE78958.1| predicted protein [Populus trichocarpa]

 Score =  269 bits (687), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 161/344 (46%), Positives = 209/344 (60%), Gaps = 40/344 (11%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRALSLWASILL 67
           YWC++CSQMVNP M   IKCPFC++G +E M  S   + + D     SDRALSLWA ILL
Sbjct: 5   YWCHMCSQMVNPIMGVEIKCPFCQNGFIEDMIDSTGDNQVPDS-EFGSDRALSLWAPILL 63

Query: 68  RMM-TGLSPSRPRIAAHEHFNNANPRVE-----EAEQEREFESLLTRRMRRN-SSASLSR 120
            M+       R R   +E   + N   E     E E ERE ES + RR R   +SA++ +
Sbjct: 64  GMVGNSHRRRRLRRVEYEEDEDGNDDGEANHAGEPEFEREIESFMRRRRRSRRNSATILQ 123

Query: 121 MLQDIRFGI-TSRSDGPEAL----------RERSGSLILVNPMNEEALIIQDHNT----- 164
           +LQ IR GI  S S+  E            RER   +IL+NP N+  ++   +++     
Sbjct: 124 LLQGIRAGILVSESENLEGDRDRDRVRDMNRERE-RVILINPFNQSIIVQGSYDSNNVQN 182

Query: 165 -----TSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVC 219
                  SLG+Y++GPGLDLLLQHL ENDPNRYG P A K  ++ALPTVT+ + LQC+VC
Sbjct: 183 QNQNAIGSLGDYVIGPGLDLLLQHLAENDPNRYGTPPAQKEAIEALPTVTVKEPLQCSVC 242

Query: 220 LEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGN----R 275
           L++FEIG EA+EMPCKHKFH  CI+PWLE+ SSCPVCR Q+P+D+ K+    S N    R
Sbjct: 243 LDDFEIGAEAREMPCKHKFHSGCILPWLELHSSCPVCRHQLPADESKLDSERSRNTFDQR 302

Query: 276 DESLGNEDAQN----NLRLGNGEDRVGNGRRYWIPIPWPFDSLF 315
           D    N ++      N+  G+GE R GNGRR+    PWPF+SLF
Sbjct: 303 DSESTNSESNISNGINVEEGDGEGRSGNGRRF--SFPWPFNSLF 344

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225435816|ref|XP_002285765.1| PREDICTED: uncharacterized protein LOC100250148 isoform 1 [Vitis vinifera] gi|225435818|ref|XP_002285766.1| PREDICTED: uncharacterized protein LOC100250148 isoform 2 [Vitis vinifera]

 Score =  253 bits (647), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 158/350 (45%), Positives = 207/350 (59%), Gaps = 34/350 (9%)

Query: 1   MGDAMVG-YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRAL 59
           M DAM G YWC+ CSQ+VNP  EA  KCP C+ G +E +  + + D  +    + SDR L
Sbjct: 1   MEDAMGGRYWCHSCSQVVNPIAEAEPKCPLCQDGFIEDIDGTASRDHNDSDSDLASDRTL 60

Query: 60  SLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRM------RRN 113
           SLWA ILL MM   +P R R    E   +     E+ E  R  E+ L R +      RR 
Sbjct: 61  SLWAPILLGMMG--NPRRRRRFRREDIEDEEEDNEDGEGRRGGETELDRELDSIIRRRRR 118

Query: 114 SSASLSRMLQDIRFGITSRSDGPE---------ALRERSGSLILVNPMNEEALIIQ---- 160
           SSA++ ++LQ IR G+ S S+  E                 LIL+NP N+  +I+Q    
Sbjct: 119 SSATILQLLQGIRAGMVSESENSENDRDRDRDRERERERERLILINPFNQ-TIIVQGSFD 177

Query: 161 -------DHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKN 213
                  + NT  SLG+Y +GP LDLLLQHL ENDPNRYG P A K  ++A+PTV I +N
Sbjct: 178 SNQAQNQNQNTIGSLGDYFIGPSLDLLLQHLAENDPNRYGTPPAQKDAIEAMPTVKIKEN 237

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGS- 272
           LQC+VCL++FEIG EA+EMPCKHKFH  CI+PWLE+ SSCPVCRFQ+ +D+ K+  + S 
Sbjct: 238 LQCSVCLDDFEIGAEAREMPCKHKFHSGCILPWLELHSSCPVCRFQIAADESKLDSDASP 297

Query: 273 -GNRDESLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQ 321
             + + S  + +   +   G+G+ R GNGRR      WPF SLFS  GSQ
Sbjct: 298 NVSSNSSERSNNGHGSSEEGDGDGRSGNGRRS--TFRWPFTSLFSSQGSQ 345

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297746512|emb|CBI16568.3| unnamed protein product [Vitis vinifera]

 Score =  251 bits (641), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 150/334 (44%), Positives = 195/334 (58%), Gaps = 48/334 (14%)

Query: 1   MGDAMVG-YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRAL 59
           M DAM G YWC+ CSQ+VNP  EA  KCP C+ G +E +  + + D  +    + SDR L
Sbjct: 1   MEDAMGGRYWCHSCSQVVNPIAEAEPKCPLCQDGFIEDIDGTASRDHNDSDSDLASDRTL 60

Query: 60  SLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQEREFESLLTRRMRRNSSASLS 119
           SLWA ILL MM G                   R  E E +RE +S    R RR SSA++ 
Sbjct: 61  SLWAPILLGMMDG----------------EGRRGGETELDRELDS--IIRRRRRSSATIL 102

Query: 120 RMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDHN----------TTSSLG 169
           ++LQ IR G+                LIL+NP N+  ++    +          T  SLG
Sbjct: 103 QLLQGIRAGM---------------RLILINPFNQTIIVQGSFDSNQAQNQNQNTIGSLG 147

Query: 170 EYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEA 229
           +Y +GP LDLLLQHL ENDPNRYG P A K  ++A+PTV I +NLQC+VCL++FEIG EA
Sbjct: 148 DYFIGPSLDLLLQHLAENDPNRYGTPPAQKDAIEAMPTVKIKENLQCSVCLDDFEIGAEA 207

Query: 230 KEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGS--GNRDESLGNEDAQNN 287
           +EMPCKHKFH  CI+PWLE+ SSCPVCRFQ+ +D+ K+  + S   + + S  + +   +
Sbjct: 208 REMPCKHKFHSGCILPWLELHSSCPVCRFQIAADESKLDSDASPNVSSNSSERSNNGHGS 267

Query: 288 LRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQ 321
              G+G+ R GNGRR      WPF SLFS  GSQ
Sbjct: 268 SEEGDGDGRSGNGRRS--TFRWPFTSLFSSQGSQ 299

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357462645|ref|XP_003601604.1| RING finger protein [Medicago truncatula] gi|355490652|gb|AES71855.1| RING finger protein [Medicago truncatula]

 Score =  249 bits (637), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 157/352 (44%), Positives = 210/352 (59%), Gaps = 35/352 (9%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDG--IHVRSDRALSLWASI 65
           YWC+ CSQ+V+P M   IKCP C+SG +E+MSS+     + +        DR+ SLWA I
Sbjct: 5   YWCHACSQIVSPVMGMEIKCPLCQSGFIEEMSSATGISDLQNTPETDFGVDRSPSLWAPI 64

Query: 66  LLRMMTG--LSPSRPRIAAHEHFNNANPRVEEA---EQEREFESLLTRRMRRNSSASLSR 120
           LL MM    L     RI   + + + N   +       +RE ES+L RR R  SSA++ +
Sbjct: 65  LLGMMGNPRLRRRLRRIELEDDYESGNRDDDHGGVGHYDRELESILRRRRR--SSATIQQ 122

Query: 121 MLQDIRFGITSRS----DGPEALRERSGS-LILVNPMNEEALIIQ-----------DHNT 164
           +LQ IR G+TS S    D  + +RER    +IL+NP N+  +I+Q           +HN 
Sbjct: 123 LLQGIRAGLTSESHENTDSDDRVREREREHVILINPFNQ-TIIVQGSYDSNRDQSDNHNP 181

Query: 165 TSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFE 224
             +LG+Y VGPGLDLLLQHL ENDPNRYG P A K  +++LPTV I++NLQC+VCL++FE
Sbjct: 182 IGALGDYFVGPGLDLLLQHLSENDPNRYGTPPAPKEAVESLPTVKINENLQCSVCLDDFE 241

Query: 225 IGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV----PSDDFKIQGNGSGNR-DESL 279
           +G+EAKEMPCKH+FH  CI+PWLE+ SSCPVCR Q+    P  D  +  N    R DE +
Sbjct: 242 VGSEAKEMPCKHRFHSACILPWLELHSSCPVCRSQLRVDEPKQDSDVSRNHRNQRDDEII 301

Query: 280 GNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSESS 331
           G+ +A      G+ E R  +G R +   PWPF+ LFS S S      N   S
Sbjct: 302 GHANANAE---GDSEGRSPSGGRRF-SFPWPFNGLFSSSSSSSNANGNGTQS 349

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463838|ref|XP_004149638.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus] gi|449519040|ref|XP_004166543.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score =  247 bits (631), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 147/350 (42%), Positives = 203/350 (58%), Gaps = 35/350 (10%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVR----------SDR 57
           YWC++CSQMVNP ++  IKCPFC SG VE++ + I+ D+ ++  +            S+R
Sbjct: 9   YWCHMCSQMVNPIVDVEIKCPFCRSGFVEEIGNGISSDNNDNNNNNNNNNELESDFGSER 68

Query: 58  ALSLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVEEAEQE-----REFESLLTRRMRR 112
           ALSLWA ILL MM   +P   R   H  F++ +   E  + E      E   L +   RR
Sbjct: 69  ALSLWAPILLGMMG--NPRGRRRFRHLEFDDDDDDNEHEDGEGNRVSSETTELDSVIRRR 126

Query: 113 NSSASLSRMLQDIRFGIT---SRSDGPEALRERSGSLILVNPMNEEALII------QDHN 163
            SSA++ ++LQ IR GI    S +            +IL+NP N+  ++       Q+ N
Sbjct: 127 RSSATILQLLQGIRAGIATAESENSYEGERSRERERVILINPFNQTIVVQGGENQNQNQN 186

Query: 164 TTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTI----DKNLQCAVC 219
           +  SLG+Y VGPGLDLLLQH+ ENDPNRYG P A K  + ALPTV +    D  LQC+VC
Sbjct: 187 SIGSLGDYFVGPGLDLLLQHIAENDPNRYGTPPAQKEAVDALPTVRVELEEDSCLQCSVC 246

Query: 220 LEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK--IQGNGSGNRDE 277
           L+EFE+  EAKEMPCKHKFH  CI+PWLE+ SSCPVCR Q+P D+ K  + G  +     
Sbjct: 247 LDEFEVDEEAKEMPCKHKFHTGCILPWLELHSSCPVCRHQLPGDESKRDVDGGSAARFMS 306

Query: 278 SLGNEDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSN 327
            L N +   +  +  G +   +GRR+    PWPF+ LF+  G+   G+++
Sbjct: 307 DLNNGNGNGSGEI-EGRNSSESGRRF--SFPWPFNGLFTSQGNSSAGSAS 353

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15241188|ref|NP_200445.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|10177832|dbj|BAB11261.1| unnamed protein product [Arabidopsis thaliana] gi|17380898|gb|AAL36261.1| unknown protein [Arabidopsis thaliana] gi|20259581|gb|AAM14133.1| unknown protein [Arabidopsis thaliana] gi|332009368|gb|AED96751.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  246 bits (629), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 160/367 (43%), Positives = 207/367 (56%), Gaps = 75/367 (20%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAG-------DSINDGIHVRSDRALS 60
           YWC++CSQMVNP ME+ IKCPFC+SG +E+MS +  G       D  +      +DRALS
Sbjct: 9   YWCHMCSQMVNPVMESEIKCPFCQSGFIEEMSGNGGGGGGRGIRDVQDSETDFGTDRALS 68

Query: 61  LWASILLRMMTGLSPSRPRIAAHEHFNNANP----------------------------R 92
           LWA ILL MM+  SP R R      F   N                             R
Sbjct: 69  LWAPILLGMMS--SPRRRRRFRRSEFGEENDDNGDDLTTNADGNGNDSNNSNNNVYRHHR 126

Query: 93  VE----EAEQEREFESLLTRRMRRNSSASLSRMLQDIRFGITSRSDGPEA----LRERSG 144
                 E + +REFES+L RR    SS ++ ++LQ IR GI S  +  +      RER  
Sbjct: 127 ARRHGGEIDLDREFESILRRRR--RSSGNILQLLQGIRAGIASEYESSDNNWDNSRERD- 183

Query: 145 SLILVNPMNEEALII----QDHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKA 200
            +I++NP N+  ++     Q+H + +SLG+Y +GPGLDLLLQHL ENDPNR G P A K 
Sbjct: 184 RVIMINPYNQSLVVPSDQNQNHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQGTPPARKE 243

Query: 201 VLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
            ++ALPTV I + LQC+VCL++FE G EAKEMPCKHKFH  CI+PWLE+ SSCPVCRF++
Sbjct: 244 AVEALPTVKIMEPLQCSVCLDDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSCPVCRFEL 303

Query: 261 PS-----DDFK-----------IQGNGSGNRDESLGNEDAQNNLRLGNGEDRVGNGRRYW 304
           PS     D+ K           ++   +GN  E++GN D     R    E R GNGRR+ 
Sbjct: 304 PSSADDDDETKTDSERVLRTRNVRETSNGNVVENVGNAD-----RGREDEVRSGNGRRF- 357

Query: 305 IPIPWPF 311
              PWPF
Sbjct: 358 -SFPWPF 363

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297793133|ref|XP_002864451.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297310286|gb|EFH40710.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  245 bits (625), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 162/370 (43%), Positives = 210/370 (56%), Gaps = 75/370 (20%)

Query: 8   YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAG-------DSINDGIHVRSDRALS 60
           YWC++CSQMVNP ME+ IKCPFC+SG +E+MS +  G       D  +      +DRALS
Sbjct: 9   YWCHMCSQMVNPIMESEIKCPFCQSGFIEEMSGNSGGGGGRGIRDVQDSETDFGTDRALS 68

Query: 61  LWASILLRMMTGLSPSRPRIAAHEHFNNANP----------------------------R 92
           LWA ILL MM+  SP R R      F   N                              
Sbjct: 69  LWAPILLGMMS--SPRRRRRFRRSEFGEENDDNGDELSNADGNDNNNNSNVYYHHRARRH 126

Query: 93  VEEAEQEREFESLLTRRMRRNSSASLSRMLQDIRFGITSRSDGPEA----LRERSGSLIL 148
             E + +REFES+L RR    SS ++ ++LQ IR GI S  +  +      RER   +I+
Sbjct: 127 GGEIDLDREFESILRRRR--RSSGNILQLLQGIRAGIASEYESSDNDWDNSRERD-RVIM 183

Query: 149 VNPMNEEALIIQ-------DHNTTSSLGEYLVGPGLDLLLQHLLENDPNRYGCPAANKAV 201
           +NP N+ +L++Q       +H + +SLG+Y +GPGLDLLLQHL ENDPNR G P A K  
Sbjct: 184 INPYNQ-SLVVQGSSDQNPNHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQGTPPARKEA 242

Query: 202 LKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261
           ++ALPTV I + LQC+VCL++FE G EAKE+PCKHKFH  CI+PWLE+ SSCPVCRF++P
Sbjct: 243 VEALPTVKIMEPLQCSVCLDDFEKGTEAKELPCKHKFHIRCIVPWLELHSSCPVCRFELP 302

Query: 262 S-----DDFKIQGN---------GSGNRD--ESLGNEDAQNNLRLGNGEDRVGNGRRYWI 305
           S     D+ KI             S NR+  E++GN +     R    E R GNGRR+  
Sbjct: 303 SSADDDDETKIDSERPPRTRNVGESNNRNIVENVGNAE-----RGRQDEARSGNGRRF-- 355

Query: 306 PIPWPFDSLF 315
             PWPF  LF
Sbjct: 356 SFPWPFSGLF 365

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	342
TAIR|locus:2161058	396	ATCRT1 [Arabidopsis thaliana (	0.640	0.553	0.456	1.3e-63
TAIR|locus:2193874	351	AT1G55530 [Arabidopsis thalian	0.944	0.920	0.387	9.9e-55
TAIR|locus:2131463	356	AT4G26400 [Arabidopsis thalian	0.611	0.587	0.379	2.9e-54
TAIR|locus:2092895	315	AT3G13430 [Arabidopsis thalian	0.540	0.587	0.427	6e-46
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.447	0.466	0.398	1.5e-35
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.225	0.194	0.536	1.2e-27
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.400	0.417	0.402	1.2e-26
TAIR|locus:2148318	407	RDUF2 "RING and Domain of Unkn	0.257	0.216	0.463	3.9e-26
UNIPROTKB|F6RQU6	293	RNF115 "Uncharacterized protei	0.271	0.317	0.397	1.1e-23
UNIPROTKB|I3LDQ5	293	LOC100739432 "Uncharacterized	0.236	0.276	0.441	6.3e-22

TAIR|locus:2161058 ATCRT1 [Arabidopsis thaliana (taxid:3702)]

 Score = 466 (169.1 bits), Expect = 1.3e-63, Sum P(2) = 1.3e-63
 Identities = 110/241 (45%), Positives = 142/241 (58%)

Query:   109 RMRRNSSASLSRMLQDIRFGITSR---SDGP-EALRERSGSLILVNPMNEEALIIQDHN- 163
             R RR SS ++ ++LQ IR GI S    SD   +  RER   +I++NP N+  ++  D N 
Sbjct:   145 RRRRRSSGNILQLLQGIRAGIASEYESSDNNWDNSRERD-RVIMINPYNQSLVVPSDQNQ 203

Query:   164 ---TTSSLGEYXXXXXXXXXXXXXXENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCL 220
                + +SLG+Y              ENDPNR G P A K  ++ALPTV I + LQC+VCL
Sbjct:   204 NHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQGTPPARKEAVEALPTVKIMEPLQCSVCL 263

Query:   221 EEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS---DDFKIQGNG-----S 272
             ++FE G EAKEMPCKHKFH  CI+PWLE+ SSCPVCRF++PS   DD + + +      +
Sbjct:   264 DDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSCPVCRFELPSSADDDDETKTDSERVLRT 323

Query:   273 GN-RDESLGN--EDAQNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNSE 329
              N R+ S GN  E+  N  R    E R GNGRR+    PWPF  LFS S S    TS S+
Sbjct:   324 RNVRETSNGNVVENVGNADRGREDEVRSGNGRRF--SFPWPFSGLFSSSSSSSSSTSGSQ 381

Query:   330 S 330
             S
Sbjct:   382 S 382

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

TAIR|locus:2193874 AT1G55530 [Arabidopsis thaliana (taxid:3702)]

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 138/356 (38%), Positives = 187/356 (52%)

Query:     1 MGDAMVG-YWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSSIAGDSINDGIHVRSDRAL 59
             M +A+V  YWC++CSQ VNP MEA IKCPFC+SG VE+M      DS +D   VR++   
Sbjct:     1 MEEAVVTRYWCHMCSQTVNPVMEAEIKCPFCQSGFVEEMEDDDDHDS-SDPADVRANN-- 57

Query:    60 SLWASILLRMMTGLSPSRPRIAAHEHFNNANPRVXXXXXXXXXXSL------LTRRMRRN 113
             SLWA IL+ +M      R   +     +N N              L      + RR RR+
Sbjct:    58 SLWAPILMELMNDPVRRRRNQSVESVEDNQNEVQTENNEDDGENDLDWQLQEILRRRRRH 117

Query:   114 SSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQ-----DHNTTSSL 168
             S+A L ++LQ IR G++  S+         G +IL+N  N+  + +Q     D     SL
Sbjct:   118 SAAVL-QLLQGIRAGLSVESESTGNGGNNPGRVILINTSNQ-TITVQNSADMDSVPAGSL 175

Query:   169 GEYXXXXXXXXXXXXXXENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNE 228
             G+Y              ENDPNRYG P A K  ++AL TV I++ LQC+VCL++FEIG E
Sbjct:   176 GDYFIGPGFEMLLQRLAENDPNRYGTPPAKKEAVEALATVKIEETLQCSVCLDDFEIGTE 235

Query:   229 AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQ---------GNGSGNRDESL 279
             AK MPC HKFH +C++PWLE+ SSCPVCR+Q+P+D+ K           G+ S +   S 
Sbjct:   236 AKLMPCTHKFHSDCLLPWLELHSSCPVCRYQLPADEAKTDSVTTTSDNNGSSSASATTSH 295

Query:   280 GNEDAQNNLRLGNGEDRVG-------NGRRYWIPIPWPFDSLFSMSGSQEGGTSNS 328
             G E++  N R    E+          N       IPWPF +LFS S      T +S
Sbjct:   296 GAENSDGNRRQEEEEEEEEEEEEENENNDGSGFSIPWPFSTLFSSSQDSNAPTDSS 351

GO:0005737 "cytoplasm" evidence=ISM

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

TAIR|locus:2131463 AT4G26400 [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 2.9e-54, Sum P(2) = 2.9e-54
 Identities = 85/224 (37%), Positives = 128/224 (57%)

Query:   109 RMRRNSSASLSRMLQDIRFGITSRSDGPEA-LRERSGSLILVNPMNEEALIIQDHNTTSS 167
             R RR SSA++ ++LQ IR GI S  +  +  L  +S  +     +N+     +++ + S+
Sbjct:   137 RRRRRSSATILQLLQGIRAGIASEYESSDRDLLNQSAVVQGSTSLNQN----RNNTSLSA 192

Query:   168 LGEYXXXXXXXXXXXXXXENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGN 227
             +G+Y              +ND  R+G   A K V+  LPTV I ++LQC++CL++F+ G+
Sbjct:   193 IGDYFVGSSLDHLLEHLADNDSIRHGSLPARKEVVDNLPTVKISESLQCSICLDDFDKGS 252

Query:   228 EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD-FKIQGNGSGNR--DESLGNEDA 284
             EAKEMPCKHKFH  CI+PWLE+ SSCPVCR+++P DD  K+       R  + ++ NE+ 
Sbjct:   253 EAKEMPCKHKFHIRCIVPWLELHSSCPVCRYELPPDDETKVNPVRPRTRTLEINVSNENV 312

Query:   285 QNNLRLGNGEDRVGNGRRYWIPIPWPFDSLFSMSGSQEGGTSNS 328
             +++ R  N  +R     R+    PWPF  LFS S S     S S
Sbjct:   313 EDDARNSNVSER-----RF--SFPWPFSGLFSSSSSSSASASGS 349

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

GO:0010200 "response to chitin" evidence=IEP

GO:0000303 "response to superoxide" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0009743 "response to carbohydrate stimulus" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

TAIR|locus:2092895 AT3G13430 [Arabidopsis thaliana (taxid:3702)]

 Score = 379 (138.5 bits), Expect = 6.0e-46, Sum P(2) = 6.0e-46
 Identities = 83/194 (42%), Positives = 115/194 (59%)

Query:   108 RRMRRNSSASLSRMLQDIRFGITSRSDGPEALRERSGSLILVNPMNEEALIIQDH-NTTS 166
             RR+R   S ++  +LQ IR G+   S+  E   + S  ++L+N  N+   + QD  +TTS
Sbjct:   110 RRIRTRHSTAIVNLLQGIRAGLLIESENNEDNPDNSELVVLINSFNQRIRVHQDSVDTTS 169

Query:   167 ----SLGEYXXXXXXXXXXXXXXEND-PNRYGCPAANKAVLKALPTVTI-DKNLQCAVCL 220
                 SLG+Y              END  NRYG P A K  ++AL  V I D  LQC+VCL
Sbjct:   170 VPSGSLGDYFIGPGFETLLQRLAENDLNNRYGTPPATKEAVEALAMVKIEDSLLQCSVCL 229

Query:   221 EEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS-DDFKIQGNGSGNRDESL 279
             ++FEIG EAKEMPCKHKFH +C++PWLE+ SSCPVCR+ +P+ DD + + +   +R++  
Sbjct:   230 DDFEIGMEAKEMPCKHKFHSDCLLPWLELHSSCPVCRYLLPTGDDDEPKTDAETSRNDD- 288

Query:   280 GNEDAQNNLRLGNG 293
              NED  N     NG
Sbjct:   289 NNEDISNASMASNG 302

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=RCA

TAIR|locus:2092231 AT3G19950 [Arabidopsis thaliana (taxid:3702)]

 Score = 334 (122.6 bits), Expect = 1.5e-35, Sum P(2) = 1.5e-35
 Identities = 69/173 (39%), Positives = 101/173 (58%)

Query:   167 SLGEYXXXXXXXXXXXXXXENDPNRYGCPAANKAVLKALPTVTIDKNL------QCAVCL 220
             + G+Y              ENDPNRYG P A+K+ + ALPTV + K++      QCAVC+
Sbjct:   161 NFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCM 220

Query:   221 EEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLG 280
             +EFE G++ K+MPCKH FH +C++PWLE+ +SCPVCRF++P+DD   +    G++    G
Sbjct:   221 DEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPTDDPDYENRSQGSQ----G 276

Query:   281 NEDAQNNLRLGNGEDRVGNGRRYWIPIPWPF---DSLFSMSGSQEGGTSNSES 330
             + D Q ++    G+       R+ I +PWPF   D   S SG+   G  N E+
Sbjct:   277 SGDGQGSVE---GQQTP----RFSIQLPWPFRRQDGSGSGSGAPGTGGGNLET 322

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

GO:0010200 "response to chitin" evidence=RCA

TAIR|locus:2075175 RDUF1 "RING and Domain of Unknown Function 1117 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 242 (90.2 bits), Expect = 1.2e-27, Sum P(2) = 1.2e-27
 Identities = 44/82 (53%), Positives = 56/82 (68%)

Query:   187 NDPNRYGCPAANKAVLKALPTVTIDK-----NLQCAVCLEEFEIGNEAKEMPCKHKFHGE 241
             N   R G P A+K+ +++LP V I          CAVC E FE G E +EMPCKH FHG+
Sbjct:   181 NGIGRSGNPPASKSAIESLPRVEISDCHTKAEANCAVCTEVFEAGIEGREMPCKHIFHGD 240

Query:   242 CIMPWLEVRSSCPVCRFQVPSD 263
             CI+PWL +R+SCPVCRF++PSD
Sbjct:   241 CIVPWLSIRNSCPVCRFELPSD 262

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

GO:0010200 "response to chitin" evidence=IEP;RCA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2058465 RHC1A "RING-H2 finger C1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 259 (96.2 bits), Expect = 1.2e-26, Sum P(2) = 1.2e-26
 Identities = 60/149 (40%), Positives = 85/149 (57%)

Query:   191 RYGCPAANKAVLKALPTVTI-DKNLQ-----CAVCLEEFEIGNEAKEMPCKHKFHGECIM 244
             R G P A ++ + ALPT+ I  ++L+     C VC +EFE+G+EAK+MPC H +H +CI+
Sbjct:   159 RRGPPPAPRSAIDALPTIKIAQRHLRSSDSNCPVCKDEFELGSEAKQMPCNHIYHSDCIV 218

Query:   245 PWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQNNLRLGNGEDRVGNGRRYW 304
             PWL   +SCPVCR ++PS       + S NR     N  + ++    N  +  GN RR  
Sbjct:   219 PWLVQHNSCPVCRQELPSASGP---SSSQNRTTPTRNYRSSSSSSSSNSREN-GNERRNP 274

Query:   305 IPIPWPFDSLFSMSGSQE--GGTSNSESS 331
                 WPF S  S S S +  GGT NS++S
Sbjct:   275 FSSFWPFRSSGSSSSSTQNRGGTRNSDTS 303

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

GO:0005618 "cell wall" evidence=IDA

TAIR|locus:2148318 RDUF2 "RING and Domain of Unknown Function 1117 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 233 (87.1 bits), Expect = 3.9e-26, Sum P(2) = 3.9e-26
 Identities = 44/95 (46%), Positives = 60/95 (63%)

Query:   191 RYGCPAANKAVLKALPTVTID-----KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP 245
             R G P A+K+ +++LP V I          CAVC E FE   EA+EMPCKH FH +CI+P
Sbjct:   169 RSGNPPASKSAIESLPRVEISDCHIGSEANCAVCTEIFETETEAREMPCKHLFHDDCIVP 228

Query:   246 WLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLG 280
             WL +R+SCPVCRF++PS+  +   N     D ++G
Sbjct:   229 WLSIRNSCPVCRFELPSEPNRRSNNNE--EDNAVG 261

GO:0005634 "nucleus" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP;RCA

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

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

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

UNIPROTKB|F6RQU6 RNF115 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 212 (79.7 bits), Expect = 1.1e-23, Sum P(2) = 1.1e-23
 Identities = 39/98 (39%), Positives = 58/98 (59%)

Query:   193 GCPAANKAVLKALPTVTI-----DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247
             G P A+K  + +LPTVT+     DK L+C VC E++ +  E +++PC H FH  CI+PWL
Sbjct:   189 GPPPADKEKITSLPTVTVTQEQVDKGLECPVCKEDYTVEEEVRQLPCNHYFHSSCIVPWL 248

Query:   248 EVRSSCPVCRFQVPSDDFKIQGNGSGNRDESLGNEDAQ 285
             E+  +CPVCR  +  +D   Q   SG    +  + D+Q
Sbjct:   249 ELHDACPVCRKSLNGEDSTQQTQRSGASASNRFSSDSQ 286

GO:0051865 "protein autoubiquitination" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|I3LDQ5 LOC100739432 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 209 (78.6 bits), Expect = 6.3e-22, Sum P(2) = 6.3e-22
 Identities = 38/86 (44%), Positives = 53/86 (61%)

Query:   193 GCPAANKAVLKALPTVTI-----DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247
             G P A+K  + +LPTVTI     DK L+C VC E++ +  E +++PC H FH  CI+PWL
Sbjct:   189 GPPPADKEKITSLPTVTITQEQVDKGLECPVCKEDYTVEEEVRQLPCNHFFHSSCIVPWL 248

Query:   248 EVRSSCPVCRFQVPSDDFKIQGNGSG 273
             E+  +CPVCR  +  +D   Q   SG
Sbjct:   249 ELHDACPVCRKSLSGEDSTQQTQTSG 274

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	342
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	7e-16
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	8e-11
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-10
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	4e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	3e-08
pfam14369	34	pfam14369, zf-RING_3, zinc-finger	4e-08
smart00184	40	smart00184, RING, Ring finger	8e-08
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	3e-07
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	5e-06
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	1e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	3e-04
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	4e-04

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

 Score = 70.5 bits (173), Expect = 7e-16
 Identities = 21/43 (48%), Positives = 29/43 (67%)

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           +C +CL+EFE G E   +PC H FH EC+  WL   ++CP+CR
Sbjct: 2   ECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 56.3 bits (136), Expect = 8e-11
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQV 260
           +C +CLEEF        +PC H F   CI  WL+    +CP+CR  +
Sbjct: 1   ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 54.4 bits (131), Expect = 3e-10
 Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 2/46 (4%)

Query: 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           + L+C +CL+     +     PC H F  ECI+ +L+ +S CP+CR
Sbjct: 1   EELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 57.7 bits (139), Expect = 2e-09
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 207 TVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVP 261
            V  DK ++CA+C+  F   +  + +PC H+FH  C+  WL    + CPVCR  +P
Sbjct: 317 AVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372

Length = 374

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

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 10/52 (19%)

Query: 216 CAVCLEEF-----EIGNEAKEMP-----CKHKFHGECIMPWLEVRSSCPVCR 257
           CA+C   F     E  +   + P     C H FH  CI  WL+ R++CP+CR
Sbjct: 22  CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 54.6 bits (131), Expect = 3e-08
 Identities = 27/103 (26%), Positives = 41/103 (39%), Gaps = 23/103 (22%)

Query: 197 ANKAVLKALPTVTIDKNLQ----CAVCLEE-FEIGNEA---------KEMPCKHKFHGEC 242
           A K +    PT T ++       C +C++E F   +E          K +PC H  H  C
Sbjct: 267 ATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHC 326

Query: 243 IMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGNRDES--LGNED 283
           +  WLE + +CP+CR  V         + S     S  + N  
Sbjct: 327 LKNWLERQQTCPICRRPV-------IFDQSSPTPASPNVRNTQ 362

Length = 491

>gnl|CDD|222714 pfam14369, zf-RING_3, zinc-finger

 Score = 48.3 bits (116), Expect = 4e-08
 Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 1/32 (3%)

Query: 8  YWCYICSQMVNP-RMEAGIKCPFCESGIVEQM 38
          YWCY C + V          CP C  G VE++
Sbjct: 3  YWCYQCDRFVRIAPSGDSDVCPRCGGGFVEEI 34

Length = 34

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

 Score = 47.5 bits (113), Expect = 8e-08
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVC 256
           C +CLEE+    +   +PC H F   CI  WLE  + +CP+C
Sbjct: 1   CPICLEEYL--KDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 3/42 (7%)

Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVC 256
           C +CLEE +  +    +PC H F  +CI+ WLE  + +CP+C
Sbjct: 1   CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 48.1 bits (114), Expect = 5e-06
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 16/79 (20%)

Query: 198  NKAVLKALPTVTIDKNLQ------CAVCLEEFEIGNEAKEMP------CKHKFHGECIMP 245
            N + +  L     + + +      CA+C     +    + +P      CK+KFH  C+  
Sbjct: 1448 NGSFMDLLGLWKKNIDEKFSGHEECAICY--SVLDMVDRSLPSKRCATCKNKFHTRCLYK 1505

Query: 246  WLEV--RSSCPVCRFQVPS 262
            W     RS+CP+CR ++  
Sbjct: 1506 WFASSARSNCPLCRSEITF 1524

Length = 1525

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)

Query: 234 CKHKFHGECIMPWLEVRSS---CPVCR 257
           CKH FH  CI+ WL   +S   CP+CR
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCR 78

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|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 234 CKHKFHGECIMPWLEVRSSCPVCR 257
           C H FH  CI  WL+ +  CP+ R
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 21/76 (27%)

Query: 199 KAVLKALPTVTID--------KNLQCAVCLEEFEIGNEAKEMP---------CKHKFHGE 241
           K  LK +P+V  +        K+ +CA+C+E+       KE+          C H F  E
Sbjct: 152 KKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVY----DKEIKNMYFGILSNCNHVFCIE 207

Query: 242 CIMPWLEVRSSCPVCR 257
           CI  W + +++CPVCR
Sbjct: 208 CIDIWKKEKNTCPVCR 223

Length = 238

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	342
PF14369	35	zf-RING_3: zinc-finger	99.51
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.42
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.4
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.2
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.11
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.09
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.08
PHA02929	238	N1R/p28-like protein; Provisional	99.06
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.95
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.92
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.91
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.83
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.82
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.77
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.73
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.72
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.66
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.63
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.62
PF14634	44	zf-RING_5: zinc-RING finger domain	98.59
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.58
PHA02926	242	zinc finger-like protein; Provisional	98.57
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.55
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.43
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.41
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.39
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.29
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.26
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.18
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.18
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.15
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.14
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.11
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.09
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.99
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.98
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.97
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.92
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.84
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.81
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.79
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.75
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.72
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.72
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.54
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.47
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.36
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.25
KOG2660	331	consensus Locus-specific chromosome binding protei	97.16
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.11
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.05
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.03
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.8
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.78
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.52
COG5152	259	Uncharacterized conserved protein, contains RING a	96.37
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.16
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.1
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.99
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	95.89
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.85
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.85
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.72
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.72
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.69
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.49
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.43
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.37
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.29
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.2
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.18
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.99
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	94.97
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.93
KOG4739	233	consensus Uncharacterized protein involved in syna	94.23
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.11
PHA03096	284	p28-like protein; Provisional	93.93
COG5236	493	Uncharacterized conserved protein, contains RING Z	93.84
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	93.78
PHA02862	156	5L protein; Provisional	93.58
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.5
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.36
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	93.26
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.25
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	93.17
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	92.99
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.68
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.51
PF04641	260	Rtf2: Rtf2 RING-finger	92.39
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	92.37
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.27
KOG1940	276	consensus Zn-finger protein [General function pred	92.23
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.22
PHA02825	162	LAP/PHD finger-like protein; Provisional	92.21
KOG1001	674	consensus Helicase-like transcription factor HLTF/	91.29
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	91.0
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	90.99
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	90.0
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	89.9
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	89.38
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	88.81
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	88.22
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	88.19
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	88.05
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	87.12
KOG4367	699	consensus Predicted Zn-finger protein [Function un	86.5
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	86.44
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	86.41
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	85.62
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	85.37
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	85.36
COG5270	202	PUA domain (predicted RNA-binding domain) [Transla	85.0
KOG3002	299	consensus Zn finger protein [General function pred	84.91
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	84.54
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	84.36
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	84.05
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	83.95
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	83.9
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	80.86
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	80.61
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	80.33

>PF14369 zf-RING_3: zinc-finger

Probab=99.51  E-value=6.5e-15  Score=96.59  Aligned_cols=32  Identities=34%  Similarity=0.995  Sum_probs=27.0

Q ss_pred             ceeeeccCceeecCC--CCCccCCCCCCCceecc
Q 043965            7 GYWCYICSQMVNPRM--EAGIKCPFCESGIVEQM   38 (342)
Q Consensus         7 ~ywCh~C~~~V~p~~--~~e~~CP~C~sGFvEE~   38 (342)
                      +||||+|++.|++..  +.+++||+|++||||||
T Consensus         2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence            499999999998653  34556999999999997

>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=99.42  E-value=5.3e-14  Score=97.01  Aligned_cols=44  Identities=52%  Similarity=1.217  Sum_probs=40.3

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcc
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR  257 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR  257 (342)
                      ++|+||++.|..++.++.++|+|+||..||.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            36999999999888999999999999999999999999999997

...

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

Probab=99.40  E-value=3.2e-13  Score=130.41  Aligned_cols=71  Identities=42%  Similarity=0.882  Sum_probs=61.3

Q ss_pred             CCCcccHHHHHcCCcccccC---c---ccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965          193 GCPAANKAVLKALPTVTIDK---N---LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD  263 (342)
Q Consensus       193 g~~~~~~~~i~~~p~~~~~~---~---~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (342)
                      ......|..++++|..++..   .   ..|+||+|+|+.|++++.|||+|.||..||.+||..+. .||+||..+...
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            45577889999999887753   1   38999999999999999999999999999999998776 599999977654

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

Probab=99.20  E-value=2.2e-11  Score=116.75  Aligned_cols=69  Identities=33%  Similarity=0.753  Sum_probs=52.6

Q ss_pred             cHHHHHcCCccccc----Ccccccccccc-cccC---------CceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          198 NKAVLKALPTVTID----KNLQCAVCLEE-FEIG---------NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       198 ~~~~i~~~p~~~~~----~~~~C~ICle~-~~~~---------~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      .|+.-+-++++..+    .+..|.||+++ |..+         .+++.|||||++|.+|++.|++++++||+||.++.-+
T Consensus       268 ~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd  347 (491)
T COG5243         268 TKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFD  347 (491)
T ss_pred             hhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccccc
Confidence            34444455555443    46789999999 4432         2579999999999999999999999999999997554


Q ss_pred             Ccc
Q 043965          264 DFK  266 (342)
Q Consensus       264 ~~~  266 (342)
                      ..+
T Consensus       348 ~~~  350 (491)
T COG5243         348 QSS  350 (491)
T ss_pred             cCC
Confidence            433

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.11  E-value=8.6e-11  Score=105.00  Aligned_cols=55  Identities=27%  Similarity=0.706  Sum_probs=45.3

Q ss_pred             ccccCcccccccccccccCCceeEecccccccccchHHHhhc----------------CCCCCCcccccCCCCc
Q 043965          208 VTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV----------------RSSCPVCRFQVPSDDF  265 (342)
Q Consensus       208 ~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~----------------~~~CP~CR~~l~~~~~  265 (342)
                      +...+..+|+||++.++   .++.++|+|.||..||.+|+..                ...||+||..+.....
T Consensus        13 ~~~~~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L   83 (193)
T PLN03208         13 VDSGGDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL   83 (193)
T ss_pred             ccCCCccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence            34446789999999987   7788999999999999999852                2479999999976554

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

Probab=99.09  E-value=3.5e-11  Score=112.82  Aligned_cols=50  Identities=36%  Similarity=1.030  Sum_probs=46.1

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhh-cCCCCCCcccccCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPS  262 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~  262 (342)
                      ..+|+|||+.|..+++.+.|||+|.||..|+.+|+. .+..||+||.+++.
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            468999999999999999999999999999999997 66799999999874

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.08  E-value=5.5e-11  Score=91.03  Aligned_cols=45  Identities=40%  Similarity=0.877  Sum_probs=35.9

Q ss_pred             ccccccccccccc----------CCceeEecccccccccchHHHhhcCCCCCCcc
Q 043965          213 NLQCAVCLEEFEI----------GNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR  257 (342)
Q Consensus       213 ~~~C~ICle~~~~----------~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR  257 (342)
                      +..|+||++.|..          .-.+...+|+|.||..||.+||+.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            4469999999932          12345567999999999999999999999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.06  E-value=1e-10  Score=108.40  Aligned_cols=64  Identities=34%  Similarity=0.671  Sum_probs=49.9

Q ss_pred             cHHHHHcCCcccc--------cCcccccccccccccCCc-----eeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          198 NKAVLKALPTVTI--------DKNLQCAVCLEEFEIGNE-----AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       198 ~~~~i~~~p~~~~--------~~~~~C~ICle~~~~~~~-----~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      .+..++.+|.+..        ..+.+|+||++.+.....     ++.++|+|.||..||.+|++.+.+||+||..+.
T Consensus       151 ~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        151 YKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             hHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            5667777776642        235789999999764321     244569999999999999999999999999875

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

Probab=98.95  E-value=6.1e-10  Score=101.36  Aligned_cols=53  Identities=30%  Similarity=0.736  Sum_probs=45.0

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCcccccCCCCccc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQVPSDDFKI  267 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~~~~~~~  267 (342)
                      ..++|.|||+.-+   +++++.|||.||+.||.+||..+.   .||+||..|..+.+..
T Consensus        46 ~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP  101 (230)
T KOG0823|consen   46 GFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP  101 (230)
T ss_pred             CceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence            4679999999877   788888999999999999997554   6999999998776543

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

Probab=98.92  E-value=5.9e-10  Score=78.88  Aligned_cols=46  Identities=30%  Similarity=0.822  Sum_probs=40.6

Q ss_pred             cccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      +..|.||++...   .+..+||+|. ||..|+..|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            568999999977   7899999999 999999999999999999999874

...

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

Probab=98.91  E-value=3.9e-10  Score=105.52  Aligned_cols=50  Identities=30%  Similarity=0.830  Sum_probs=45.3

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      ...|.+||+...   .+..+||||+||..||..|+..+..||+||..+...+.
T Consensus       239 ~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  239 TRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            478999999987   88999999999999999999999999999998876543

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

Probab=98.83  E-value=1.5e-09  Score=72.89  Aligned_cols=39  Identities=44%  Similarity=1.031  Sum_probs=32.9

Q ss_pred             ccccccccccCCceeEecccccccccchHHHhhcCCCCCCc
Q 043965          216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVC  256 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C  256 (342)
                      |+||++.+..  .++.++|||+||..||.+|++.+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999882  33788999999999999999998899998

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

Probab=98.82  E-value=1.7e-09  Score=73.94  Aligned_cols=38  Identities=37%  Similarity=0.993  Sum_probs=30.8

Q ss_pred             ccccccccccCCceeEecccccccccchHHHhhcCC----CCCCc
Q 043965          216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVC  256 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~C  256 (342)
                      |+||++.|.   +++.|+|||+||..||..|++...    .||+|
T Consensus         1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            899999999   999999999999999999996542    69988

>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=98.77  E-value=3.7e-09  Score=71.39  Aligned_cols=44  Identities=41%  Similarity=1.104  Sum_probs=36.3

Q ss_pred             cccccccccccCCceeEecccccccccchHHHhhc-CCCCCCccccc
Q 043965          215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQV  260 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l  260 (342)
                      .|+||++.+.  +....++|+|.||..|+..|++. ...||+||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999984  24445559999999999999987 67899998754

>smart00504 Ubox Modified RING finger domain

Probab=98.73  E-value=6.1e-09  Score=76.58  Aligned_cols=48  Identities=21%  Similarity=0.484  Sum_probs=42.8

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      +.|+||++.+.   .++.++|||+|+..||.+|++.+.+||+|+..+..++
T Consensus         2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~   49 (63)
T smart00504        2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED   49 (63)
T ss_pred             cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence            57999999998   6788999999999999999988889999999885544

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=98.72  E-value=3.8e-09  Score=92.60  Aligned_cols=51  Identities=25%  Similarity=0.664  Sum_probs=43.2

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      ...|+|||+.+... .++.+.|||+||..||...++....||+|++.|..+.
T Consensus       131 ~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  131 TYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             ccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            46899999999832 2355789999999999999999999999999887654

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

Probab=98.66  E-value=1.2e-08  Score=79.74  Aligned_cols=51  Identities=31%  Similarity=0.767  Sum_probs=39.0

Q ss_pred             Cccccccccccccc--------CC--ceeEecccccccccchHHHhhc---CCCCCCcccccCC
Q 043965          212 KNLQCAVCLEEFEI--------GN--EAKEMPCKHKFHGECIMPWLEV---RSSCPVCRFQVPS  262 (342)
Q Consensus       212 ~~~~C~ICle~~~~--------~~--~~~~lpC~H~Fh~~Ci~~Wl~~---~~~CP~CR~~l~~  262 (342)
                      +++.|.||...|..        |+  .++.-.|+|.||..||.+||..   +..||+||++...
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            47789999988862        22  2333459999999999999975   3589999998753

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

Probab=98.63  E-value=8.5e-09  Score=106.80  Aligned_cols=49  Identities=39%  Similarity=1.018  Sum_probs=43.8

Q ss_pred             cccccccccccccCCc--eeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          213 NLQCAVCLEEFEIGNE--AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      +..|+||+|.+..+..  ++.|+|+|+||..|+..|+++.++||+||..+.
T Consensus       291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~  341 (543)
T KOG0802|consen  291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLY  341 (543)
T ss_pred             CCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhh
Confidence            6789999999985543  899999999999999999999999999999543

>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=98.62  E-value=1.6e-08  Score=68.29  Aligned_cols=38  Identities=45%  Similarity=1.215  Sum_probs=33.1

Q ss_pred             ccccccccccCCcee-EecccccccccchHHHhh--cCCCCCCc
Q 043965          216 CAVCLEEFEIGNEAK-EMPCKHKFHGECIMPWLE--VRSSCPVC  256 (342)
Q Consensus       216 C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~--~~~~CP~C  256 (342)
                      |+||++.+.   .+. .++|+|.||..||.+|++  ....||+|
T Consensus         1 C~iC~~~~~---~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFE---DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCS---SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCcccc---CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999988   445 888999999999999998  44589998

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 ....

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.59  E-value=2.4e-08  Score=68.79  Aligned_cols=44  Identities=25%  Similarity=0.740  Sum_probs=38.3

Q ss_pred             cccccccccccCCceeEecccccccccchHHHhhcCCCCCCccc
Q 043965          215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF  258 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~  258 (342)
                      .|.||++.|.....+..++|+|+||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            49999999955567889999999999999999866679999984

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.58  E-value=2.3e-08  Score=99.03  Aligned_cols=51  Identities=29%  Similarity=0.722  Sum_probs=45.0

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +...+.|+||++.|.   .++.++|+|.||..||..|+.....||+||..+...
T Consensus        23 Le~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            445689999999998   677899999999999999998888999999988654

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

>PHA02926 zinc finger-like protein; Provisional

Probab=98.57  E-value=2.5e-08  Score=90.53  Aligned_cols=50  Identities=30%  Similarity=0.672  Sum_probs=37.9

Q ss_pred             CcccccccccccccCC-----c-eeEecccccccccchHHHhhcC------CCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIGN-----E-AKEMPCKHKFHGECIMPWLEVR------SSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~-----~-~~~lpC~H~Fh~~Ci~~Wl~~~------~~CP~CR~~l~  261 (342)
                      ++.+|+||+|..-...     . ....+|+|.||..||..|.+.+      .+||+||..+.
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            4688999999864221     1 2344699999999999999753      36999999764

>smart00184 RING Ring finger

Probab=98.55  E-value=3.7e-08  Score=64.14  Aligned_cols=38  Identities=42%  Similarity=1.206  Sum_probs=33.5

Q ss_pred             ccccccccccCCceeEecccccccccchHHHhh-cCCCCCCc
Q 043965          216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVC  256 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~C  256 (342)
                      |+||++...   .+..++|+|.||..|+..|++ ....||+|
T Consensus         1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999854   788899999999999999998 56689987

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)

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

Probab=98.43  E-value=6.5e-08  Score=89.69  Aligned_cols=51  Identities=33%  Similarity=0.791  Sum_probs=43.9

Q ss_pred             CcccccccccccccCCceeEecccccccccchHH-HhhcCCC-CCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP-WLEVRSS-CPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~-Wl~~~~~-CP~CR~~l~~~~~  265 (342)
                      .+..|+||++...   .+..++|||+||..||.. |-..+.. ||+||+.+..+..
T Consensus       214 ~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccC---CcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            4778999999988   889999999999999999 8777665 9999998765543

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

Probab=98.41  E-value=7.3e-08  Score=96.54  Aligned_cols=59  Identities=31%  Similarity=0.638  Sum_probs=46.6

Q ss_pred             ccccCcccccccccccccCCceeEecccccccccchHHHhhcC-----CCCCCcccccCCCCcccCC
Q 043965          208 VTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-----SSCPVCRFQVPSDDFKIQG  269 (342)
Q Consensus       208 ~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-----~~CP~CR~~l~~~~~~~~~  269 (342)
                      +.+..+..|+|||+...   .+..+.|||+||..||.++|...     ..||+||..|..+++....
T Consensus       181 v~~~t~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  181 VYGSTDMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF  244 (513)
T ss_pred             hhcCcCCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence            33333778999999987   67777899999999999987544     3799999999887665443

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

Probab=98.39  E-value=6.4e-08  Score=92.31  Aligned_cols=51  Identities=33%  Similarity=0.813  Sum_probs=46.1

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      ..+.|.||.++|.   .+.++||+|.||..||..+|..+..||+|+.++....+
T Consensus        22 ~lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   22 DLLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence            4568999999999   88999999999999999999999999999998876553

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

Probab=98.29  E-value=3.7e-07  Score=69.83  Aligned_cols=31  Identities=35%  Similarity=0.826  Sum_probs=27.9

Q ss_pred             ecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          232 MPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       232 lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      -.|.|.||..||.+||..++.||++|+....
T Consensus        52 G~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          52 GVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             EecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            3499999999999999999999999987743

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

Probab=98.26  E-value=4.2e-07  Score=69.42  Aligned_cols=51  Identities=22%  Similarity=0.470  Sum_probs=40.7

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~  265 (342)
                      +.+.|+||.+.+.   +++.++|||+|.+.||..||+. +.+||+|+..+...+.
T Consensus         3 ~~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l   54 (73)
T PF04564_consen    3 DEFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDL   54 (73)
T ss_dssp             GGGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGS
T ss_pred             cccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccc
Confidence            4578999999999   8999999999999999999988 7799999998876543

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 ....

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

Probab=98.18  E-value=4.3e-07  Score=84.37  Aligned_cols=60  Identities=30%  Similarity=0.739  Sum_probs=46.4

Q ss_pred             cCCcccccCcccccccccccccCC-------ceeEecccccccccchHHHh--hcCCCCCCcccccCCCC
Q 043965          204 ALPTVTIDKNLQCAVCLEEFEIGN-------EAKEMPCKHKFHGECIMPWL--EVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       204 ~~p~~~~~~~~~C~ICle~~~~~~-------~~~~lpC~H~Fh~~Ci~~Wl--~~~~~CP~CR~~l~~~~  264 (342)
                      .+|+..+ ++..|+||-..+....       +...|.|+|+||..||.-|.  .++++||.|+..+..+.
T Consensus       216 glPtkhl-~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  216 GLPTKHL-SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCCCCCC-CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            3444444 3567999998886544       66789999999999999997  56679999999876543

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

Probab=98.18  E-value=7.5e-07  Score=61.16  Aligned_cols=38  Identities=32%  Similarity=0.836  Sum_probs=22.7

Q ss_pred             cccccccccc-CCceeEecccccccccchHHHhhcCC----CCC
Q 043965          216 CAVCLEEFEI-GNEAKEMPCKHKFHGECIMPWLEVRS----SCP  254 (342)
Q Consensus       216 C~ICle~~~~-~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP  254 (342)
                      |+||++ |.. ...++.|+|||+|+.+||.++++...    .||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 753 34588999999999999999997542    576

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

Probab=98.15  E-value=6.9e-07  Score=83.81  Aligned_cols=48  Identities=31%  Similarity=0.602  Sum_probs=43.2

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      ..+.|-||-+.|.   .+..++|||.||..||...|..+..||+||.+...
T Consensus        24 s~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          24 SMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             hHHHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            3568999999999   78889999999999999999999999999987643

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

Probab=98.14  E-value=6.7e-07  Score=89.06  Aligned_cols=50  Identities=30%  Similarity=0.974  Sum_probs=39.9

Q ss_pred             cccccccccccccCC--------------ceeEecccccccccchHHHhh-cCCCCCCcccccCC
Q 043965          213 NLQCAVCLEEFEIGN--------------EAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPS  262 (342)
Q Consensus       213 ~~~C~ICle~~~~~~--------------~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~  262 (342)
                      ...|+||+..+....              .-..+||.|+||..|+.+|+. .+..||+||.+|+.
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            467999999885211              133568999999999999998 56699999999874

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

Probab=98.11  E-value=5.4e-07  Score=68.40  Aligned_cols=49  Identities=33%  Similarity=0.836  Sum_probs=36.7

Q ss_pred             ccccccccccccc--------C-CceeEec-ccccccccchHHHhhcC---CCCCCcccccC
Q 043965          213 NLQCAVCLEEFEI--------G-NEAKEMP-CKHKFHGECIMPWLEVR---SSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~--------~-~~~~~lp-C~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~  261 (342)
                      +..|.||.-.|..        + +.+.++- |.|.||..||.+|+...   ..||+||+.+.
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            4589999888852        2 2333333 99999999999999643   47999998764

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

Probab=98.09  E-value=8e-07  Score=94.01  Aligned_cols=54  Identities=28%  Similarity=0.820  Sum_probs=40.6

Q ss_pred             ccccCcccccccccccccCC---cee-EecccccccccchHHHhhcCC--CCCCcccccC
Q 043965          208 VTIDKNLQCAVCLEEFEIGN---EAK-EMPCKHKFHGECIMPWLEVRS--SCPVCRFQVP  261 (342)
Q Consensus       208 ~~~~~~~~C~ICle~~~~~~---~~~-~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~  261 (342)
                      .++.+..+|+||+..+..-+   .-+ .-.|+|.||..|+.+|++...  +||+||.+++
T Consensus      1464 ~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1464 EKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            34556789999998886221   122 334999999999999997654  8999998775

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

Probab=97.99  E-value=1.9e-06  Score=79.90  Aligned_cols=45  Identities=42%  Similarity=0.941  Sum_probs=39.4

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR  257 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR  257 (342)
                      +.+...|+||++.|.   .++.++|+|.||..||..++.....||.||
T Consensus        10 ~~~~~~C~iC~~~~~---~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   10 LQEELTCPICLEYFR---EPVLLPCGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             ccccccChhhHHHhh---cCccccccchHhHHHHHHhcCCCcCCcccC
Confidence            345688999999999   558999999999999999888555899999

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

Probab=97.98  E-value=3.9e-06  Score=59.25  Aligned_cols=42  Identities=24%  Similarity=0.790  Sum_probs=33.5

Q ss_pred             cccccccccccCCceeEeccc-----ccccccchHHHhhcCC--CCCCcc
Q 043965          215 QCAVCLEEFEIGNEAKEMPCK-----HKFHGECIMPWLEVRS--SCPVCR  257 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~~--~CP~CR  257 (342)
                      .|-||++ ...++.+..+||.     |.+|..|+.+|+..+.  +||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998 4445567788985     8999999999996554  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

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

Probab=97.97  E-value=2.3e-06  Score=63.25  Aligned_cols=51  Identities=29%  Similarity=0.733  Sum_probs=26.4

Q ss_pred             cCcccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (342)
                      ++...|++|.+.++   .++.| .|.|+||..||..-+.  ..||+|+.+.-..+.+
T Consensus         5 e~lLrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    5 EELLRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             HHTTS-SSS-S--S---S-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS--
T ss_pred             HHhcCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHH
Confidence            44578999999998   66554 5999999999988654  3599999877666554

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

Probab=97.92  E-value=2.2e-06  Score=65.01  Aligned_cols=50  Identities=28%  Similarity=0.657  Sum_probs=23.3

Q ss_pred             cccccccccccc-cCCce-eEe---cccccccccchHHHhhc----C-------CCCCCcccccCC
Q 043965          213 NLQCAVCLEEFE-IGNEA-KEM---PCKHKFHGECIMPWLEV----R-------SSCPVCRFQVPS  262 (342)
Q Consensus       213 ~~~C~ICle~~~-~~~~~-~~l---pC~H~Fh~~Ci~~Wl~~----~-------~~CP~CR~~l~~  262 (342)
                      +..|.||+..+. .+..+ +.-   .|++.||..||.+||..    +       ..||.|+.+|..
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            357999999876 33222 222   49999999999999952    1       159999998753

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.84  E-value=8.4e-06  Score=78.14  Aligned_cols=54  Identities=19%  Similarity=0.428  Sum_probs=38.9

Q ss_pred             cccccccccccccCCc--eeEecccccccccchHHHh-hcCCCCCCcccccCCCCcc
Q 043965          213 NLQCAVCLEEFEIGNE--AKEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~  266 (342)
                      +..|+||+..-.....  ....+|||.||..||...+ .....||.|+..+......
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            3579999995332222  2233799999999999965 4455899999988766543

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).

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

Probab=97.81  E-value=2.6e-06  Score=82.03  Aligned_cols=51  Identities=29%  Similarity=0.699  Sum_probs=41.8

Q ss_pred             ccCcccccccccccccCCceeEec-ccccccccchHHHhhc-CCCCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEV-RSSCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~  263 (342)
                      +.....|+|||+.++   ..+.++ |.|.||..||..-++. .+.||.||+.+..+
T Consensus        40 ~~~~v~c~icl~llk---~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   40 FDIQVICPICLSLLK---KTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhhhccHHHHHHHH---hhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            345678999999998   555555 9999999999988865 45899999988655

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

Probab=97.79  E-value=8.3e-06  Score=80.71  Aligned_cols=54  Identities=37%  Similarity=0.896  Sum_probs=41.3

Q ss_pred             CcccccCcccccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          206 PTVTIDKNLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       206 p~~~~~~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      +...+.+-.+|+||||.+.... .++.+.|.|.||..|+.+|.  ..+||+||.-..
T Consensus       168 ~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  168 PPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             CCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            3344456678999999997543 23445599999999999994  568999998665

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

Probab=97.75  E-value=1.3e-05  Score=77.60  Aligned_cols=47  Identities=26%  Similarity=0.728  Sum_probs=41.7

Q ss_pred             cccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      ..+|.||+.+..   +..+|||.|. .|..|.+..--+++.||+||+++..
T Consensus       290 gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  290 GKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             CCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            568999999988   8999999999 8999998877788999999998854

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

Probab=97.72  E-value=1.1e-05  Score=76.24  Aligned_cols=49  Identities=29%  Similarity=0.564  Sum_probs=41.1

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcC-CCCCCcccccCCCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQVPSDD  264 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (342)
                      ..+|+||+....   .++.|+|+|.||..||.--.+.. .+|++||.+++...
T Consensus         7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence            457999998876   77899999999999998766544 47999999998764

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

Probab=97.72  E-value=1.4e-05  Score=64.25  Aligned_cols=30  Identities=37%  Similarity=0.778  Sum_probs=26.7

Q ss_pred             ecccccccccchHHHhhcCCCCCCcccccC
Q 043965          232 MPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       232 lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      --|.|.||..||.+||+.++.||+|.++..
T Consensus        79 G~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   79 GVCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             eecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            349999999999999999999999987653

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

Probab=97.54  E-value=1.5e-05  Score=56.86  Aligned_cols=45  Identities=22%  Similarity=0.606  Sum_probs=36.5

Q ss_pred             ccccccccccccCCceeEeccccc-ccccchHHHhh-cCCCCCCcccccC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLE-VRSSCPVCRFQVP  261 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~-~~~~CP~CR~~l~  261 (342)
                      .+|.||+|.-.   +.+...|||. .|..|-.+.++ .+..||+||.++.
T Consensus         8 dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            68999998765   4556669998 88999876554 8889999999875

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

Probab=97.47  E-value=3.8e-05  Score=72.61  Aligned_cols=92  Identities=22%  Similarity=0.448  Sum_probs=61.1

Q ss_pred             CchhHHHHHHHhcCCCCCCCCcccHHHHHcCCcc---cccCcccccccccccccCCceeEecccccccccchHHHhhc--
Q 043965          175 PGLDLLLQHLLENDPNRYGCPAANKAVLKALPTV---TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--  249 (342)
Q Consensus       175 ~~l~~l~~~L~~~~~~~~g~~~~~~~~i~~~p~~---~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--  249 (342)
                      +.|..|.+++.+......|.| .--+.++.....   .-.....|.|||.-|..++....++|-|.||..|+-++|..  
T Consensus        75 ~~~~~i~~~~~~iikq~~g~p-ii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~  153 (368)
T KOG4445|consen   75 PEFREIQRQIQEIIKQNSGMP-IICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL  153 (368)
T ss_pred             HHHHHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence            456666666665444445543 333333332221   11235689999999998888899999999999999887631  


Q ss_pred             ---------------------CCCCCCcccccCCCCccc
Q 043965          250 ---------------------RSSCPVCRFQVPSDDFKI  267 (342)
Q Consensus       250 ---------------------~~~CP~CR~~l~~~~~~~  267 (342)
                                           ...||+||..|..+.-.+
T Consensus       154 ~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~sl  192 (368)
T KOG4445|consen  154 TGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENSL  192 (368)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccce
Confidence                                 125999999887665433

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

Probab=97.37  E-value=0.0001  Score=72.11  Aligned_cols=51  Identities=29%  Similarity=0.768  Sum_probs=38.1

Q ss_pred             cCcccccccccccccCC----ceeEec-ccccccccchHHHh--hc-----CCCCCCcccccC
Q 043965          211 DKNLQCAVCLEEFEIGN----EAKEMP-CKHKFHGECIMPWL--EV-----RSSCPVCRFQVP  261 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl--~~-----~~~CP~CR~~l~  261 (342)
                      ..+..|.||++......    .-.+|| |.|.||..||..|-  .+     ...||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            56778999999976322    012345 99999999999998  33     458999998653

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

Probab=97.37  E-value=6.1e-05  Score=73.46  Aligned_cols=48  Identities=27%  Similarity=0.853  Sum_probs=36.2

Q ss_pred             ccccccccccccCCceeEec-ccccccccchHHHhhcCC---CCCCcccccC
Q 043965          214 LQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRS---SCPVCRFQVP  261 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~  261 (342)
                      ..|.||.+-+.....+..+. |||+||..|+.+|++.-.   .||+|+-.++
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            46999966555444555555 999999999999997644   7999994443

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

Probab=97.36  E-value=4.7e-05  Score=79.96  Aligned_cols=52  Identities=29%  Similarity=0.673  Sum_probs=43.6

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhh-cCCCCCCcccccCCCCc
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~~  265 (342)
                      .+.+.|++|-..++   .++++.|+|+||..|+.+-+. ++..||.|...|-..++
T Consensus       641 K~~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  641 KELLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             HhceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            34678999998887   788888999999999999885 55699999998866554

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

Probab=97.25  E-value=5.3e-05  Score=79.31  Aligned_cols=53  Identities=28%  Similarity=0.490  Sum_probs=45.0

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      ...|++|+..+..+......+|+|.||..||..|-+...+||+||..+....+
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V  175 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKV  175 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeee
Confidence            35799999999866666667799999999999999999999999998865443

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

Probab=97.16  E-value=0.0001  Score=70.72  Aligned_cols=51  Identities=25%  Similarity=0.707  Sum_probs=42.8

Q ss_pred             ccCcccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +....+|.+|..+|.   ++..+. |-|.||..||...|....+||.|...+-..
T Consensus        12 ~n~~itC~LC~GYli---DATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLI---DATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             cccceehhhccceee---cchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            445678999999998   555555 999999999999999999999998776443

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

Probab=97.11  E-value=0.00017  Score=71.77  Aligned_cols=49  Identities=29%  Similarity=0.697  Sum_probs=44.0

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      ..++.|.||+..+.   .++.+||||.||..||.+-+.....||+||..+..
T Consensus        82 ~sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcC---CCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            34688999999998   88888999999999999988888899999999875

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

Probab=97.05  E-value=0.00026  Score=70.80  Aligned_cols=52  Identities=29%  Similarity=0.835  Sum_probs=44.5

Q ss_pred             ccCcccccccccccccCCceeE-ecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      +.+++.|+||...+.   .+.. +.|+|.||..|+..|+..+..||.|+..+....
T Consensus        18 ~~~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCcccccccc---CCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            567789999999998   5555 579999999999999999999999988775443

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

Probab=97.03  E-value=0.0002  Score=70.09  Aligned_cols=50  Identities=26%  Similarity=0.731  Sum_probs=42.0

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhc--CCCCCCcccccCCCCcc
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--RSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~~~~~  266 (342)
                      ..|.||-|.-+   ++++-||||..|..|+..|-..  .++||.||.++...+..
T Consensus       370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            35999988755   8889999999999999999843  46999999999876643

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

Probab=96.80  E-value=0.00047  Score=50.21  Aligned_cols=41  Identities=34%  Similarity=0.834  Sum_probs=27.9

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcC--CCCCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--SSCPV  255 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~  255 (342)
                      ...|+|.+..|+  +.++...|+|+|-+..|.+||..+  ..||+
T Consensus        11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            578999999998  344455799999999999999443  37998

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

Probab=96.78  E-value=0.00062  Score=67.01  Aligned_cols=48  Identities=27%  Similarity=0.827  Sum_probs=36.7

Q ss_pred             cccccccccccccCC--ceeEecccccccccchHHHhhc--CCCCCCccccc
Q 043965          213 NLQCAVCLEEFEIGN--EAKEMPCKHKFHGECIMPWLEV--RSSCPVCRFQV  260 (342)
Q Consensus       213 ~~~C~ICle~~~~~~--~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l  260 (342)
                      ..+|+||++.+....  ....+.|+|.|...||.+||.+  ...||.|..+-
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            357999999997543  3445569999999999999952  23799997644

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

Probab=96.52  E-value=0.00071  Score=66.26  Aligned_cols=48  Identities=38%  Similarity=0.796  Sum_probs=38.5

Q ss_pred             cccccccccccccCC-ceeEecccccccccchHHHhhcCC--CCCCccccc
Q 043965          213 NLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRS--SCPVCRFQV  260 (342)
Q Consensus       213 ~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l  260 (342)
                      .+-|..|-+.+-..+ ....|||.|+||..|+...|.++.  +||.||+-.
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr  415 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR  415 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            467999999885433 566789999999999999996655  899999533

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

Probab=96.37  E-value=0.00093  Score=59.95  Aligned_cols=46  Identities=22%  Similarity=0.574  Sum_probs=40.7

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      +.|.||.++|+   .++.+.|||.||..|...-++....|-+|-+....
T Consensus       197 F~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G  242 (259)
T COG5152         197 FLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG  242 (259)
T ss_pred             eeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence            57999999999   78888999999999999998888999999765543

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

Probab=96.16  E-value=0.0035  Score=60.84  Aligned_cols=50  Identities=24%  Similarity=0.428  Sum_probs=43.4

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      .++..|+||...-.   .++..||+|.-|+.||.+.|...+.|=.|+..+...
T Consensus       420 sEd~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~  469 (489)
T KOG4692|consen  420 SEDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDV  469 (489)
T ss_pred             cccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence            45678999987655   788899999999999999999999999999887643

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

Probab=96.10  E-value=0.0017  Score=61.51  Aligned_cols=46  Identities=24%  Similarity=0.514  Sum_probs=41.2

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      +.|-||...|.   .++...|+|.||..|...-++....|.+|-+....
T Consensus       242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            56999999999   88899999999999999999988999999876543

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

Probab=95.99  E-value=0.0032  Score=69.94  Aligned_cols=52  Identities=33%  Similarity=0.680  Sum_probs=41.5

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCC----------CCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----------SCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----------~CP~CR~~l~~  262 (342)
                      ..++.|.||+.+--.....+.|.|+|+||..|....|+..-          +||+|+.++..
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            34678999998766566788999999999999987765432          79999988753

>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]

Probab=95.89  E-value=0.0041  Score=51.58  Aligned_cols=39  Identities=23%  Similarity=0.497  Sum_probs=30.5

Q ss_pred             CCCCCceeeeccCceeecCCCCCccCCCCCCCceeccccC
Q 043965            2 GDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSS   41 (342)
Q Consensus         2 ~~~~~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~~~   41 (342)
                      ++..+..||..|.+++.+..- ++.||.|+|..+.-+...
T Consensus        65 e~~p~~~~C~~C~~~~~~e~~-~~~CP~C~s~~~~i~~G~  103 (115)
T COG0375          65 EEEPAECWCLDCGQEVELEEL-DYRCPKCGSINLRIIGGD  103 (115)
T ss_pred             EEeccEEEeccCCCeecchhh-eeECCCCCCCceEEecCC
Confidence            344556999999999976543 777999999998877644

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

Probab=95.85  E-value=0.0038  Score=43.75  Aligned_cols=44  Identities=30%  Similarity=0.612  Sum_probs=22.1

Q ss_pred             ccccccccccCCceeEec--ccccccccchHHHhh-cCCCCCCccccc
Q 043965          216 CAVCLEEFEIGNEAKEMP--CKHKFHGECIMPWLE-VRSSCPVCRFQV  260 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l  260 (342)
                      |++|.+++... ....+|  |++.+|..|...-++ ....||-||.+.
T Consensus         1 cp~C~e~~d~~-d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDET-DKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CC-CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccC-CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            78999999433 334455  899999999888876 467999999864

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

Probab=95.85  E-value=0.0052  Score=57.79  Aligned_cols=48  Identities=25%  Similarity=0.394  Sum_probs=36.6

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhc--CCCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--RSSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~  261 (342)
                      .+.+|++|-+.-.  ..-...+|+|+||+.||..-+..  ..+||.|-.++.
T Consensus       238 ~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  238 SDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             CCceeeccCCCCC--CCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            4578999998866  23344559999999999886643  359999987665

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

Probab=95.72  E-value=0.0058  Score=59.53  Aligned_cols=43  Identities=35%  Similarity=0.681  Sum_probs=33.0

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ...|.||++..+   ..+.+||||.-|  |..--. .-.+||+||..+.
T Consensus       305 p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  305 PDLCVVCLDEPK---SAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIR  347 (355)
T ss_pred             CCceEEecCCcc---ceeeecCCcEEE--chHHHh-hCCCCchhHHHHH
Confidence            467999999988   789999999966  654432 2335999998764

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

Probab=95.72  E-value=0.003  Score=64.13  Aligned_cols=51  Identities=31%  Similarity=0.720  Sum_probs=41.2

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhc-----CCCCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-----RSSCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-----~~~CP~CR~~l~~~~~  265 (342)
                      +...|.+|-+.-+   +.+...|.|.||+.||..++..     .-+||+|-..|..+..
T Consensus       535 ~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDls  590 (791)
T KOG1002|consen  535 GEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLS  590 (791)
T ss_pred             CceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccccc
Confidence            3467999999877   7888899999999999888742     3489999888876643

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=95.69  E-value=0.0049  Score=49.60  Aligned_cols=37  Identities=30%  Similarity=0.602  Sum_probs=30.5

Q ss_pred             cccccCcccccccccccccCCceeEecccccccccchH
Q 043965          207 TVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIM  244 (342)
Q Consensus       207 ~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~  244 (342)
                      .+.+.+...|+||...+.. ......||+|+||..|+.
T Consensus        72 ~v~i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   72 SVVITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             eEEECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            3455677889999999875 577788999999999974

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 [].

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

Probab=95.49  E-value=0.0037  Score=54.48  Aligned_cols=28  Identities=32%  Similarity=0.877  Sum_probs=26.2

Q ss_pred             cccccccccccccCCceeEecccccccc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHG  240 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~  240 (342)
                      ..+|.||||+++.++.+..|||-.+||+
T Consensus       177 kGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  177 KGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             CCcEEEEhhhccCCCceeccceEEEeec
Confidence            4689999999999999999999999996

>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=95.43  E-value=0.0051  Score=52.19  Aligned_cols=35  Identities=14%  Similarity=0.537  Sum_probs=30.2

Q ss_pred             cccccccccccccCCceeEeccc------ccccccchHHHh
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCK------HKFHGECIMPWL  247 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~------H~Fh~~Ci~~Wl  247 (342)
                      ..+|.||++.+...+.++.++|+      |.||..|+.+|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence            46899999999875677888886      899999999994

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

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

Probab=95.37  E-value=0.0093  Score=54.64  Aligned_cols=49  Identities=22%  Similarity=0.584  Sum_probs=38.9

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhc--------CCCCCCcccccCCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--------RSSCPVCRFQVPSD  263 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--------~~~CP~CR~~l~~~  263 (342)
                      .-|..|--.+..++.+ .|-|-|.||.+|+..|-..        ...||.|..+|...
T Consensus        51 pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   51 PNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            4599999999877655 5669999999999999743        22799999888544

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

Probab=95.29  E-value=0.0093  Score=41.62  Aligned_cols=40  Identities=30%  Similarity=0.839  Sum_probs=26.7

Q ss_pred             ccccccccccCCceeEeccc--c---cccccchHHHhhc--CCCCCCc
Q 043965          216 CAVCLEEFEIGNEAKEMPCK--H---KFHGECIMPWLEV--RSSCPVC  256 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~--~~~CP~C  256 (342)
                      |-||++.-.... ....||+  -   ..|..|+.+|+..  ..+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679998876443 5667754  3   6899999999964  4479887

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

Probab=95.20  E-value=0.008  Score=59.48  Aligned_cols=46  Identities=26%  Similarity=0.636  Sum_probs=37.2

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcC--------CCCCCccc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--------SSCPVCRF  258 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--------~~CP~CR~  258 (342)
                      ...|.||++........+.+||+|+||..|+..++..+        -.||-|..
T Consensus       184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            46899999998755788999999999999999988532        25877654

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

Probab=95.18  E-value=0.0087  Score=63.85  Aligned_cols=50  Identities=26%  Similarity=0.679  Sum_probs=36.7

Q ss_pred             cCcccccccccccccCCcee-EecccccccccchHHHhhcCC-------CCCCccccc
Q 043965          211 DKNLQCAVCLEEFEIGNEAK-EMPCKHKFHGECIMPWLEVRS-------SCPVCRFQV  260 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~~~~-------~CP~CR~~l  260 (342)
                      ....+|.||++.+.....+- .-.|-|+||..||..|-....       .||.|+...
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            35678999999997544332 234889999999999985422       599998433

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.99  E-value=0.017  Score=53.60  Aligned_cols=57  Identities=16%  Similarity=0.219  Sum_probs=46.9

Q ss_pred             cccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCCCcccCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQG  269 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  269 (342)
                      ...|+||.+.+........| ||||+|+..|+.+.+.....||+|-.++...++....
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq  278 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ  278 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence            46899999999865544444 5999999999999999999999999999877664433

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

Probab=94.97  E-value=0.014  Score=56.19  Aligned_cols=47  Identities=21%  Similarity=0.499  Sum_probs=37.3

Q ss_pred             CcccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ....|+||+....   .+..+. -|.+||+.||.+.+..++.||+=-.+..
T Consensus       299 ~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  299 DREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS  346 (357)
T ss_pred             ccccChhHHhccC---CCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence            3567999998876   333443 6999999999999999999998765543

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

Probab=94.93  E-value=0.0057  Score=57.99  Aligned_cols=42  Identities=24%  Similarity=0.626  Sum_probs=33.6

Q ss_pred             cccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ...|.||++...   +.+.|+|||. -|..|-...    +.||+||+.+.
T Consensus       300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCc---ceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence            457999999877   8899999997 677776442    38999998764

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

Probab=94.23  E-value=0.018  Score=53.33  Aligned_cols=47  Identities=19%  Similarity=0.482  Sum_probs=34.7

Q ss_pred             cccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      .|-.|..--. ++...++.|.|+||..|...-.  ...||+|+..+....
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQ   51 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhcccCC--ccccccccceeeeee
Confidence            5777766544 6677778899999999986522  228999999875543

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

Probab=94.11  E-value=0.027  Score=53.93  Aligned_cols=47  Identities=23%  Similarity=0.627  Sum_probs=39.0

Q ss_pred             ccccccccccccCC---ceeEecccccccccchHHHhhcCC-CCCCccccc
Q 043965          214 LQCAVCLEEFEIGN---EAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQV  260 (342)
Q Consensus       214 ~~C~ICle~~~~~~---~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l  260 (342)
                      ..|-||-++|...+   .++.|.|||.||..|+.+.+.... .||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            47999999998653   577888999999999988775444 799999985

>PHA03096 p28-like protein; Provisional

Probab=93.93  E-value=0.022  Score=54.56  Aligned_cols=45  Identities=27%  Similarity=0.458  Sum_probs=31.6

Q ss_pred             ccccccccccccCC----ceeEec-ccccccccchHHHhhcCC---CCCCccc
Q 043965          214 LQCAVCLEEFEIGN----EAKEMP-CKHKFHGECIMPWLEVRS---SCPVCRF  258 (342)
Q Consensus       214 ~~C~ICle~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl~~~~---~CP~CR~  258 (342)
                      ..|.||++......    .-..|+ |.|.||..||..|-....   +||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            57999999876432    233566 999999999999985432   4444443

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

Probab=93.84  E-value=0.034  Score=53.98  Aligned_cols=48  Identities=25%  Similarity=0.721  Sum_probs=39.7

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHH--HhhcCCCCCCcccccC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP--WLEVRSSCPVCRFQVP  261 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~--Wl~~~~~CP~CR~~l~  261 (342)
                      ++...|.||.+.+.   -...+||+|..|-.|..+  -|.....||+||.+..
T Consensus        59 Een~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          59 EENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             cccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            34567999999887   678899999999999865  4677889999998653

>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=93.78  E-value=0.045  Score=47.72  Aligned_cols=52  Identities=23%  Similarity=0.559  Sum_probs=36.7

Q ss_pred             cccccccccccccCCceeEeccc-------------ccccccchHHHhhc------------------------------
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCK-------------HKFHGECIMPWLEV------------------------------  249 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~-------------H~Fh~~Ci~~Wl~~------------------------------  249 (342)
                      +..|+||||.-.   .++.|-|.             -.-|..|+.+.-+.                              
T Consensus         2 d~~CpICme~PH---NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (162)
T PF07800_consen    2 DVTCPICMEHPH---NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ   78 (162)
T ss_pred             CccCceeccCCC---ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence            567999999877   66666553             22477899887431                              


Q ss_pred             -CCCCCCcccccCCCCccc
Q 043965          250 -RSSCPVCRFQVPSDDFKI  267 (342)
Q Consensus       250 -~~~CP~CR~~l~~~~~~~  267 (342)
                       +..||+||.+|..+....
T Consensus        79 ~~L~CPLCRG~V~GWtvve   97 (162)
T PF07800_consen   79 PELACPLCRGEVKGWTVVE   97 (162)
T ss_pred             ccccCccccCceeceEEch
Confidence             125999999998876543

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.

>PHA02862 5L protein; Provisional

Probab=93.58  E-value=0.036  Score=47.59  Aligned_cols=45  Identities=18%  Similarity=0.551  Sum_probs=33.5

Q ss_pred             ccccccccccccCCceeEeccc-----ccccccchHHHhhcC--CCCCCcccccCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCK-----HKFHGECIMPWLEVR--SSCPVCRFQVPS  262 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~  262 (342)
                      ..|=||.+.-.  +.  .-||.     ..-|..|+.+|+...  ..|++|+.++.-
T Consensus         3 diCWIC~~~~~--e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCD--ER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCC--CC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            57999999843  22  35654     468999999999644  389999988753

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

Probab=93.50  E-value=0.029  Score=53.42  Aligned_cols=42  Identities=33%  Similarity=0.757  Sum_probs=35.0

Q ss_pred             ccccccccccccCCceeEec-ccccccccchHHHh-hcCCCCCCccc
Q 043965          214 LQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWL-EVRSSCPVCRF  258 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl-~~~~~CP~CR~  258 (342)
                      +.|+.|...+.   .+..++ |+|.||..||..-| .....||.|..
T Consensus       275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            68999999887   666777 99999999998765 56669999954

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

Probab=93.36  E-value=0.037  Score=61.65  Aligned_cols=84  Identities=24%  Similarity=0.472  Sum_probs=55.6

Q ss_pred             ccccCchhHHHHHHHhcCCCCCCCCcccHHHHHcCCcccccCcccccccccccccCCceeEecccccccccchHHHhhcC
Q 043965          171 YLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR  250 (342)
Q Consensus       171 ~~~g~~l~~l~~~L~~~~~~~~g~~~~~~~~i~~~p~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~  250 (342)
                      +...+|+-.++..|.+.........+..++.+.-  ...+.....|.||++.+..  ...+..|+|.+|..|+..|+..+
T Consensus      1113 ~ls~~G~~r~lk~l~e~~~~~~~~i~~~es~~~y--~~~~~~~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~ 1188 (1394)
T KOG0298|consen 1113 FLSIPGLLRYLKGLKESKADTPCKIAQTESDVRY--LMNLSGHFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYAS 1188 (1394)
T ss_pred             hhccchHHHHHHHHHHHhccCccccCCccchHHH--HHHhhcccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHh
Confidence            3444677777777776554333222222222221  1222345589999999873  33455699999999999999999


Q ss_pred             CCCCCccc
Q 043965          251 SSCPVCRF  258 (342)
Q Consensus       251 ~~CP~CR~  258 (342)
                      ..||.|+.
T Consensus      1189 s~~~~~ks 1196 (1394)
T KOG0298|consen 1189 SRCPICKS 1196 (1394)
T ss_pred             ccCcchhh
Confidence            99999984

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

Probab=93.26  E-value=0.039  Score=48.97  Aligned_cols=51  Identities=24%  Similarity=0.576  Sum_probs=36.5

Q ss_pred             cccccccccccccCCce----eEecccccccccchHHHhhcC-----------CCCCCcccccCCC
Q 043965          213 NLQCAVCLEEFEIGNEA----KEMPCKHKFHGECIMPWLEVR-----------SSCPVCRFQVPSD  263 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~----~~lpC~H~Fh~~Ci~~Wl~~~-----------~~CP~CR~~l~~~  263 (342)
                      ...|.||+.+-..|..+    --..|+..||.-|+..||+.-           ..||.|-.++..+
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            34699998776544422    234599999999999999632           1599998877543

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

Probab=93.25  E-value=0.0063  Score=59.74  Aligned_cols=50  Identities=22%  Similarity=0.630  Sum_probs=42.6

Q ss_pred             ccccccccccccC-CceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          214 LQCAVCLEEFEIG-NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       214 ~~C~ICle~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      ..|+||.+.++.. +....+-|+|.+|..||.+||.....||.|+.+|+..
T Consensus       197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            4699999988754 4566777999999999999999999999999988654

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=93.17  E-value=0.062  Score=38.66  Aligned_cols=45  Identities=24%  Similarity=0.516  Sum_probs=33.1

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      ..|..|...-.   ....+||+|+.+..|..-  ++-+-||+|-.++...
T Consensus         8 ~~~~~~~~~~~---~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    8 QPCVFCGFVGT---KGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFD   52 (55)
T ss_pred             eeEEEcccccc---ccccccccceeeccccCh--hhccCCCCCCCcccCC
Confidence            34666655433   678899999999999643  4667899998888654

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

Probab=92.99  E-value=0.034  Score=38.07  Aligned_cols=41  Identities=29%  Similarity=0.821  Sum_probs=23.2

Q ss_pred             ccccccccccCCceeEecccccccccchHHHhhcCC--CCCCc
Q 043965          216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS--SCPVC  256 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~C  256 (342)
                      |.+|.+....|..-....|+-.+|..|+..++....  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            678888877543333334888999999999997666  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=92.68  E-value=0.048  Score=58.42  Aligned_cols=43  Identities=21%  Similarity=0.683  Sum_probs=34.4

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCccccc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV  260 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l  260 (342)
                      ...|.+|--.+..  ..+...|+|.||.+|+.   .....||.|+.++
T Consensus       840 ~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            3579999888773  56777899999999997   4556899998844

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.51  E-value=0.06  Score=52.21  Aligned_cols=57  Identities=19%  Similarity=0.513  Sum_probs=40.6

Q ss_pred             CcccccccccccccCC-ceeEecccccccccchHHHh-hcCCCCCCcccccCCCCcccC
Q 043965          212 KNLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVPSDDFKIQ  268 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~~~  268 (342)
                      +++.|+.|+|++...+ ...-.+||...|.-|....- .....||.||.....+..++.
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~   71 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV   71 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence            3456999999997655 34455699888888865433 245689999998877765543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=92.39  E-value=0.091  Score=49.69  Aligned_cols=53  Identities=23%  Similarity=0.422  Sum_probs=40.6

Q ss_pred             cccccccccccccCCcee-EecccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965          213 NLQCAVCLEEFEIGNEAK-EMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (342)
                      ...|||....|......+ ..+|||+|...+|...- ....||+|-.++...+..
T Consensus       113 ~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI  166 (260)
T PF04641_consen  113 RFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDII  166 (260)
T ss_pred             eeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEE
Confidence            468999999995443444 44799999999998872 355899999999866654

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=92.37  E-value=0.067  Score=32.05  Aligned_cols=22  Identities=32%  Similarity=0.871  Sum_probs=18.8

Q ss_pred             eeccCceeecCC-CCCccCCCCC
Q 043965           10 CYICSQMVNPRM-EAGIKCPFCE   31 (342)
Q Consensus        10 Ch~C~~~V~p~~-~~e~~CP~C~   31 (342)
                      |..|.+.|.|.- ...++||.|+
T Consensus         1 C~sC~~~i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    1 CTSCGRPIAPREQAVPFPCPNCG   23 (24)
T ss_pred             CccCCCcccCcccCceEeCCCCC
Confidence            889999998775 5689999996

It is likely to bind zinc via its four well-conserved cysteine residues.

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

Probab=92.27  E-value=0.056  Score=51.85  Aligned_cols=43  Identities=30%  Similarity=0.621  Sum_probs=30.2

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCccccc
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV  260 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l  260 (342)
                      -.|.-|--.+.  .--+.+||+|+||.+|...  ..-+.||.|-..|
T Consensus        91 HfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            35777765554  1346779999999999754  3456899996655

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

Probab=92.23  E-value=0.061  Score=51.20  Aligned_cols=45  Identities=24%  Similarity=0.658  Sum_probs=37.9

Q ss_pred             ccccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCccc
Q 043965          214 LQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRF  258 (342)
Q Consensus       214 ~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~  258 (342)
                      ..|+||.+.+.... .+..++|+|..|..|.......+-+||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            34999999886544 5678899999999999888877789999988

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

Probab=92.22  E-value=0.047  Score=38.04  Aligned_cols=44  Identities=23%  Similarity=0.605  Sum_probs=26.1

Q ss_pred             cccccccccccCCceeEeccc-ccccccchHHHhhcCCCCCCcccccCCC
Q 043965          215 QCAVCLEEFEIGNEAKEMPCK-HKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      -|.-|+-..+     ..+.|. |..|..|+...|.....||+|..+||.+
T Consensus         4 nCKsCWf~~k-----~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFANK-----GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S--S-----SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhcCC-----CeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            3666664433     455675 8899999999999999999999999865

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=92.21  E-value=0.089  Score=45.97  Aligned_cols=48  Identities=23%  Similarity=0.628  Sum_probs=34.6

Q ss_pred             CcccccccccccccCCceeEeccc--c---cccccchHHHhhcCC--CCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCK--H---KFHGECIMPWLEVRS--SCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~  263 (342)
                      .+..|=||.+.-.  .  ...||.  .   .-|..|+..|+..+.  .|++|+.++...
T Consensus         7 ~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          7 MDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4567999998843  2  234654  4   459999999996544  899999877544

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

Probab=91.29  E-value=0.069  Score=57.04  Aligned_cols=49  Identities=22%  Similarity=0.590  Sum_probs=39.8

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCC--CCCCcccccCCCCcc
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS--SCPVCRFQVPSDDFK  266 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~~~~  266 (342)
                      ..|.||++ .   +.+...+|+|.||..|+..-+....  .||+||..+..+...
T Consensus       455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~  505 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLL  505 (674)
T ss_pred             cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHh
Confidence            78999999 3   3788889999999999998775433  699999988766443

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=91.00  E-value=0.13  Score=36.15  Aligned_cols=31  Identities=39%  Similarity=0.909  Sum_probs=24.2

Q ss_pred             CCCCceeeeccCceee-cCCCCCccCCCCCCC
Q 043965            3 DAMVGYWCYICSQMVN-PRMEAGIKCPFCESG   33 (342)
Q Consensus         3 ~~~~~ywCh~C~~~V~-p~~~~e~~CP~C~sG   33 (342)
                      +++..|=|-.|.+.|. .....++.||+|++-
T Consensus         2 ~~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           2 EAMMEYKCARCGREVELDQETRGIRCPYCGSR   33 (49)
T ss_pred             cceEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence            4556699999999996 223467999999984

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

Probab=90.99  E-value=0.21  Score=49.41  Aligned_cols=31  Identities=32%  Similarity=0.795  Sum_probs=23.7

Q ss_pred             ccccccccchHHHhhcCC-------------CCCCcccccCCCC
Q 043965          234 CKHKFHGECIMPWLEVRS-------------SCPVCRFQVPSDD  264 (342)
Q Consensus       234 C~H~Fh~~Ci~~Wl~~~~-------------~CP~CR~~l~~~~  264 (342)
                      |...+|..|+-+|+..++             .||+||+.+..-|
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence            556678999999985332             6999999887554

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

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

Probab=90.00  E-value=0.18  Score=49.89  Aligned_cols=48  Identities=21%  Similarity=0.376  Sum_probs=40.0

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCcccc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQ  259 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~  259 (342)
                      ..+.|||=.+.-.....+..|.|||+....-|.+..+...   .||+|-..
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            4578999888888888999999999999999988776544   79999543

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

Probab=89.90  E-value=0.11  Score=43.99  Aligned_cols=49  Identities=22%  Similarity=0.558  Sum_probs=37.4

Q ss_pred             cccccccccccccCCceeEec----ccccccccchHHHhh---cCCCCCCcccccCCCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMP----CKHKFHGECIMPWLE---VRSSCPVCRFQVPSDD  264 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lp----C~H~Fh~~Ci~~Wl~---~~~~CP~CR~~l~~~~  264 (342)
                      -.+|-||.|...   +.+.|+    ||-..|..|-...|+   .+..||+|+..+....
T Consensus        80 lYeCnIC~etS~---ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   80 LYECNICKETSA---EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             ceeccCcccccc---hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            468999999876   333343    999999999887654   4568999999886553

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=89.38  E-value=0.23  Score=41.17  Aligned_cols=33  Identities=27%  Similarity=0.512  Sum_probs=25.1

Q ss_pred             CceeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965            6 VGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMS   39 (342)
Q Consensus         6 ~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~   39 (342)
                      +..||+.|...+.+. ...+.||.|+|..++-+.
T Consensus        69 ~~~~C~~Cg~~~~~~-~~~~~CP~Cgs~~~~i~~  101 (115)
T TIGR00100        69 VECECEDCSEEVSPE-IDLYRCPKCHGIMLQVRA  101 (115)
T ss_pred             cEEEcccCCCEEecC-CcCccCcCCcCCCcEEec
Confidence            339999999988643 336789999998766554

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=88.81  E-value=0.25  Score=41.15  Aligned_cols=34  Identities=26%  Similarity=0.310  Sum_probs=23.9

Q ss_pred             CceeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965            6 VGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMS   39 (342)
Q Consensus         6 ~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~   39 (342)
                      +.+||..|...+.+.......||.|+|-.++-+.
T Consensus        70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~  103 (117)
T PRK00564         70 VELECKDCSHVFKPNALDYGVCEKCHSKNVIITQ  103 (117)
T ss_pred             CEEEhhhCCCccccCCccCCcCcCCCCCceEEec
Confidence            3499999998875432223459999998776544

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=88.22  E-value=0.28  Score=35.23  Aligned_cols=39  Identities=26%  Similarity=0.676  Sum_probs=30.6

Q ss_pred             cccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPV  255 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~  255 (342)
                      ...|.+|-+.|+.++++++-| |+-.+|+.|...    ...|-+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            346999999998778888888 999999999533    445544

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

Probab=88.19  E-value=0.27  Score=45.10  Aligned_cols=40  Identities=33%  Similarity=0.688  Sum_probs=30.8

Q ss_pred             ccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCC
Q 043965          216 CAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      |-+|.+.=.   .+..+||.|. +|..|-..    -..||+|+.....
T Consensus       161 Cr~C~~~~~---~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGEREA---TVLLLPCRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcCCc---eEEeecccceEeccccccc----CccCCCCcChhhc
Confidence            889987755   7999999987 88888643    4469999876543

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=88.05  E-value=0.33  Score=40.20  Aligned_cols=34  Identities=24%  Similarity=0.654  Sum_probs=23.8

Q ss_pred             CceeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965            6 VGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMS   39 (342)
Q Consensus         6 ~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~   39 (342)
                      +.+||..|...+......-..||.|+|.-++-+.
T Consensus        69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~  102 (114)
T PRK03681         69 AECWCETCQQYVTLLTQRVRRCPQCHGDMLRIVA  102 (114)
T ss_pred             cEEEcccCCCeeecCCccCCcCcCcCCCCcEEcc
Confidence            3399999998885332212669999988766544

>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]

Probab=87.12  E-value=0.29  Score=36.06  Aligned_cols=29  Identities=28%  Similarity=0.605  Sum_probs=21.9

Q ss_pred             eeccCceeecCCCCCccCCCCCCC-ceeccccC
Q 043965           10 CYICSQMVNPRMEAGIKCPFCESG-IVEQMSSS   41 (342)
Q Consensus        10 Ch~C~~~V~p~~~~e~~CP~C~sG-FvEE~~~~   41 (342)
                      |+.|.+.+.   ++.-+||.|+|- |.||-...
T Consensus         7 C~~Ck~l~~---~d~e~CP~Cgs~~~te~W~G~   36 (64)
T COG2093           7 CKNCKRLTP---EDTEICPVCGSTDLTEEWFGL   36 (64)
T ss_pred             HhhccccCC---CCCccCCCCCCcccchhhccE
Confidence            899998874   224579999996 88886543

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

Probab=86.50  E-value=0.3  Score=48.95  Aligned_cols=36  Identities=28%  Similarity=0.638  Sum_probs=31.0

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhc
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV  249 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~  249 (342)
                      ++.+.|+||..-|.   ++++|||+|..|..|...-+..
T Consensus         2 eeelkc~vc~~f~~---epiil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFYR---EPIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhcc---CceEeecccHHHHHHHHhhccc
Confidence            46788999999999   8999999999999998866543

>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=86.44  E-value=0.44  Score=45.46  Aligned_cols=53  Identities=19%  Similarity=0.584  Sum_probs=37.1

Q ss_pred             cccccccccccCCcee--EecccccccccchHHHhhcCC-CCCCcccccCCCCccc
Q 043965          215 QCAVCLEEFEIGNEAK--EMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSDDFKI  267 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~--~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~~~~~  267 (342)
                      .|++|....-.....+  .-+|+|..|..|....+.... .||.|-..+.......
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~   57 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRV   57 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccch
Confidence            4888876543332332  336999999999999886554 8999988776555443

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

Probab=86.41  E-value=0.27  Score=53.24  Aligned_cols=37  Identities=24%  Similarity=0.610  Sum_probs=30.0

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHh
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL  247 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl  247 (342)
                      ++....|.+|...+... .-...||||.||..||.+..
T Consensus       814 ~ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             ecCccchHHhcchhhcC-cceeeeccchHHHHHHHHHH
Confidence            45678899999988643 66677899999999998764

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

Probab=85.62  E-value=0.73  Score=31.66  Aligned_cols=32  Identities=31%  Similarity=0.730  Sum_probs=24.0

Q ss_pred             CCceeeeccCceeecCCC-CCccCCCCCCCcee
Q 043965            5 MVGYWCYICSQMVNPRME-AGIKCPFCESGIVE   36 (342)
Q Consensus         5 ~~~ywCh~C~~~V~p~~~-~e~~CP~C~sGFvE   36 (342)
                      |..|=|-.|...+..... ..++||+|++-++-
T Consensus         1 ~~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~   33 (46)
T PRK00398          1 MAEYKCARCGREVELDEYGTGVRCPYCGYRILF   33 (46)
T ss_pred             CCEEECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence            345889999998854332 26899999988774

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=85.37  E-value=0.66  Score=38.37  Aligned_cols=31  Identities=29%  Similarity=0.786  Sum_probs=23.6

Q ss_pred             eeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965            8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS   39 (342)
Q Consensus         8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~   39 (342)
                      +||..|.....+. ...+.||.|+|.-++-+.
T Consensus        71 ~~C~~Cg~~~~~~-~~~~~CP~Cgs~~~~i~~  101 (113)
T PRK12380         71 AWCWDCSQVVEIH-QHDAQCPHCHGERLRVDT  101 (113)
T ss_pred             EEcccCCCEEecC-CcCccCcCCCCCCcEEcc
Confidence            9999999888643 346779999987665543

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=85.36  E-value=0.41  Score=39.56  Aligned_cols=31  Identities=32%  Similarity=0.538  Sum_probs=22.3

Q ss_pred             eeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965            8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS   39 (342)
Q Consensus         8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~   39 (342)
                      +||..|.....+... .+.||.|++..++-+.
T Consensus        71 ~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~  101 (113)
T PF01155_consen   71 ARCRDCGHEFEPDEF-DFSCPRCGSPDVEIIS  101 (113)
T ss_dssp             EEETTTS-EEECHHC-CHH-SSSSSS-EEEEE
T ss_pred             EECCCCCCEEecCCC-CCCCcCCcCCCcEEcc
Confidence            999999999975543 5889999998775544

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]

Probab=85.00  E-value=0.57  Score=41.96  Aligned_cols=25  Identities=36%  Similarity=0.930  Sum_probs=20.1

Q ss_pred             eeeeccCceeecCCCCCccCCCCCCCceec
Q 043965            8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQ   37 (342)
Q Consensus         8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE   37 (342)
                      |||-.|+-++.     .-.|+-|+++|-|-
T Consensus        15 yWCe~cNlPl~-----~~~c~~cg~~~~~l   39 (202)
T COG5270          15 YWCEKCNLPLL-----GRRCSVCGSKVEEL   39 (202)
T ss_pred             eehhhCCCccc-----cccccccCCcceEE
Confidence            99999998773     45899999776544

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

Probab=84.91  E-value=0.58  Score=45.27  Aligned_cols=44  Identities=27%  Similarity=0.697  Sum_probs=34.0

Q ss_pred             cCcccccccccccccCCceeEecc--cccccccchHHHhhcCCCCCCcccccC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPC--KHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC--~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      .+-++|+||.+.+.   .+ ++.|  ||.-|..|-.   +..+.||.||.++.
T Consensus        46 ~~lleCPvC~~~l~---~P-i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLS---PP-IFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hhhccCchhhccCc---cc-ceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            35578999999988   33 3446  6888888865   46779999999886

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=84.54  E-value=0.74  Score=31.66  Aligned_cols=29  Identities=21%  Similarity=0.447  Sum_probs=23.5

Q ss_pred             ceeeeccCceeecCCCCCccCCCCCCCce
Q 043965            7 GYWCYICSQMVNPRMEAGIKCPFCESGIV   35 (342)
Q Consensus         7 ~ywCh~C~~~V~p~~~~e~~CP~C~sGFv   35 (342)
                      .|=|-.|..+|.......+.||+|++--+
T Consensus         2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIl   30 (44)
T smart00659        2 IYICGECGRENEIKSKDVVRCRECGYRIL   30 (44)
T ss_pred             EEECCCCCCEeecCCCCceECCCCCceEE
Confidence            48899999999866556799999997533

present in RNA polymerase I, II and III

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

Probab=84.36  E-value=0.58  Score=46.84  Aligned_cols=38  Identities=26%  Similarity=0.721  Sum_probs=28.1

Q ss_pred             cccccccc-cccccCCceeEecccccccccchHHHhhcC
Q 043965          213 NLQCAVCL-EEFEIGNEAKEMPCKHKFHGECIMPWLEVR  250 (342)
Q Consensus       213 ~~~C~ICl-e~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~  250 (342)
                      ..+|.||. +............|+|.||..|+.+.++.+
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            56899999 444433344456699999999999988644

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=84.05  E-value=0.8  Score=39.08  Aligned_cols=33  Identities=27%  Similarity=0.389  Sum_probs=23.6

Q ss_pred             ceeeeccCceeecCC--------------------CCCccCCCCCCCceeccc
Q 043965            7 GYWCYICSQMVNPRM--------------------EAGIKCPFCESGIVEQMS   39 (342)
Q Consensus         7 ~ywCh~C~~~V~p~~--------------------~~e~~CP~C~sGFvEE~~   39 (342)
                      .|||..|...+....                    ...+.||.|++.-++-+.
T Consensus        70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~  122 (135)
T PRK03824         70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK  122 (135)
T ss_pred             EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence            399999998876431                    234779999987665443

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

Probab=83.95  E-value=0.28  Score=52.05  Aligned_cols=49  Identities=29%  Similarity=0.734  Sum_probs=39.0

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcC---CCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR---SSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~  263 (342)
                      ...+|+||+..+.   .+..+.|.|.|+..|+..-|...   ..||+|+..+...
T Consensus        20 k~lEc~ic~~~~~---~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~   71 (684)
T KOG4362|consen   20 KILECPICLEHVK---EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR   71 (684)
T ss_pred             hhccCCceeEEee---ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence            3578999999998   55788899999999997766444   3799999766544

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

Probab=83.90  E-value=0.48  Score=50.52  Aligned_cols=39  Identities=31%  Similarity=0.749  Sum_probs=28.5

Q ss_pred             ccccccccccCCceeEecccccccccchHHHhhcCCCCCC
Q 043965          216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPV  255 (342)
Q Consensus       216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~  255 (342)
                      |.||--.+. +.......|+|+.|..|...|++....||.
T Consensus      1031 C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeEeeEee-ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            444433322 334456679999999999999999999985

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=80.86  E-value=0.99  Score=37.93  Aligned_cols=32  Identities=19%  Similarity=0.369  Sum_probs=22.2

Q ss_pred             ceeeeccCceeecCCCC------CccCCCCCCCceeccc
Q 043965            7 GYWCYICSQMVNPRMEA------GIKCPFCESGIVEQMS   39 (342)
Q Consensus         7 ~ywCh~C~~~V~p~~~~------e~~CP~C~sGFvEE~~   39 (342)
                      .+|| .|.....+....      -+.||.|+|..++-+.
T Consensus        70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~  107 (124)
T PRK00762         70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG  107 (124)
T ss_pred             eEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence            3999 999886533110      1569999998876554

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=80.61  E-value=1.5  Score=28.12  Aligned_cols=26  Identities=31%  Similarity=0.660  Sum_probs=19.7

Q ss_pred             eeeeccCceeecCCCCCccCCCCCCC
Q 043965            8 YWCYICSQMVNPRMEAGIKCPFCESG   33 (342)
Q Consensus         8 ywCh~C~~~V~p~~~~e~~CP~C~sG   33 (342)
                      |-|-.|..+|.....+.+.||.|+.-
T Consensus         1 Y~C~~Cg~~~~~~~~~~irC~~CG~R   26 (32)
T PF03604_consen    1 YICGECGAEVELKPGDPIRCPECGHR   26 (32)
T ss_dssp             EBESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred             CCCCcCCCeeEcCCCCcEECCcCCCe
Confidence            77999999998555567999999853

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=80.33  E-value=1.5  Score=28.89  Aligned_cols=25  Identities=24%  Similarity=0.586  Sum_probs=19.2

Q ss_pred             eeeeccCceeecCC----CCCccCCCCCC
Q 043965            8 YWCYICSQMVNPRM----EAGIKCPFCES   32 (342)
Q Consensus         8 ywCh~C~~~V~p~~----~~e~~CP~C~s   32 (342)
                      |-|..|...+....    +..+.||.|++
T Consensus         6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (41)
T smart00834        6 YRCEDCGHTFEVLQKISDDPLATCPECGG   34 (41)
T ss_pred             EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence            99999999764332    34588999998

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	342
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		9e-11
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		6e-10
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		1e-09
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-09
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		5e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-06
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		1e-04
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		1e-04
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		2e-04
2y43_A	99	Rad18 Ubiquitin Ligase Ring Domain Structure Length		4e-04

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 32/48 (66%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           +   L+C VC E++ +G   +++PC H FH  CI+PWLE   SCPVCR
Sbjct: 12  VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/52 (50%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQV 260
           +D  ++CAVCL E E G EA+ +P C H FH EC+  WL   S+CP+CR  V
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3 Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4710b Length = 91

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 195 PAANKAVLKALPTVTIDKN-------LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247
           P A+K  + ALP + + ++       + C +C  E+  G+ A E+PC H FH  C+  WL
Sbjct: 15  PPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWL 74
Query: 248 EVRSSCPVCRFQVP 261
           +   +CPVCR   P
Sbjct: 75  QKSGTCPVCRCMFP 88

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 24/45 (53%), Positives = 31/45 (68%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
           CAVCLE+F+  +E    PCKH FH +C++ WLEVR  CP+C   V
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF----QVPSD 263
           +C +CL   E G + + +PC H FH  C+  WL     CP+CR     Q+PS+
Sbjct: 16  KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSE 68

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           C VC+ +FE     + +PC H+FH +C+  WL+   +CP+CR
Sbjct: 26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67

>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 195 PAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCP 254
            A  + VL  +  V ++  LQC +C E F    EA  + C H F   CI  W++ +  CP
Sbjct: 36  QAQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECP 91
Query: 255 VCRFQVPSDDFKIQGNGSGNR 275
           +CR  + S  + +  +   N+
Sbjct: 92  ICRKDIKSKTYSLVLDNXINK 112

>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 195 PAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCP 254
            A  + VL  +  V ++  LQC +C E F    EA  + C H F   CI  W++ +  CP
Sbjct: 36  QAQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECP 91
Query: 255 VCRFQVPSDDFKIQGNGSGNR 275
           +CR  + S  + +  +   N+
Sbjct: 92  ICRKDIKSKTYSLVLDNCINK 112

>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HETERODIMER Length = 149

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 196 AANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPV 255
           A  + VL  +  V ++  LQC +C E F    EA  + C H F   CI  W++ +  CP+
Sbjct: 48  AQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECPI 103
Query: 256 CRFQVPSDDFKIQGNGSGNR 275
           CR  + S  + +  +   N+
Sbjct: 104 CRKDIKSKTYSLVLDNCINK 123

>pdb|2Y43|A Chain A, Rad18 Ubiquitin Ligase Ring Domain Structure Length = 99

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK 266
           TID  L+C +C E F I   A  +P C H +   CI  +L  ++ CP C   V   D K
Sbjct: 18  TIDDLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	342
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	7e-40
2ect_A	78	Ring finger protein 126; metal binding protein, st	3e-28
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-25
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-23
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	8e-23
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-18
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-17
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	8e-17
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	1e-13
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	9e-13
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	4e-12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-11
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	1e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-10
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-10
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	6e-09
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	4e-08
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	6e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	8e-08
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-07
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	2e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	4e-07
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-07
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	7e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-06
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	2e-06
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	4e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	5e-06
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	6e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	9e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	3e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	5e-05
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	9e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	9e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	1e-04
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	2e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	3e-04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	3e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	3e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	5e-04

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

 Score =  134 bits (340), Expect = 7e-40
 Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 7/88 (7%)

Query: 181 LQHLLENDPNRYGCPAANKAVLKALPTVTIDK-------NLQCAVCLEEFEIGNEAKEMP 233
           + H   +  +    P A+K  + ALP + + +        + C +C  E+  G+ A E+P
Sbjct: 1   MGHHHHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP 60

Query: 234 CKHKFHGECIMPWLEVRSSCPVCRFQVP 261
           C H FH  C+  WL+   +CPVCR   P
Sbjct: 61  CHHYFHKPCVSIWLQKSGTCPVCRCMFP 88

>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 =  104 bits (260), Expect = 3e-28
 Identities = 23/56 (41%), Positives = 34/56 (60%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
            +   L+C VC E++ +G   +++PC H FH  CI+PWLE   SCPVCR  +   +
Sbjct: 11  HVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN 66

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

 Score = 95.9 bits (239), Expect = 3e-25
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 197 ANKAVLKALPTVTIDKN------LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR 250
            +      LP+   + N        C VC+ +FE     + +PC H+FH +C+  WL+  
Sbjct: 1   GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 251 SSCPVCRFQV 260
            +CP+CR   
Sbjct: 61  RTCPICRADS 70

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

 Score = 91.4 bits (227), Expect = 1e-23
 Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQ 268
            ++ +  CAVCLE+F+  +E    PCKH FH +C++ WLEVR  CP+C   V     ++ 
Sbjct: 11  ELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA-QLS 69

Query: 269 GNGSG 273
           G  SG
Sbjct: 70  GPSSG 74

>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 = 89.3 bits (222), Expect = 8e-23
 Identities = 18/54 (33%), Positives = 27/54 (50%)

Query: 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
           D   +C +CL   E G + + +PC H FH  C+  WL     CP+CR  + +  
Sbjct: 12  DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQL 65

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

 Score = 77.6 bits (192), Expect = 1e-18
 Identities = 26/52 (50%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQV 260
           +D  ++CAVCL E E G EA+ +P C H FH EC+  WL   S+CP+CR  V
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 75.8 bits (187), Expect = 5e-18
 Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 215 QCAVCLEEFEIGNE-AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
            C +CLE+       A  +PC H  H  C    L+    CP+C    
Sbjct: 7   GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 74.7 bits (184), Expect = 2e-17
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 4/56 (7%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
            +    +C +C++          +PC H F  +CI  W +   +CP+CR Q+   +
Sbjct: 11  QLTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN 62

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

 Score = 72.8 bits (179), Expect = 8e-17
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGSGN 274
           +C +CLE+    N +  +PC H F   CI  W+    +CP+C+  V S    I+ +    
Sbjct: 7   RCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSEFG 64

Query: 275 R 275
            
Sbjct: 65  D 65

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

 Score = 64.2 bits (156), Expect = 1e-13
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 211 DKNLQCAVCLEEFE----IGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260
              + C +C++ +      G       C H F  +C+   L+  ++CP CR ++
Sbjct: 13  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

>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 = 63.3 bits (154), Expect = 3e-13
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 211 DKNLQCAVCLEEFE----IGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265
              + C +C++ +      G       C H F  +C+   L+  ++CP CR ++    +
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 66

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

 Score = 61.7 bits (150), Expect = 9e-13
 Identities = 11/56 (19%), Positives = 26/56 (46%), Gaps = 4/56 (7%)

Query: 214 LQCAVCLEEFEIGNEAKEM----PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265
           + C +C++ +    +   +     C H F  +C+   L+  ++CP CR ++    +
Sbjct: 4   VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 59

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

 Score = 60.3 bits (146), Expect = 4e-12
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 216 CAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCR 257
           C  C  E +  +       C H FH  C+  W++  + CP+C+
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 59.0 bits (143), Expect = 1e-11
 Identities = 11/56 (19%), Positives = 18/56 (32%), Gaps = 2/56 (3%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
            +   + C++C       +      C H F   CI+      + CP C   V    
Sbjct: 11  ELTPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ 64

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

 Score = 56.0 bits (135), Expect = 1e-10
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265
            +CA+CL+          +PCKH F   C+     +   C +CR ++P D  
Sbjct: 16  PECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFL 64

>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 = 56.4 bits (136), Expect = 2e-10
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWL-EVRSSCPVCRFQVPSDDFK 266
           +I +  +C +C+E+     +A+  P C       CI  WL E R+ CP CR  +   +  
Sbjct: 18  SIAEVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELV 74

>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 = 55.6 bits (134), Expect = 4e-10
 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
           ++ +L C +C   F   +    + C H F   CI+ +LE    CP+C  QV    
Sbjct: 12  LNPHLMCVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64

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

 Score = 51.8 bits (124), Expect = 5e-09
 Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 3/47 (6%)

Query: 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           +   +C +C + F+         C+H F   C +        C +C 
Sbjct: 13  EIPFRCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICD 56

>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 = 51.1 bits (122), Expect = 6e-09
 Identities = 11/55 (20%), Positives = 18/55 (32%), Gaps = 4/55 (7%)

Query: 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--SSCPVCRFQVPSD 263
           D    C +C      G   +   C  + H  C+  + +      CP C    P +
Sbjct: 13  DAVKICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE 65

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

 Score = 52.0 bits (124), Expect = 2e-08
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQG 269
           ++  LQC +C E F    EA  + C H F   CI  W++ +  CP+CR  + S  + +  
Sbjct: 61  LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 117

Query: 270 N 270
           +
Sbjct: 118 D 118

>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 = 54.4 bits (130), Expect = 2e-08
 Identities = 14/55 (25%), Positives = 20/55 (36%), Gaps = 4/55 (7%)

Query: 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSDD 264
                C +C E      + K  PC H     C+  W E     CP CR ++   +
Sbjct: 330 STFQLCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 381

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

 Score = 51.3 bits (122), Expect = 2e-08
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 211 DKNLQCAVCLEEFEIGNEAKE----MPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK 266
              + C +C++ +    +         C H F  +C+   L+  ++CP CR ++    + 
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH 64

Query: 267 IQGNGSGNRDESLGNEDAQ 285
               GSG     +  +   
Sbjct: 65  PIYIGSGTVSCPICMDGYS 83

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

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 6/74 (8%)

Query: 190 NRYGCPAANKAVLKALPTV--TIDKNLQCAVCLEEF----EIGNEAKEMPCKHKFHGECI 243
           N   CP   K +              + C +C++ +    + G       C H F  +C+
Sbjct: 47  NANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCL 106

Query: 244 MPWLEVRSSCPVCR 257
              L+  ++CP CR
Sbjct: 107 RDSLKNANTCPTCR 120

>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 = 49.9 bits (119), Expect = 4e-08
 Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 4/71 (5%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS-CPVCRFQVPSDDFKIQ 268
             K++ C +C        +  E  CKH F   CI+  L+V  S CP CR+     D +  
Sbjct: 20  FVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESP 76

Query: 269 GNGSGNRDESL 279
                N   SL
Sbjct: 77  VKSFLNILNSL 87

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 49.4 bits (117), Expect = 6e-08
 Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 1/44 (2%)

Query: 215 QCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCR 257
           +C                  C H FH  CI  WL+ R  CP+  
Sbjct: 53  ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 48.6 bits (116), Expect = 8e-08
 Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKI 267
           TID  L+C +C E F   N A  +P C H +   CI  +L  ++ CP C   V   D K 
Sbjct: 18  TIDDLLRCGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKN 74

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 49.1 bits (116), Expect = 1e-07
 Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 1/44 (2%)

Query: 215 QCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCR 257
           +C                  C H FH  CI  WL+ R  CP+  
Sbjct: 64  ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 48.7 bits (115), Expect = 1e-07
 Identities = 13/83 (15%), Positives = 27/83 (32%), Gaps = 20/83 (24%)

Query: 195 PAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEM---------------PCKHKFH 239
               + + K    + +     C +C+E+  + +   +M                C H FH
Sbjct: 7   GEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFH 66

Query: 240 GECIMPWLEVRS-----SCPVCR 257
             C++      +      CP C+
Sbjct: 67  LLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS-CPVCRFQVPSDDF 265
            ++   +C +CL       EA + PC H+F   CI+  +      CPV    +  +  
Sbjct: 14  PLESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQL 68

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

 Score = 45.5 bits (108), Expect = 4e-07
 Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 4/57 (7%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVPSDD 264
           T++   +C  C          K+  C H+F   C+   L      C  C+  +  D 
Sbjct: 11  TVEDKYKCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK 64

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

 Score = 46.4 bits (110), Expect = 7e-07
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 9/80 (11%)

Query: 188 DPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247
           +P+  G  A ++A L  L     +K L+C+ C              C+H F   C+   +
Sbjct: 2   EPDGRGAWAHSRAALDRL-----EKLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCI 54

Query: 248 EVRSSCPVCRFQVPSDDFKI 267
              + CPVC       D KI
Sbjct: 55  G--TGCPVCYTPAWIQDLKI 72

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

 Score = 44.7 bits (106), Expect = 7e-07
 Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 6/48 (12%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261
           L+C  C  E       K +PC H     C+         CP+C+   P
Sbjct: 7   LRCQQCQAEA---KCPKLLPCLHTLCSGCLE---ASGMQCPICQAPWP 48

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

 Score = 47.9 bits (113), Expect = 2e-06
 Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 16/66 (24%)

Query: 211 DKNLQCAVCLEEFEIGNEAKEM-----PCKHKFHGECIMPWLE-----------VRSSCP 254
           ++ L+C +C      G E   +      C  K H  C+  W +               CP
Sbjct: 306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCP 365

Query: 255 VCRFQV 260
            C+ ++
Sbjct: 366 FCKAKL 371

>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 = 46.2 bits (109), Expect = 2e-06
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 4/59 (6%)

Query: 209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS-CPVCRFQVPSDDFK 266
            ++   +C +CL       EA + PC H+F   CI+  +      CPV    +  +   
Sbjct: 14  PLESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLF 69

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

 Score = 43.2 bits (102), Expect = 4e-06
 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 6/58 (10%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRS--SCPVCRFQVPSDD 264
           I   L C +C +      +A  +P C + +  ECI   L      +CP C     S D
Sbjct: 12  IPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 66

>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 = 44.1 bits (104), Expect = 4e-06
 Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 4/50 (8%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPS 262
            QC +C+E      E   +PC H     C    +E  S  CP CR +V S
Sbjct: 16  CQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS 62

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

 Score = 43.2 bits (101), Expect = 5e-06
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 211 DKNLQCAVCLEEFEIGNEA-KEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVPSDDFK 266
           +  ++C +C+E  EI +       C ++    C      +    CP CR   P D   
Sbjct: 9   EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV 66

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

 Score = 42.7 bits (101), Expect = 6e-06
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 6/56 (10%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE---VRSSCPVCRFQVPSDDFK 266
           + C +CL+  +   +   + C H F  +CI    E       CP+C+  V  +  +
Sbjct: 21  VICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAIR 73

>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 = 43.8 bits (103), Expect = 9e-06
 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPS 262
           +++  QC  C E            C+H    +C+      +  SCP CR+ +  
Sbjct: 49  VEETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR 99

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

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 18/91 (19%), Positives = 29/91 (31%), Gaps = 6/91 (6%)

Query: 177 LDLLLQHLLENDPNRYGCPAANKAVLKALPTVTID--KNLQCAVCLEEFEIGNEAKEMPC 234
           L    QHL+  D           + L   P       ++  C  C E      +     C
Sbjct: 40  LTPQQQHLIREDCQNQKLWDEVLSHLVEGPNFLKKLEQSFMCVCCQELVY---QPVTTEC 96

Query: 235 KHKFHGECIMPWLEVRS-SCPVCRFQVPSDD 264
            H    +C+    + +  SCP CR  +  + 
Sbjct: 97  FHNVCKDCLQRSFKAQVFSCPACRHDLGQNY 127

>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 = 42.4 bits (99), Expect = 3e-05
 Identities = 8/56 (14%), Positives = 18/56 (32%), Gaps = 4/56 (7%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS-CPVCRFQVPSDD 264
           ++    C+ C           +  C H++   C+   L      C  C  +   ++
Sbjct: 28  LEAKYLCSACRNVLR---RPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEE 80

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

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 4/56 (7%)

Query: 210 IDKNLQCAVCLEEFEIGNEA-KEMPCKHKFHGECIMPWLEVRS---SCPVCRFQVP 261
           + + L+C +C+E F       K + C H    +C+   L        CP C     
Sbjct: 12  LREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITR 67

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

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 18/62 (29%), Positives = 23/62 (37%), Gaps = 9/62 (14%)

Query: 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR------SSCPVCRFQVPSDDF 265
           + + C +CLE      E     C H F   CI    E         +CPVCR   P  + 
Sbjct: 18  EEVTCPICLELL---KEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNL 74

Query: 266 KI 267
           K 
Sbjct: 75  KP 76

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

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 6/58 (10%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEV--RSSCPVCRFQVPSDD 264
           I   L C +C +      +A  +P C + +  ECI   L      +CP C     S D
Sbjct: 10  IPDELLCLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 64

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens} Length = 238

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 4/55 (7%)

Query: 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS--CPVCRFQVPSD 263
           D    C +C      G   +   C  + H  C+  + +  +   CP C    P +
Sbjct: 178 DAVKICNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE 230

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 3/59 (5%)

Query: 213 NLQCAVCLEEFEIGNEAKEM--PCKHKFHGECIMPWLEVRS-SCPVCRFQVPSDDFKIQ 268
           +  C  C          K M   C H     C+       + +CP C   +   +F++Q
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ 61

>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 = 41.5 bits (96), Expect = 2e-04
 Identities = 32/189 (16%), Positives = 55/189 (29%), Gaps = 10/189 (5%)

Query: 87  NNANPRVEEAEQEREFESLLTRRMR-RNSSASLSRMLQDIRFGITSRSDGPEALRERSGS 145
           + +   +   EQ  +  S         + S S    ++D++      SD    +   +  
Sbjct: 51  STSPSTIGIEEQVADITSTYKLLSTYESESNSFDEHIKDLKKNFKQSSDACPQIDLSTWD 110

Query: 146 LILVNPMNEEAL--IIQDHNTTSSLGEYLVGPGLDLLLQHLLE-NDPNRYGCPAANKAVL 202
                 +    L  +  +  T            L +L       NDP        N A  
Sbjct: 111 KYRTGELTAPKLSELYLNMPTPEPATMVNNTDTLKILKVLPYIWNDPTCVIPDLQNPADE 170

Query: 203 KALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS--CPV--CRF 258
             L        L C +  + +E         C H F  + I  +L+  ++  CP   C  
Sbjct: 171 DDLQIEGGKIELTCPITCKPYE--APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQ 228

Query: 259 QVPSDDFKI 267
            V   DF  
Sbjct: 229 VVSMRDFVR 237

>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 = 40.0 bits (93), Expect = 3e-04
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 204 ALPTVTIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEV-RSSCPVCRFQVP 261
            +   ++   L C +CL+  +          C H+F  +CI+  L      CP CR ++ 
Sbjct: 45  VVSPRSLHSELMCPICLDMLK---NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 101

Query: 262 SDD 264
           S  
Sbjct: 102 SKR 104

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 9/66 (13%)

Query: 215 QCAVCLEEFEIGNEAKEMPCK-----HKFHGECIMPWLEVRSS--CPVCRFQVPSDDFKI 267
            C +C  E +  +     PC      H  H  C+  W++   +  C +C+++    + K+
Sbjct: 17  ICRICHCEGDDESPLI-TPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIM-ETKL 74

Query: 268 QGNGSG 273
            G  SG
Sbjct: 75  SGPSSG 80

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 12/62 (19%)

Query: 212 KNLQCAVCLEEFEIGNEAKE---MPCKHKFHGECIMPWLE---VRSSCPVCRFQVPSDDF 265
           K L+C +CLE        KE     C H F   C++  L      S CP+C+  +     
Sbjct: 20  KILECPICLELI------KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL 73

Query: 266 KI 267
           + 
Sbjct: 74  QE 75

>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 = 37.6 bits (88), Expect = 5e-04
 Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 10/61 (16%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECI-------MPWLEVRSSCPVCRFQVPSDDFK 266
           + C +CLE      E   + C H     CI       +  +  +SSCPVC      +  +
Sbjct: 13  VTCPICLELLT---EPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQ 69

Query: 267 I 267
            
Sbjct: 70  A 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	342
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.56
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.46
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.43
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.42
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.41
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.39
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.31
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.31
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.3
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.3
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.3
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.26
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.26
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.25
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.25
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.25
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.24
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.23
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.22
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.22
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.21
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.2
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.2
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.19
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.17
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.16
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.16
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.16
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.11
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.1
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.09
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.09
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.09
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.08
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.02
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.02
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.0
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.0
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.0
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.99
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.99
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.99
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.98
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.97
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.94
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.93
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.9
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.9
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.89
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.88
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.85
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.81
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.79
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.75
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.75
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.71
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.65
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.61
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.49
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.48
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.47
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.45
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.45
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.4
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.32
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.3
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.88
3nw0_A	238	Non-structural maintenance of chromosomes element	97.57
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.3
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	92.49
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	92.35
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	91.26
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	88.06
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	85.38
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	84.86
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	83.76
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.44
1we9_A	64	PHD finger family protein; structural genomics, PH	83.43
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	83.1
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	82.62
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	82.24
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	81.7
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	80.79
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	80.23

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

Probab=99.56  E-value=2.3e-15  Score=118.53  Aligned_cols=73  Identities=36%  Similarity=0.873  Sum_probs=63.8

Q ss_pred             CCCCCCcccHHHHHcCCcccccC-------cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          190 NRYGCPAANKAVLKALPTVTIDK-------NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       190 ~~~g~~~~~~~~i~~~p~~~~~~-------~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      ...+..+++++.++.+|.+.+.+       ...|+||++.|..++.++.++|+|.||..||.+|++.+.+||+||..+..
T Consensus        10 ~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           10 HMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             CSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            34567789999999999876642       45799999999988889999999999999999999999999999998864

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

Probab=99.46  E-value=6.1e-14  Score=106.58  Aligned_cols=58  Identities=40%  Similarity=1.070  Sum_probs=50.6

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCccc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKI  267 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  267 (342)
                      ..+...|+||++.|.....++.++|+|+||..||.+|++.+.+||+||..+.......
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCC
Confidence            3456789999999987777888999999999999999999999999999998765543

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

Probab=99.43  E-value=4.8e-14  Score=99.93  Aligned_cols=51  Identities=51%  Similarity=1.129  Sum_probs=46.3

Q ss_pred             cCcccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ++...|+||++.|..++.+..++ |+|.||..||.+|++.+.+||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            45678999999999888888898 9999999999999999999999999874

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

Probab=99.42  E-value=7.5e-14  Score=105.47  Aligned_cols=52  Identities=33%  Similarity=0.931  Sum_probs=47.1

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +...|+||++.|..++.++.++|+|+||..||.+|++.+.+||+||+.+...
T Consensus        22 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           22 EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             SCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             CCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            4578999999999888889999999999999999999999999999988643

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

Probab=99.41  E-value=1.5e-13  Score=103.36  Aligned_cols=54  Identities=44%  Similarity=0.993  Sum_probs=48.0

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +.+...|+||++.|.....++.++|+|+||..||.+|++.+.+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            345678999999999877888889999999999999999999999999988653

>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=99.39  E-value=1.8e-13  Score=101.53  Aligned_cols=53  Identities=34%  Similarity=0.973  Sum_probs=47.7

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      .....|+||++.|..+..++.++|+|.||..||.+|++.+.+||+||..+...
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            34578999999998777889999999999999999999999999999988654

>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=99.31  E-value=9.4e-13  Score=93.07  Aligned_cols=50  Identities=28%  Similarity=0.646  Sum_probs=43.3

Q ss_pred             CcccccccccccccC-CceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIG-NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ....|+||++.|..+ ..++.++|+|.||..||.+|++.+.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            356899999999643 35778899999999999999999999999999874

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

Probab=99.31  E-value=6.4e-13  Score=98.76  Aligned_cols=56  Identities=20%  Similarity=0.592  Sum_probs=47.0

Q ss_pred             ccCcccccccccccccC----CceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIG----NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      ..+...|+||++.+...    ..++.++|+|.||..||.+|++.+.+||+||..+...+.
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   66 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhe
Confidence            34567899999999732    344888999999999999999999999999999876544

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

Probab=99.30  E-value=1.4e-12  Score=97.77  Aligned_cols=55  Identities=22%  Similarity=0.549  Sum_probs=46.7

Q ss_pred             cccCcccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (342)
                      .+.+...|+||++.+.   .++.+ +|+|.||..||..|++.+..||+||..+...+..
T Consensus        11 ~~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           11 ELTPYILCSICKGYLI---DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CCCGGGSCTTTSSCCS---SCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSC
T ss_pred             hcCCCCCCCCCChHHH---CcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccc
Confidence            3456788999999998   56665 8999999999999999999999999998766543

>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=99.30  E-value=1.6e-12  Score=105.77  Aligned_cols=53  Identities=21%  Similarity=0.615  Sum_probs=42.4

Q ss_pred             cCcccccccccccccCC---------------ceeEecccccccccchHHHh-----hcCCCCCCcccccCCC
Q 043965          211 DKNLQCAVCLEEFEIGN---------------EAKEMPCKHKFHGECIMPWL-----EVRSSCPVCRFQVPSD  263 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~---------------~~~~lpC~H~Fh~~Ci~~Wl-----~~~~~CP~CR~~l~~~  263 (342)
                      ..+..|+||++.|....               .++.++|+|+||..||.+||     ..+.+||+||..+...
T Consensus        23 ~~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            34568999999996432               33478899999999999999     4567999999988644

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

Probab=99.30  E-value=7.4e-13  Score=97.67  Aligned_cols=53  Identities=21%  Similarity=0.592  Sum_probs=44.8

Q ss_pred             ccCcccccccccccccC----CceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          210 IDKNLQCAVCLEEFEIG----NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      +.+...|+||++.|...    ..++.++|+|.||..||..|++.+.+||+||..|..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            34567899999999842    234788999999999999999999999999998753

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

Probab=99.26  E-value=3.8e-12  Score=95.98  Aligned_cols=54  Identities=30%  Similarity=0.627  Sum_probs=45.4

Q ss_pred             cccCcccccccccccccCCceeEec-ccccccccchHHHhhcC--CCCCCcccccCCCCc
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVR--SSCPVCRFQVPSDDF  265 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~~  265 (342)
                      .+.+...|+||++.|.   .++.++ |+|.||..||..|+..+  ..||+||..+...+.
T Consensus        11 ~~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           11 PIPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             CSCGGGSCSSSCCCCT---TCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             cCCCCCCCcCCChHHh---CCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            3456789999999998   778899 99999999999999866  589999997654443

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

Probab=99.26  E-value=1.8e-12  Score=96.82  Aligned_cols=51  Identities=29%  Similarity=0.618  Sum_probs=45.2

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      .+...|+||++.+.   .++.++|+|.||..||..|+..+..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           13 LTVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDF   63 (71)
T ss_dssp             SSCCBCSSSSSBCS---SEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHH
T ss_pred             CCCCCCccCCcccC---CCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhh
Confidence            35678999999997   7788999999999999999999999999999986543

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

Probab=99.25  E-value=1.6e-12  Score=94.38  Aligned_cols=54  Identities=20%  Similarity=0.614  Sum_probs=45.7

Q ss_pred             CcccccccccccccC----CceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIG----NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      +...|+||++.+...    ..++.++|+|.||..||.+|++.+.+||+||..+...+.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   59 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   59 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccce
Confidence            456899999999732    344788999999999999999999999999999876643

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

Probab=99.25  E-value=1.4e-12  Score=100.39  Aligned_cols=52  Identities=23%  Similarity=0.588  Sum_probs=41.9

Q ss_pred             Cccccccccccccc-----------CCceeEec-ccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEI-----------GNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~-----------~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      ++..|+||++.|..           ++.++.++ |+|.||..||.+||+.+.+||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            35568888888753           34466666 999999999999999999999999987643

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

Probab=99.25  E-value=3.5e-12  Score=95.34  Aligned_cols=53  Identities=25%  Similarity=0.639  Sum_probs=45.2

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhh---cCCCCCCcccccCCCC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE---VRSSCPVCRFQVPSDD  264 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---~~~~CP~CR~~l~~~~  264 (342)
                      .+.+...|+||++.+.   .++.++|+|.||..||..|++   ....||+||..+..++
T Consensus        16 ~~~~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           16 KLQEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCCBCTTTCSBCS---SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             hCccCCEeccCCcccC---CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            3456789999999998   788889999999999999997   4558999999987654

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

Probab=99.24  E-value=3.7e-12  Score=93.97  Aligned_cols=50  Identities=34%  Similarity=0.834  Sum_probs=43.5

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      ....|+||++.+.  +.++.++|+|.||..||.+|++.+.+||+||..+...
T Consensus         4 ~~~~C~IC~~~~~--~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCcccc--CCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            4568999999987  2358899999999999999999999999999988643

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

Probab=99.23  E-value=2.4e-12  Score=95.69  Aligned_cols=51  Identities=27%  Similarity=0.843  Sum_probs=45.0

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      .+...|+||++.+.   . +.++|+|.||..||.+|+..+.+||+||..+...+.
T Consensus        13 ~~~~~C~IC~~~~~---~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           13 TDEEECCICMDGRA---D-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCSSSCCSCC---S-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             CCCCCCeeCCcCcc---C-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            45678999999988   3 789999999999999999999999999999876543

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

Probab=99.22  E-value=6.1e-12  Score=97.22  Aligned_cols=57  Identities=23%  Similarity=0.552  Sum_probs=47.3

Q ss_pred             ccccCcccccccccccccCCc-eeEecccccccccchHHHhhcC---CCCCCcccccCCCC
Q 043965          208 VTIDKNLQCAVCLEEFEIGNE-AKEMPCKHKFHGECIMPWLEVR---SSCPVCRFQVPSDD  264 (342)
Q Consensus       208 ~~~~~~~~C~ICle~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~~  264 (342)
                      ..+.+...|+||++.|...+. ++.++|+|.||..||..|++.+   ..||+||..+...+
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           10 DALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             hhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            344567899999999985443 8889999999999999999876   69999999886553

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

Probab=99.22  E-value=4.2e-12  Score=93.37  Aligned_cols=52  Identities=21%  Similarity=0.608  Sum_probs=44.2

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhh-cCCCCCCcccccCCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPSDD  264 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~  264 (342)
                      +.+...|+||++.+.   .++.++|+|.||..||.+|+. ....||+||..+..++
T Consensus        12 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEES---SCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CCcCCCCCCCChHhc---CeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            345688999999998   666789999999999999994 5669999999987653

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

Probab=99.21  E-value=5.8e-12  Score=95.53  Aligned_cols=52  Identities=15%  Similarity=0.457  Sum_probs=45.8

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDD  264 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (342)
                      +.+.+.|+||++.|.   .++.++|||+||..||..|+.. +.+||+||..+....
T Consensus         5 ~~~~~~C~IC~~~~~---~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            5 FPEYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             CSSSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             CcccCCCCCcccccc---CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            456789999999998   7888999999999999999987 779999999987553

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

Probab=99.20  E-value=3e-12  Score=108.08  Aligned_cols=49  Identities=39%  Similarity=0.916  Sum_probs=44.3

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      ++..|+||++.|.   .++.++|||.||..||..|+..+.+||+||..+...
T Consensus        52 ~~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           52 NELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHSBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             ccCCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            4568999999998   788999999999999999999999999999988644

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

Probab=99.20  E-value=5.5e-12  Score=102.21  Aligned_cols=50  Identities=28%  Similarity=0.504  Sum_probs=42.4

Q ss_pred             CcccccccccccccCC---------------ceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIGN---------------EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~---------------~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ++..|+||++.|...-               .++.++|+|.||..||.+||..+.+||+||..+.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            4578999999987431               2566889999999999999999999999999864

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

Probab=99.19  E-value=7.2e-12  Score=95.85  Aligned_cols=48  Identities=19%  Similarity=0.610  Sum_probs=43.6

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      .....|+||++.|.   .++.++|+|+||..||..|++....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCC---SEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhc---CeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34678999999997   6788999999999999999999999999999885

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

Probab=99.17  E-value=1.2e-11  Score=94.48  Aligned_cols=53  Identities=34%  Similarity=0.812  Sum_probs=45.7

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhc------CCCCCCcccccCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV------RSSCPVCRFQVPSDDF  265 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~~~~  265 (342)
                      +.+...|+||++.+.   .++.++|+|.||..||..|+..      ...||+||..+..++.
T Consensus        16 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecw_A           16 IKEEVTCPICLELLK---EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNL   74 (85)
T ss_dssp             CCTTTSCTTTCSCCS---SCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCC
T ss_pred             CccCCCCcCCChhhC---cceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhC
Confidence            456789999999998   6778999999999999999987      6689999999876543

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

Probab=99.16  E-value=4.1e-12  Score=101.46  Aligned_cols=52  Identities=27%  Similarity=0.699  Sum_probs=45.2

Q ss_pred             ccCcccccccccccccCCceeE-ecccccccccchHHHhhcC-CCCCCcccccCCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWLEVR-SSCPVCRFQVPSDD  264 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (342)
                      +.+...|+||++.|.   .++. ++|||.||..||..|+..+ ..||+||..+...+
T Consensus        19 l~~~~~C~IC~~~~~---~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           19 IAEVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHHHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCccCCcccc---CccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            445788999999998   6777 8999999999999999888 69999999986544

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

Probab=99.16  E-value=5.1e-12  Score=95.77  Aligned_cols=53  Identities=28%  Similarity=0.684  Sum_probs=45.4

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhhc-------CCCCCCcccccCCCC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-------RSSCPVCRFQVPSDD  264 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-------~~~CP~CR~~l~~~~  264 (342)
                      .+.+...|+||++.|.   .++.++|||.||..||..|+..       ...||+||..+...+
T Consensus         8 ~~~~~~~C~IC~~~~~---~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   67 (79)
T 2egp_A            8 NVQEEVTCPICLELLT---EPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH   67 (79)
T ss_dssp             CCCCCCEETTTTEECS---SCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSG
T ss_pred             hcccCCCCcCCCcccC---CeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhh
Confidence            3456789999999998   6778999999999999999976       568999999987643

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

Probab=99.16  E-value=1.5e-11  Score=93.95  Aligned_cols=53  Identities=28%  Similarity=0.762  Sum_probs=45.6

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhhc------CCCCCCcccccCCCC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV------RSSCPVCRFQVPSDD  264 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~~~  264 (342)
                      .+.+...|+||++.+.   .++.++|+|.||..||..|+..      ...||+||..+...+
T Consensus        15 ~~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           15 NVKEEVTCPICLELLT---QPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCCCCTTTCSCCS---SCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             HccCCCCCCCCCcccC---CceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            3456788999999998   6778899999999999999987      679999999987654

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

Probab=99.11  E-value=3.5e-11  Score=87.54  Aligned_cols=45  Identities=27%  Similarity=0.714  Sum_probs=39.2

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhh---cCCCCCCc
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE---VRSSCPVC  256 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---~~~~CP~C  256 (342)
                      .+.+...|+||++.+.   .++.++|+|+||..||.+|++   ....||+|
T Consensus        16 ~~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBCS---SCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             hCccCCCCCcCCchhC---CeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3456789999999998   778889999999999999998   45589998

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

Probab=99.10  E-value=1.5e-11  Score=97.56  Aligned_cols=50  Identities=32%  Similarity=0.790  Sum_probs=43.8

Q ss_pred             cCcccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      .+...|+||++.|.   .++.+ +|||.||..||..|+..+..||+||..+...
T Consensus        20 ~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           20 DDLLRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HHHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CCCCCcccCChhhC---CcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChh
Confidence            34678999999998   56676 8999999999999999889999999988653

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

Probab=99.09  E-value=2.9e-11  Score=99.91  Aligned_cols=49  Identities=24%  Similarity=0.658  Sum_probs=43.3

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~  262 (342)
                      .+...|+||++.|.   .++.++|||.||..||..|+..+. .||+||..+..
T Consensus        50 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHc---CcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            34678999999998   788899999999999999998555 89999998865

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

Probab=99.09  E-value=6.6e-11  Score=91.03  Aligned_cols=52  Identities=21%  Similarity=0.627  Sum_probs=43.3

Q ss_pred             CcccccccccccccCCceeEeccc-----ccccccchHHHhhcCC--CCCCcccccCCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCK-----HKFHGECIMPWLEVRS--SCPVCRFQVPSDD  264 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~~  264 (342)
                      +...|.||++++..++. .++||+     |.||..||.+||..+.  +||+||..+..+.
T Consensus        14 ~~~~C~IC~~~~~~~~~-l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           14 SQDICRICHCEGDDESP-LITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             TSCCCSSSCCCCCSSSC-EECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCeEcCccccCCCe-eEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            45689999999976655 468996     9999999999997764  8999999987553

>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=99.09  E-value=3.5e-11  Score=97.04  Aligned_cols=51  Identities=33%  Similarity=0.794  Sum_probs=45.0

Q ss_pred             ccCcccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +.+...|+||++.|.   .++.+ +|||.||..||..|+..+..||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFI---DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HGGGTBCTTTSSBCS---SEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCcCCCccCChHHh---CcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            446789999999998   67776 9999999999999999999999999988654

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

Probab=99.09  E-value=4.7e-11  Score=93.32  Aligned_cols=50  Identities=28%  Similarity=0.651  Sum_probs=43.3

Q ss_pred             cccCcccccccccccccCCceeEec-ccccccccchHHHhhcC--CCCCCcccccC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVR--SSCPVCRFQVP  261 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~  261 (342)
                      .+.+.+.|+||++.|.   .++.++ |||.||..||..|+..+  ..||+||..+.
T Consensus         9 ~~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A            9 PIPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCCTTTEETTTTEECS---SCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             cCCcCCCCCCCChhhc---CceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            3456789999999998   788999 99999999999999754  48999999873

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=99.08  E-value=1.3e-11  Score=101.69  Aligned_cols=50  Identities=28%  Similarity=0.521  Sum_probs=0.9

Q ss_pred             CcccccccccccccC-------------C--ceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIG-------------N--EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~-------------~--~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ++..|+||++.|...             +  .+..++|+|.||..||.+||+.+.+||+||.++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            357899999999742             1  2334589999999999999999999999999864

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

Probab=99.04  E-value=6.1e-11  Score=84.42  Aligned_cols=44  Identities=39%  Similarity=0.918  Sum_probs=37.7

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhh---cCCCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE---VRSSCPVC  256 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---~~~~CP~C  256 (342)
                      +.+...|+||++.+.   .++.++|+|+||..||.+|+.   ....||+|
T Consensus        12 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLK---EPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCS---SCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccC---ccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            445678999999998   667899999999999999954   56689998

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

Probab=99.04  E-value=5.7e-11  Score=98.12  Aligned_cols=55  Identities=20%  Similarity=0.619  Sum_probs=46.7

Q ss_pred             CcccccccccccccC----CceeEecccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965          212 KNLQCAVCLEEFEIG----NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       212 ~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (342)
                      +...|+||++.|...    ..++.++|||+||..||.+|++.+.+||+||..+......
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~   64 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   64 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEE
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccccc
Confidence            467899999999732    3348899999999999999999999999999999766543

>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=99.04  E-value=5.6e-11  Score=95.94  Aligned_cols=51  Identities=29%  Similarity=0.768  Sum_probs=43.7

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~~~~~  265 (342)
                      +...|+||++.+.   .++.++|||.||..||..|+..+.   .||+||..+.....
T Consensus        20 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   73 (112)
T 1jm7_A           20 KILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (112)
T ss_dssp             HHTSCSSSCCCCS---SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CCCCCcccChhhc---CeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhc
Confidence            4568999999997   677789999999999999998654   89999998876543

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

Probab=99.02  E-value=9.8e-11  Score=85.73  Aligned_cols=54  Identities=17%  Similarity=0.453  Sum_probs=42.3

Q ss_pred             ccccccccc-ccccCCc-eeEecccccccccchHHHhhc-CCCCCCcccccCCCCcc
Q 043965          213 NLQCAVCLE-EFEIGNE-AKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       213 ~~~C~ICle-~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~  266 (342)
                      +..|+||++ .+..... .+.++|||+||..||.+|+.. ...||+||..+...+..
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   59 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCE
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccce
Confidence            567999999 7774322 246789999999999999754 45899999998766543

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

Probab=99.02  E-value=1e-10  Score=90.84  Aligned_cols=51  Identities=10%  Similarity=0.116  Sum_probs=46.1

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +.+.+.|+||++.|.   +++.++|||+|+..||..||..+.+||+|+..+...
T Consensus        11 ~p~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           11 APDEFRDPLMDTLMT---DPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CCTTTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CchheECcccCchhc---CCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            345789999999999   899999999999999999999889999999988654

>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=99.00  E-value=1.8e-10  Score=92.22  Aligned_cols=53  Identities=9%  Similarity=0.109  Sum_probs=47.1

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      +.+.+.|+||++.|.   +++.++|||+||..||..||..+.+||+||.++...++
T Consensus        26 ~p~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L   78 (100)
T 2kre_A           26 APDEFRDPLMDTLMT---DPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESML   78 (100)
T ss_dssp             CSTTTBCTTTCSBCS---SEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSS
T ss_pred             CcHhhCCcCccCccc---CCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhc
Confidence            345789999999999   89999999999999999999988899999999876543

>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=99.00  E-value=1.1e-10  Score=100.20  Aligned_cols=49  Identities=22%  Similarity=0.623  Sum_probs=43.7

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (342)
                      +...|+||++.|.   .++.++|+|.||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhc---CCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4578999999998   788899999999999999998765 899999998765

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

Probab=99.00  E-value=2.1e-10  Score=86.93  Aligned_cols=52  Identities=19%  Similarity=0.459  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcC--CCCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--SSCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~~  265 (342)
                      ....|+||++.+..+.  +...|+|.||..||.+||+.+  .+||+||..+..+..
T Consensus        14 ~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~   67 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP   67 (74)
T ss_dssp             SSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCC
T ss_pred             CCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCC
Confidence            3568999999998543  333799999999999999887  799999988765543

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=98.99  E-value=2e-10  Score=91.64  Aligned_cols=53  Identities=11%  Similarity=0.082  Sum_probs=47.2

Q ss_pred             ccCcccccccccccccCCceeEeccc-ccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCK-HKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      +.+.+.|+||++.|.   +++.++|| |+||+.||..||..+.+||+||.++...++
T Consensus        19 ~p~~~~CpI~~~~m~---dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L   72 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             CCTTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             CcHhcCCcCcccccc---CCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhc
Confidence            345789999999999   89999999 999999999999988899999999876543

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

Probab=98.99  E-value=9.5e-11  Score=101.50  Aligned_cols=49  Identities=31%  Similarity=0.808  Sum_probs=42.4

Q ss_pred             cCcccccccccccccCCceeEe-cccccccccchHHHhhc-CCCCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEV-RSSCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~  262 (342)
                      .+...|+||++.|.   .++.+ +|||.||..||..|+.. +..||+||..+..
T Consensus        52 ~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDMLK---NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBCS---SEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHhh---CcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            45678999999998   56666 89999999999999987 6789999998854

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

Probab=98.99  E-value=4.7e-11  Score=97.28  Aligned_cols=49  Identities=33%  Similarity=0.736  Sum_probs=43.2

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~  262 (342)
                      .+++.|+||++.|.   .++.++|||.||..||..|+.. +..||+||..+..
T Consensus        13 ~~~~~C~iC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBCS---SCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCccCCcccC---ceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            45678999999998   7888999999999999999976 5689999998864

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

Probab=98.98  E-value=1e-10  Score=95.94  Aligned_cols=51  Identities=27%  Similarity=0.690  Sum_probs=44.7

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (342)
                      +.+...|+||++.+.   .++.++|||.||..||..|+.... +||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           15 LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcCChhhc---CeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            456689999999998   778899999999999999998766 999999988654

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

Probab=98.97  E-value=6.6e-11  Score=96.57  Aligned_cols=51  Identities=35%  Similarity=0.765  Sum_probs=44.6

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDD  264 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (342)
                      .+...|+||++.+.   .++.++|||.||..||..|+.. ..+||+||..+...+
T Consensus        21 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           21 VKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cCCCCCCCCCcHhc---CcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            34678999999998   7788999999999999999987 679999999987543

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

Probab=98.94  E-value=1.8e-10  Score=95.08  Aligned_cols=53  Identities=23%  Similarity=0.676  Sum_probs=45.1

Q ss_pred             Cccccccccccccc----CCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          212 KNLQCAVCLEEFEI----GNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       212 ~~~~C~ICle~~~~----~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      +...|+||++.|..    +..++.++|+|.||..||.+|++.+.+||+||..+..++
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            45689999999973    223478899999999999999999999999999987654

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

Probab=98.93  E-value=2.7e-10  Score=93.29  Aligned_cols=48  Identities=27%  Similarity=0.647  Sum_probs=42.2

Q ss_pred             cCcccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      .+...|+||++.|.   .++.+ +|||.||..||..|+.  ..||+||..+...
T Consensus        20 ~~~~~C~IC~~~~~---~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           20 EKLLRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (117)
T ss_dssp             HHTTSCSSSCSCCS---SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             hhCCCCCCCChHhh---CccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccc
Confidence            45688999999998   77788 8999999999999998  8899999988543

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

Probab=98.90  E-value=3.4e-10  Score=110.63  Aligned_cols=47  Identities=30%  Similarity=0.796  Sum_probs=42.7

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhh-cCCCCCCcccccCCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPSD  263 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~  263 (342)
                      ..|+||++.+.   .++.+||||.||..||..|+. .+.+||+||..+...
T Consensus       333 ~~C~ICle~~~---~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          333 QLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SBCTTTSSSBC---CEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCccCcCCC---CeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            68999999987   788999999999999999998 678999999988654

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

Probab=98.90  E-value=3.6e-10  Score=95.92  Aligned_cols=52  Identities=15%  Similarity=0.507  Sum_probs=44.6

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD  263 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (342)
                      .+.+.+.|+||++.|.   .++.++|||.||..||..|+.... .||+||.++..+
T Consensus        27 ~l~~~~~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           27 KLEAKYLCSACRNVLR---RPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             GCCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             cCCcCcCCCCCChhhc---CcEECCCCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            3456789999999998   778899999999999999998665 899999987543

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

Probab=98.89  E-value=5.3e-10  Score=79.75  Aligned_cols=46  Identities=28%  Similarity=0.673  Sum_probs=39.9

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +...|+||++.|.   .++.++|+|.||..||..|   ...||+||..+...
T Consensus         5 ~~~~C~IC~~~~~---~p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            5 QFLRCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCB---CCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             cCCCceEeCCccC---CeEEcCCCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            4578999999998   6789999999999999884   56899999988654

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

Probab=98.88  E-value=1e-09  Score=83.87  Aligned_cols=56  Identities=25%  Similarity=0.570  Sum_probs=43.6

Q ss_pred             ccCcccccccccccccCCceeEec--ccccccccchHHHhh-cCCCCCCcccccCCCCcc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMP--CKHKFHGECIMPWLE-VRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~~~  266 (342)
                      +.++..|+||++.+... .++.+|  |||.||..|+..|+. ....||+||+.+......
T Consensus         8 ~~~~~~CpICle~~~~~-d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEID-DINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCCBCTTTCCBCCTT-TTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             cccCCcCCccCccCccc-cccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            45678999999988643 334454  999999999999874 356899999999776553

>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=98.85  E-value=1.1e-09  Score=80.44  Aligned_cols=47  Identities=19%  Similarity=0.359  Sum_probs=41.3

Q ss_pred             CcccccccccccccCCceeEe--ccccc-ccccchHHHhhcCCCCCCcccccC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEM--PCKHK-FHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~l--pC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ++..|.||++.+.   .++.+  ||||. ||..|+..|++.+..||+||.++.
T Consensus         7 ~~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPK---NGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCS---CEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCC---CEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            4568999999987   66666  99999 899999999998899999999874

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.81  E-value=1.2e-09  Score=101.00  Aligned_cols=52  Identities=19%  Similarity=0.192  Sum_probs=44.8

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD  263 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (342)
                      .+...+.|+||++.|.   +++.++|||+||..||..|+..+. +||+||.++...
T Consensus       204 ~~~~~~~c~i~~~~~~---dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~  256 (281)
T 2c2l_A          204 DIPDYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE  256 (281)
T ss_dssp             CCCSTTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             CCCcccCCcCcCCHhc---CCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchh
Confidence            3445789999999999   899999999999999999997644 599999988644

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

Probab=98.79  E-value=7.9e-10  Score=83.36  Aligned_cols=45  Identities=20%  Similarity=0.544  Sum_probs=39.9

Q ss_pred             cCcccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      .+...|+||++.+.   .++.+||||. ||..|+..|    ..||+||..+..
T Consensus        22 ~~~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           22 QEEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHHTBCTTTSSSBC---CEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             ccCCCCCCCCCCCC---CEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            34578999999988   7889999999 999999998    889999998854

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

Probab=98.75  E-value=1.7e-09  Score=85.31  Aligned_cols=51  Identities=24%  Similarity=0.636  Sum_probs=42.5

Q ss_pred             cCcccccccccccccCCceeEec-ccccccccchHHHhhcC------CCCCC--cccc-cCCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVR------SSCPV--CRFQ-VPSDD  264 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~------~~CP~--CR~~-l~~~~  264 (342)
                      .+.+.|+||++.|.   +++.++ |||+||..||..||..+      .+||+  |+.. +...+
T Consensus         5 ~~~~~CPI~~~~~~---dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~   65 (94)
T 2yu4_A            5 SSGFTCPITKEEMK---KPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSD   65 (94)
T ss_dssp             SSCCBCTTTCSBCS---SEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGG
T ss_pred             CcEeECcCcCchhc---CCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhh
Confidence            35678999999999   888996 99999999999999754      48999  9876 54443

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

Probab=98.75  E-value=3.4e-09  Score=77.46  Aligned_cols=46  Identities=17%  Similarity=0.432  Sum_probs=40.2

Q ss_pred             cccccccccccccCCceeEe--ccccc-ccccchHHHhhcCCCCCCcccccC
Q 043965          213 NLQCAVCLEEFEIGNEAKEM--PCKHK-FHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~l--pC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      ...|.||++...   .+..+  ||||. ||..|+..|.+....||+||.++.
T Consensus         7 ~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPR---DGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBS---CEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCCCcccCCcCC---CeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            467999999876   55566  99998 999999999988889999999884

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

Probab=98.71  E-value=3.3e-09  Score=92.09  Aligned_cols=51  Identities=27%  Similarity=0.690  Sum_probs=44.4

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD  263 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (342)
                      +.+.+.|+||++.|.   .++.++|||+||..||.+|+.... +||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           15 LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCChhhc---CcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            456789999999998   778899999999999999997654 999999988654

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

Probab=98.65  E-value=1.1e-08  Score=90.06  Aligned_cols=53  Identities=21%  Similarity=0.193  Sum_probs=45.4

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHHhhcC-CCCCCcccccCCCC
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQVPSDD  264 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (342)
                      .+.+.+.|+||++.|.   +++.++|||+|+..||..|+..+ .+||+|+.++...+
T Consensus       102 ~ip~~f~CPI~~elm~---DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~  155 (179)
T 2f42_A          102 EIPDYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQ  155 (179)
T ss_dssp             CCCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCcHhhcccCccccCC---CCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhh
Confidence            3456789999999999   88999999999999999999764 47999999886543

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

Probab=98.61  E-value=7e-09  Score=78.18  Aligned_cols=45  Identities=20%  Similarity=0.546  Sum_probs=38.3

Q ss_pred             CcccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +...|+||++.+.   .++.+||+|. ||..|+..    ...||+||..+...
T Consensus        24 ~~~~C~IC~~~~~---~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           24 EEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHHSCSSSCSSCC---CBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCCcCCCCCC---CEEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            4567999999987   7888999999 99999954    37899999988654

>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=98.49  E-value=1.9e-08  Score=76.88  Aligned_cols=45  Identities=36%  Similarity=0.685  Sum_probs=39.2

Q ss_pred             CcccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +...|+||++.+.   .++.+||||. ||..|+..|.    .||+||..+...
T Consensus        17 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~~~----~CP~Cr~~i~~~   62 (79)
T 2yho_A           17 EAMLCMVCCEEEI---NSTFCPCGHTVCCESCAAQLQ----SCPVCRSRVEHV   62 (79)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCBCCBCHHHHTTCS----BCTTTCCBCCEE
T ss_pred             CCCEeEEeCcccC---cEEEECCCCHHHHHHHHHhcC----cCCCCCchhhCe
Confidence            4568999999987   8899999999 9999998873    999999988654

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

Probab=98.48  E-value=6.4e-08  Score=71.81  Aligned_cols=45  Identities=27%  Similarity=0.651  Sum_probs=38.7

Q ss_pred             CcccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      +...|.||++...   .++.+||+|. ||..|+..    ...||+||..+...
T Consensus        14 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           14 NSKDCVVCQNGTV---NWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CSSCCSSSSSSCC---CCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCcCcCCC---CEEEECCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            4568999999887   7899999999 99999973    47899999988654

>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=98.47  E-value=3.2e-08  Score=95.66  Aligned_cols=45  Identities=27%  Similarity=0.669  Sum_probs=40.2

Q ss_pred             cCcccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      .+...|+||++.+.   .++.+||||. ||..|+..|    ..||+||..+..
T Consensus       293 ~~~~~C~IC~~~~~---~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEV---SVVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBC---CEEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCC---ceEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            45678999999998   8889999999 999999988    789999998854

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.45  E-value=3.9e-08  Score=71.52  Aligned_cols=51  Identities=8%  Similarity=0.164  Sum_probs=44.7

Q ss_pred             cccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965          213 NLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (342)
                      .+.|+||++.+.   +++.+ +|||+|.+.||.+||+.+.+||+++.+|..+++.
T Consensus         3 ~~~CpIs~~~m~---dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Li   54 (61)
T 2bay_A            3 HMLCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   54 (61)
T ss_dssp             -CCCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             eEEecCCCCCCC---CCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcE
Confidence            357999999999   77888 8999999999999999888999999999766543

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

Probab=98.45  E-value=4.3e-08  Score=93.79  Aligned_cols=52  Identities=23%  Similarity=0.674  Sum_probs=39.8

Q ss_pred             CcccccccccccccCC-cee----EecccccccccchHHHhhcC-----------CCCCCcccccCCC
Q 043965          212 KNLQCAVCLEEFEIGN-EAK----EMPCKHKFHGECIMPWLEVR-----------SSCPVCRFQVPSD  263 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~-~~~----~lpC~H~Fh~~Ci~~Wl~~~-----------~~CP~CR~~l~~~  263 (342)
                      ...+|+||++.+..+. .+.    ..+|+|.||..||.+||+..           ++||+||.++...
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            3468999999998622 221    23699999999999999653           4699999988654

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

Probab=98.40  E-value=6.3e-08  Score=89.69  Aligned_cols=53  Identities=26%  Similarity=0.527  Sum_probs=43.7

Q ss_pred             ccCcccccccccccccCCceeE-ecccccccccchHHHhhcC--CCCCC--cccccCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWLEVR--SSCPV--CRFQVPSDDF  265 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~--~~CP~--CR~~l~~~~~  265 (342)
                      ......|+||++.|.   .++. +.|||+||+.||..|+..+  ..||+  |+..+...++
T Consensus       178 ~~~el~CPIcl~~f~---DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL  235 (267)
T 3htk_C          178 GKIELTCPITCKPYE---APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDF  235 (267)
T ss_dssp             SBCCSBCTTTSSBCS---SEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGE
T ss_pred             CceeeECcCccCccc---CCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhC
Confidence            345689999999998   6666 4899999999999999764  37999  9998866544

>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=98.32  E-value=1.5e-07  Score=73.79  Aligned_cols=51  Identities=25%  Similarity=0.603  Sum_probs=38.7

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcC--------CCCCC--cccc--cCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--------SSCPV--CRFQ--VPS  262 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--------~~CP~--CR~~--l~~  262 (342)
                      +..+|+||++.+.........+|+|.||..|+..++..+        ..||.  |+..  +..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            356899999998744333334799999999999998531        27999  9987  543

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.30  E-value=2.6e-07  Score=66.97  Aligned_cols=48  Identities=23%  Similarity=0.666  Sum_probs=37.2

Q ss_pred             CcccccccccccccCCceeEeccc--c---cccccchHHHhhc--CCCCCCcccccCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCK--H---KFHGECIMPWLEV--RSSCPVCRFQVPS  262 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~  262 (342)
                      +...|.||++...   ....+||.  |   .||..||.+|+..  +.+||+|+..+..
T Consensus         5 ~~~~CrIC~~~~~---~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEELG---NERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECS---CCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCCC---CceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            4568999999743   33468854  4   8999999999964  5689999998753

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.88  E-value=4.6e-06  Score=65.99  Aligned_cols=47  Identities=26%  Similarity=0.494  Sum_probs=38.8

Q ss_pred             cccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCC
Q 043965          215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSD  263 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~  263 (342)
                      .|.+|--.+.  .-.+.+||+|+||.+|+..|.+. .++||.|+.++..-
T Consensus         3 fC~~C~~Pi~--iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCS--EEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeE--EEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            4888887776  35678899999999999999854 57999999988543

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=97.57  E-value=2.7e-05  Score=71.41  Aligned_cols=51  Identities=20%  Similarity=0.469  Sum_probs=40.4

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCC--CCCCcccccCCCCc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS--SCPVCRFQVPSDDF  265 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~~~  265 (342)
                      ...|.||.+.+..+  .+.-.|+|.||..|+.+|++.+.  .||.|+...+....
T Consensus       180 i~~C~iC~~iv~~g--~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          180 VKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             CCBCTTTCSBCSSC--EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCcCcchhhHHhCC--cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            46799999998853  22233999999999999997765  89999998766543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=92.49  E-value=0.042  Score=42.69  Aligned_cols=33  Identities=18%  Similarity=0.547  Sum_probs=25.1

Q ss_pred             CcccccccccccccCCceeE--ecccccccccchHHH
Q 043965          212 KNLQCAVCLEEFEIGNEAKE--MPCKHKFHGECIMPW  246 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~--lpC~H~Fh~~Ci~~W  246 (342)
                      ++..|.||++.+..  .++.  +.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~--~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQ--DAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCC--BCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCC--CceEECCcCChHHhHHHCHHH
Confidence            34679999976432  3344  889999999999983

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=92.35  E-value=0.069  Score=40.71  Aligned_cols=37  Identities=19%  Similarity=0.407  Sum_probs=24.5

Q ss_pred             cccCcccccccccccccCCceeEecccccccccchHHH
Q 043965          209 TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPW  246 (342)
Q Consensus       209 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~W  246 (342)
                      .+..+..|.||-- +..++....--|+-+||..|+.+.
T Consensus        11 ~~~~D~~C~VC~~-~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           11 PVVNDEMCDVCEV-WTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTTCC-CCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCCcccCcccc-ccccceeccccccccccHhhcccc
Confidence            3446788999953 332222222238999999999986

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=91.26  E-value=0.092  Score=42.47  Aligned_cols=33  Identities=27%  Similarity=0.425  Sum_probs=25.6

Q ss_pred             CceeeeccCceeecCCCCCc-cCCCCCCCceeccc
Q 043965            6 VGYWCYICSQMVNPRMEAGI-KCPFCESGIVEQMS   39 (342)
Q Consensus         6 ~~ywCh~C~~~V~p~~~~e~-~CP~C~sGFvEE~~   39 (342)
                      +.|||..|...+... .... +||.|++..++-+.
T Consensus        72 ~~~~C~~CG~~~e~~-~~~~~~CP~Cgs~~~~i~~  105 (119)
T 2kdx_A           72 VELECKDCSHVFKPN-ALDYGVCEKCHSKNVIITQ  105 (119)
T ss_dssp             CEEECSSSSCEECSC-CSTTCCCSSSSSCCCEEEE
T ss_pred             ceEEcCCCCCEEeCC-CCCCCcCccccCCCcEEec
Confidence            349999999998743 3467 89999999776544

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=88.06  E-value=0.28  Score=35.60  Aligned_cols=44  Identities=25%  Similarity=0.541  Sum_probs=31.5

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCcccc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRFQ  259 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~  259 (342)
                      ...|.||.+.   ++.+.--.|...||..|+.+.|....    .||.|+..
T Consensus        12 ~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           12 GARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             TCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            4569999753   33333334999999999998886543    79999753

>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=85.38  E-value=0.39  Score=51.67  Aligned_cols=50  Identities=14%  Similarity=0.202  Sum_probs=44.2

Q ss_pred             CcccccccccccccCCceeEeccc-ccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCK-HKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      +.+.|+|-++.+.   +++.+|.| +.|-+.+|.+||..+.+||+=|.++....
T Consensus       890 ~~F~cPIs~~lM~---DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          890 DEFLDPLMYTIMK---DPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLED  940 (968)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             HHhCCcchhhHHh---CCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccc
Confidence            3578999999999   89999987 68999999999999999999999887554

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=84.86  E-value=0.67  Score=34.06  Aligned_cols=37  Identities=24%  Similarity=0.498  Sum_probs=29.7

Q ss_pred             CCCCCCceeeeccCceeecC----------------CCCCccCCCCCC---Cceec
Q 043965            1 MGDAMVGYWCYICSQMVNPR----------------MEAGIKCPFCES---GIVEQ   37 (342)
Q Consensus         1 m~~~~~~ywCh~C~~~V~p~----------------~~~e~~CP~C~s---GFvEE   37 (342)
                      |+.+|..|-|-.|--...+.                ++++.+||.|+-   -|+..
T Consensus         1 m~~~m~~y~C~vCGyiYd~~~Gdp~~gi~pGT~f~~lPddw~CP~Cga~K~~F~~~   56 (70)
T 1dx8_A            1 MEIDEGKYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSPKNQFKSI   56 (70)
T ss_dssp             CBCCSSCEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCBGGGEEEC
T ss_pred             CCCCCceEEeCCCCEEEcCCCCCcccCcCCCCchhhCCCCCcCCCCCCCHHHceEc
Confidence            89999999999999887764                455789999997   56553

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=83.76  E-value=0.49  Score=33.58  Aligned_cols=45  Identities=31%  Similarity=0.629  Sum_probs=30.9

Q ss_pred             cCcccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccc
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRF  258 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~  258 (342)
                      ..+..|.||...   ++-+.--.|...||..|+.+-+....    .||.|+.
T Consensus         9 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            345789999873   22333334889999999988654322    7999975

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=83.44  E-value=0.63  Score=35.75  Aligned_cols=47  Identities=30%  Similarity=0.615  Sum_probs=32.6

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCcccc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRFQ  259 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~  259 (342)
                      ...+..|.||...   ++-+..-.|.-.||..|+.+-|....    .||.|+..
T Consensus        22 d~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           22 DDSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            3456789999864   32333334889999999988764433    69999764

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=83.43  E-value=0.33  Score=34.57  Aligned_cols=47  Identities=26%  Similarity=0.480  Sum_probs=31.2

Q ss_pred             CcccccccccccccCCceeE-ecccccccccchHHHhh-----cCCCCCCccc
Q 043965          212 KNLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWLE-----VRSSCPVCRF  258 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~-----~~~~CP~CR~  258 (342)
                      +...|+||...+..+...+. -.|...||..|+.--..     ..-.||.|+.
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            45679999988753332222 24899999999853221     3347999975

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=83.10  E-value=0.59  Score=33.15  Aligned_cols=46  Identities=26%  Similarity=0.515  Sum_probs=31.0

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccccc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRFQV  260 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~l  260 (342)
                      .+..|.||.+.   ++.+.--.|...||..|+.+-|....    .||.|+...
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            35679999863   22333334889999999987654322    699997643

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=82.62  E-value=0.56  Score=31.66  Aligned_cols=33  Identities=27%  Similarity=0.696  Sum_probs=20.9

Q ss_pred             CCceeeeccCceeecC-C--CCCccCCCCCCCceec
Q 043965            5 MVGYWCYICSQMVNPR-M--EAGIKCPFCESGIVEQ   37 (342)
Q Consensus         5 ~~~ywCh~C~~~V~p~-~--~~e~~CP~C~sGFvEE   37 (342)
                      |+.|=|-.|-+++.-. +  -.+++||+|+=--|.-
T Consensus         1 ~~iY~C~rCg~~fs~~el~~lP~IrCpyCGyrii~K   36 (48)
T 4ayb_P            1 MAVYRCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFM   36 (48)
T ss_dssp             ----CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEEC
T ss_pred             CcEEEeeccCCCccHHHHhhCCCcccCccCcEEEEE
Confidence            3458999999998532 1  1489999998655543

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=82.24  E-value=0.52  Score=39.19  Aligned_cols=34  Identities=24%  Similarity=0.379  Sum_probs=24.6

Q ss_pred             CceeeeccCceeecCC----------CC----------CccCCCCCCCceeccc
Q 043965            6 VGYWCYICSQMVNPRM----------EA----------GIKCPFCESGIVEQMS   39 (342)
Q Consensus         6 ~~ywCh~C~~~V~p~~----------~~----------e~~CP~C~sGFvEE~~   39 (342)
                      +.+||..|...+....          ..          ..+||.|++.-++-+.
T Consensus        69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i~~  122 (139)
T 3a43_A           69 AVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVK  122 (139)
T ss_dssp             CEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEEEE
T ss_pred             CcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEEec
Confidence            3499999999886432          02          5789999998776433

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=81.70  E-value=0.77  Score=33.05  Aligned_cols=28  Identities=21%  Similarity=0.532  Sum_probs=24.1

Q ss_pred             eeeeccCceeecCCCCCccCCCCCCCce
Q 043965            8 YWCYICSQMVNPRMEAGIKCPFCESGIV   35 (342)
Q Consensus         8 ywCh~C~~~V~p~~~~e~~CP~C~sGFv   35 (342)
                      |-|-.|..+|.......|.||+|+.-.+
T Consensus        22 Y~C~~Cg~~~~l~~~~~iRC~~CG~RIL   49 (63)
T 3h0g_L           22 YLCADCGARNTIQAKEVIRCRECGHRVM   49 (63)
T ss_dssp             CBCSSSCCBCCCCSSSCCCCSSSCCCCC
T ss_pred             EECCCCCCeeecCCCCceECCCCCcEEE
Confidence            9999999999876666799999998654

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=80.79  E-value=0.51  Score=31.96  Aligned_cols=44  Identities=30%  Similarity=0.540  Sum_probs=28.3

Q ss_pred             cccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccc
Q 043965          215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRF  258 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~  258 (342)
                      .|.||...-..++-+.--.|...||..|+.+=|....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            4888986533222233334889999999976554322    6999964

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.23  E-value=0.34  Score=33.71  Aligned_cols=44  Identities=27%  Similarity=0.594  Sum_probs=29.9

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRF  258 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~  258 (342)
                      .+..|.||...   ++.+.--.|...||..|+.+-|....    .||.|..
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            45679999874   32333334899999999987654322    5888854

---

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	342
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-18
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-15
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	5e-12
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	6e-12
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-11
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-10
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-10
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	8e-09
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	5e-08
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	6e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	2e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	2e-05

>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 = 76.1 bits (187), Expect = 2e-18
 Identities = 26/52 (50%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQV 260
           +D  ++CAVCL E E G EA+ +P C H FH EC+  WL   S+CP+CR  V
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 67.7 bits (165), Expect = 3e-15
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQGNGS 272
           +C +CLE+    N +  +PC H F   CI  W+    +CP+C+  V S    I+ +  
Sbjct: 7   RCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSE 62

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 5e-12
 Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 4/50 (8%)

Query: 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS-CPVCRFQVPSDD 264
           C +C E  +   + K  PC H     C+  W E     CP CR ++   +
Sbjct: 26  CKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 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 = 58.3 bits (140), Expect = 6e-12
 Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 3/59 (5%)

Query: 213 NLQCAVCLEEFEIGNEAKEM--PCKHKFHGECIMPWLEVRS-SCPVCRFQVPSDDFKIQ 268
           +  C  C          K M   C H     C+       + +CP C   +   +F++Q
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ 61

>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 = 55.3 bits (133), Expect = 5e-11
 Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 6/50 (12%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263
           L+C  C  E +     K +PC H     C+         CP+C+   P  
Sbjct: 7   LRCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG 50

>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 = 55.9 bits (134), Expect = 7e-11
 Identities = 14/57 (24%), Positives = 17/57 (29%), Gaps = 15/57 (26%)

Query: 216 CAVCLEEF---------------EIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257
           CA+C                             C H FH  CI  WL+ R  CP+  
Sbjct: 24  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 2e-10
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 214 LQCAVCLEEFEIGNEA-KEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD 263
           ++C +C+E  EI +       C ++    C        +  CP CR   P D
Sbjct: 1   VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQVPSDDFK 266
           + K L+C +CLE  +   E     C H F   C++  L  +     CP+C+  +     +
Sbjct: 18  MQKILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQ 74

>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 = 50.2 bits (119), Expect = 8e-09
 Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 9/80 (11%)

Query: 188 DPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247
           +P+  G  A ++A L  L     +K L+C+ C              C+H F   C+   +
Sbjct: 2   EPDGRGAWAHSRAALDRL-----EKLLRCSRCTNILREPV--CLGGCEHIFCSNCVSDCI 54

Query: 248 EVRSSCPVCRFQVPSDDFKI 267
                CPVC       D KI
Sbjct: 55  GTG--CPVCYTPAWIQDLKI 72

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.1 bits (117), Expect = 1e-08
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSS-CPVCRFQVPSDDFK 266
             K++ C +C        +  E  CKH F   CI+  L+V  S CP CR+     D +
Sbjct: 20  FVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 74

>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 = 46.8 bits (110), Expect = 5e-08
 Identities = 10/50 (20%), Positives = 16/50 (32%), Gaps = 4/50 (8%)

Query: 214 LQCAVCLEEFEIGNEAKEMP--CKHKFHGECIMPWLEVR--SSCPVCRFQ 259
             C +C EE                  H  C+  WL +   ++C +C   
Sbjct: 7   PVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 6e-06
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 10/65 (15%)

Query: 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS--------SCP--VCRFQVPSDD 264
            C +CL E+ +        C+  F   C+  ++E+          SCP   C  Q    +
Sbjct: 7   GCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE 66

Query: 265 FKIQG 269
            +I+ 
Sbjct: 67  NEIEC 71

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.8 bits (94), Expect = 2e-05
 Identities = 12/79 (15%), Positives = 26/79 (32%), Gaps = 20/79 (25%)

Query: 199 KAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKE---------------MPCKHKFHGECI 243
           + + K    + +     C +C+E+  + +   +                 C H FH  C+
Sbjct: 11  QVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCL 70

Query: 244 MPWLEVRS-----SCPVCR 257
           +      +      CP C+
Sbjct: 71  LAMYCNGNKDGSLQCPSCK 89

>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 = 39.4 bits (91), Expect = 2e-05
 Identities = 4/51 (7%), Positives = 17/51 (33%), Gaps = 2/51 (3%)

Query: 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264
           + CA+  +             +  F    +  +++   + P+    +  ++
Sbjct: 1   MLCAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 49

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	342
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.55
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.4
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.31
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.29
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.25
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.25
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.23
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.21
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.17
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.16
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.11
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.05
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.03
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.01
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.86
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.77
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.22
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	89.2
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	86.87
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	86.03
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	84.83
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	82.13

>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=99.55  E-value=7.5e-16  Score=108.80  Aligned_cols=51  Identities=51%  Similarity=1.129  Sum_probs=46.2

Q ss_pred             cCcccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      +++.+|+||+++|..++.+..++ |+|.||..||.+||+.+.+||+||+.|.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            45678999999999888888876 9999999999999999999999999774

>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=99.40  E-value=5.5e-14  Score=103.15  Aligned_cols=48  Identities=35%  Similarity=0.900  Sum_probs=42.3

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS  262 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (342)
                      ...|+||++.|.  +.++.++|+|.||..||.+|++.+.+||+||.++..
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            457999999986  356778999999999999999999999999998753

>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=99.31  E-value=1.1e-12  Score=105.35  Aligned_cols=70  Identities=17%  Similarity=0.492  Sum_probs=48.5

Q ss_pred             CCcccHHHHHcC-CcccccCcccccccccccccC---------------CceeEecccccccccchHHHhhcC-----CC
Q 043965          194 CPAANKAVLKAL-PTVTIDKNLQCAVCLEEFEIG---------------NEAKEMPCKHKFHGECIMPWLEVR-----SS  252 (342)
Q Consensus       194 ~~~~~~~~i~~~-p~~~~~~~~~C~ICle~~~~~---------------~~~~~lpC~H~Fh~~Ci~~Wl~~~-----~~  252 (342)
                      .....+++++++ ..+....+..|+||++.|...               ..+..++|+|+||..||..||+..     .+
T Consensus         5 ss~~pe~v~~~~~e~~~~~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~   84 (114)
T d1v87a_           5 SSGEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ   84 (114)
T ss_dssp             SSCCHHHHHHHHEEECSSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCB
T ss_pred             CCCCCHHHHHHHHHHhcccccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCc
Confidence            334445555442 223334467899999998532               234567899999999999999753     37


Q ss_pred             CCCcccccCCC
Q 043965          253 CPVCRFQVPSD  263 (342)
Q Consensus       253 CP~CR~~l~~~  263 (342)
                      ||+||..+..+
T Consensus        85 CP~CR~~~~~~   95 (114)
T d1v87a_          85 CPSCKTIYGEK   95 (114)
T ss_dssp             CTTTCCBSSSC
T ss_pred             cccccchhccC
Confidence            99999877544

>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=99.29  E-value=3.2e-13  Score=93.87  Aligned_cols=49  Identities=24%  Similarity=0.542  Sum_probs=40.8

Q ss_pred             ccccccccccccCCc-eeEecccccccccchHHHhhcCC-CCCCcccccCC
Q 043965          214 LQCAVCLEEFEIGNE-AKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPS  262 (342)
Q Consensus       214 ~~C~ICle~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~  262 (342)
                      .+|+||+++|..++. ++.++|+|.||..||.+|++.+. +||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            379999999976554 45568999999999999998644 79999998864

>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=99.25  E-value=1.2e-12  Score=95.11  Aligned_cols=55  Identities=16%  Similarity=0.399  Sum_probs=42.9

Q ss_pred             CcccccccccccccCC--ceeEecccccccccchHHHhhc-CCCCCCcccccCCCCcc
Q 043965          212 KNLQCAVCLEEFEIGN--EAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDDFK  266 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~--~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~  266 (342)
                      ++..|+||++.+....  ....++|+|.||..||.+|+.. +.+||+||+.+...+.+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~~   59 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCE
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccccc
Confidence            4578999999864332  3456689999999999999965 45899999998766544

>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=99.25  E-value=1.2e-12  Score=98.70  Aligned_cols=48  Identities=29%  Similarity=0.805  Sum_probs=42.2

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCCC
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDD  264 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (342)
                      ..|+||++.+.   .++.++|||.||..||..||.. +.+||+||..|....
T Consensus        24 ~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          24 QLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TBCTTTSSSBC---CEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCccCCCcCC---CeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            46999999988   7889999999999999999974 568999999997543

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.6e-12  Score=99.95  Aligned_cols=49  Identities=29%  Similarity=0.525  Sum_probs=41.3

Q ss_pred             cccccccccccccCC---------------ceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965          213 NLQCAVCLEEFEIGN---------------EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP  261 (342)
Q Consensus       213 ~~~C~ICle~~~~~~---------------~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (342)
                      +..|+||++.+....               .+..++|+|+||..||.+||+.+.+||+||+++.
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            456999998885322               3567889999999999999999999999999875

>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=99.21  E-value=1e-12  Score=92.58  Aligned_cols=49  Identities=10%  Similarity=0.230  Sum_probs=43.5

Q ss_pred             ccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          214 LQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      +.|+||++.++   .++.++ |||+||..||.+||+.+.+||+||.++..+++
T Consensus         1 l~C~Ic~~~~~---~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           1 MLCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCCccCCchHH---hcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            36999999998   777775 99999999999999999999999999876654

>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=99.17  E-value=3e-12  Score=101.03  Aligned_cols=51  Identities=29%  Similarity=0.768  Sum_probs=43.5

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~~~~~  265 (342)
                      +.+.|+||++.|.   .++.++|||+||..||..|+....   .||+||..+...+.
T Consensus        20 ~~l~CpIC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          20 KILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HHTSCSSSCCCCS---SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             cCcCCCccCchhC---CeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            4578999999998   778899999999999999997654   89999998865543

>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=99.16  E-value=2.8e-12  Score=98.18  Aligned_cols=50  Identities=36%  Similarity=0.795  Sum_probs=43.3

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcC-CCCCCcccccCCCC
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQVPSDD  264 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (342)
                      +...|+||++.+.   .++.++|||.||..||.+|++.+ .+||+||.++...+
T Consensus        22 ~~l~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          22 KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cCcCCccCCcchh---cceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            3468999999998   88999999999999999999755 58999999886554

>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=99.11  E-value=7e-12  Score=88.33  Aligned_cols=45  Identities=29%  Similarity=0.676  Sum_probs=39.5

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD  263 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (342)
                      .+.|+||++.+.   .++.++|+|+||..||.+|   +.+||+||.++...
T Consensus         6 ~l~C~IC~~~~~---~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCB---CCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCcccCcccC---CCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            468999999998   7889999999999999876   66899999988654

>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=99.05  E-value=4e-11  Score=93.37  Aligned_cols=49  Identities=29%  Similarity=0.623  Sum_probs=40.2

Q ss_pred             cCcccccccccccccCCceeE-ecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD  264 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (342)
                      .+.+.|+||++.|.   .++. .+|||.||..||.+|+.  ..||+||..+...+
T Consensus        20 ~~~l~C~IC~~~~~---~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          20 EKLLRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (97)
T ss_dssp             HHTTSCSSSCSCCS---SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hhcCCCccCCchhh---cCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhh
Confidence            35678999999998   5555 47999999999999984  46999998876544

>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=99.03  E-value=4.5e-11  Score=89.88  Aligned_cols=52  Identities=19%  Similarity=0.200  Sum_probs=44.8

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCCC
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDD  264 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (342)
                      +.+.+.|+||++.|.   +++.++|||+||..||.+||.. +..||+||.++...+
T Consensus         4 iP~~l~CpIc~~l~~---dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           4 IPDYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             CCSTTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CCccccCcCcCchhh---hhcccCCcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            446789999999999   7889999999999999999975 458999999886543

>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=99.01  E-value=8.5e-11  Score=87.84  Aligned_cols=53  Identities=15%  Similarity=0.451  Sum_probs=46.0

Q ss_pred             ccCcccccccccccccCCceeEecccccccccchHHHhhcC-CCCCCcccccCCCCc
Q 043965          210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQVPSDDF  265 (342)
Q Consensus       210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~~  265 (342)
                      +.+++.|+||++.|.   +++.++|||.||+.||..|+..+ ..||.|+..+...+.
T Consensus         5 iP~~l~CpIc~~~m~---dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l   58 (78)
T d1t1ha_           5 FPEYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGL   58 (78)
T ss_dssp             CSSSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCC
T ss_pred             CCccCCCcCcCchhh---CceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccc
Confidence            346789999999999   78899999999999999999765 579999999876554

>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=98.86  E-value=4e-10  Score=79.97  Aligned_cols=49  Identities=20%  Similarity=0.518  Sum_probs=37.5

Q ss_pred             cCcccccccccccccCCceeEec-----ccccccccchHHHhh--cCCCCCCcccccCC
Q 043965          211 DKNLQCAVCLEEFEIGNEAKEMP-----CKHKFHGECIMPWLE--VRSSCPVCRFQVPS  262 (342)
Q Consensus       211 ~~~~~C~ICle~~~~~~~~~~lp-----C~H~Fh~~Ci~~Wl~--~~~~CP~CR~~l~~  262 (342)
                      ++...|.||++.+..   ....+     |+|.||..||.+|+.  .+.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~---~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGN---ERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSC---CCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCC---ceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            355789999998863   23333     469999999999995  34589999998753

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=1.6e-09  Score=84.47  Aligned_cols=51  Identities=12%  Similarity=0.111  Sum_probs=45.3

Q ss_pred             CcccccccccccccCCceeEeccc-ccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCK-HKFHGECIMPWLEVRSSCPVCRFQVPSDDF  265 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (342)
                      +.+.|+||++.|.   ++++++|+ |.|++.||..||..+..||+|+.+|..+++
T Consensus        21 ~~f~CPI~~~lm~---dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L   72 (98)
T d1wgma_          21 DEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             HHhCCcCchhHHH---HHHhcccccchhhHHHHHHHHHhcCCcccccccccchhh
Confidence            4689999999999   89999965 589999999999999999999999876654

>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=98.22  E-value=9.5e-08  Score=73.08  Aligned_cols=47  Identities=23%  Similarity=0.562  Sum_probs=36.7

Q ss_pred             CcccccccccccccCCceeEecccccccccchHHHhhcC----C----CCCCccc
Q 043965          212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR----S----SCPVCRF  258 (342)
Q Consensus       212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~----~CP~CR~  258 (342)
                      ....|+||++++...+.+..++|+|.||..||..|++.+    .    .||.|+-
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            346899999999765556666899999999999999532    1    5998643

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.20  E-value=0.054  Score=35.37  Aligned_cols=44  Identities=30%  Similarity=0.540  Sum_probs=29.3

Q ss_pred             cccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccc
Q 043965          215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRF  258 (342)
Q Consensus       215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~  258 (342)
                      .|.||...-..+.-+.--.|...||..|+.+-+....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            4888876543322222234899999999988764332    6999974

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.87  E-value=0.22  Score=34.63  Aligned_cols=44  Identities=30%  Similarity=0.637  Sum_probs=29.6

Q ss_pred             ccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccccc
Q 043965          214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRFQV  260 (342)
Q Consensus       214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~l  260 (342)
                      ..|.||.+.   ++.+.--.|...||..|+.+.+....    .||.|+..-
T Consensus         8 ~~C~~C~~~---~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           8 TICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCc---CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            457777643   33333334999999999998875443    699996543

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.03  E-value=0.15  Score=36.87  Aligned_cols=39  Identities=21%  Similarity=0.422  Sum_probs=26.8

Q ss_pred             cccccCcccccccccccccCCceeEecccccccccchHHH
Q 043965          207 TVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPW  246 (342)
Q Consensus       207 ~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~W  246 (342)
                      ...+..+..|.|| +.+......-.--|+.+||..|+.+.
T Consensus         9 re~v~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_           9 REPVVNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             ccCCCcCcccccc-CcccccceecceeecchhhHHHHHHh
Confidence            3345567889999 77764332222228899999999886

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.83  E-value=0.093  Score=35.81  Aligned_cols=46  Identities=28%  Similarity=0.523  Sum_probs=31.3

Q ss_pred             cccccccccccccCCceeE-ecccccccccchHHH---hh--cCCCCCCccc
Q 043965          213 NLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPW---LE--VRSSCPVCRF  258 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~W---l~--~~~~CP~CR~  258 (342)
                      ...|.||......++..+. -.|+..||..|+..-   ..  .+-.||.|+.
T Consensus         6 ~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_           6 SGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             CCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcC
Confidence            4579999987765444333 349999999999532   11  2347999975

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.13  E-value=0.25  Score=33.33  Aligned_cols=44  Identities=27%  Similarity=0.505  Sum_probs=29.7

Q ss_pred             cccccccccccccCCceeEecccccccccchHHHhhcC----CCCCCcccc
Q 043965          213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR----SSCPVCRFQ  259 (342)
Q Consensus       213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~~CP~CR~~  259 (342)
                      ...|.||.+.   ++.+.--.|.-.||..|+...+...    -.||.|+..
T Consensus         9 ~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_           9 MEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             CSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             cCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            4569999753   3233333499999999997665432    279999754