Citrus Sinensis ID: 036250

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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
MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRNSSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPFDGLLSMSGSQEGGTSNSESSAAGTAVAGAGTAAHIDET
Secondary Structure (PSIPRED)
ccccccccEEccccccEEcccccccccccccccccEEEcccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccHHHHHHcccHHHHHHHcccccccccccccccccccccccccccHHHHcccccccccccccHHHHHHHcccccccccHHHccHHHHHHHHHHHHccccccccccccHHHHHccccEEEcccccccccccccccccEEEEcccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEccEEEccccccccEccccccccEEEcccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccEEEEcccccccccccccccccccccHcccccHHHHHHHHHHccccccccccccHHHHHccccEEEcccccccccHHHccccHHHcccccccccccccEcHHHHHccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mgdatvgsYWCYICSRmvnprmeagikcpfcetgfveqmsssitddsinngihvgsdralSLWAPILLRMMtglapsrpritahehissnnsrieeAEQEGEFESLLRRRrrnssaplSRMLQDIRFgiasrpndpealRERSgslilvnpmneeaLIIQGENAAsslgeylvgpgLDLLLQHLLendpnrygslpaQKEVVKAlptvaidqdlQCAVCLEefvmgneakempckhkfhgecimpwlelqsscpicryqlpsddlkvqgngsgnredsagnedagntlrlangevgngrrnwipipwpfdgllsmsgsqeggtsnsessaagtavagagtaahidet
Flexible Loop (DISEMBL)
mgdatvgsYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMMTGLAPSRPRITAHehissnnsrieeaeqegEFESLLrrrrrnssaplsrmlqdirfgiasrpndpeALRERSGSLILVNPMNEEALIIQGENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNRedsagnedagntLRLAngevgngrrNWIPIPWPFDGLLSMSGSQEGGTSNSESSAAGTAVAGAGTAAHIDET
Low Complexity Region (SEG)
MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFEsllrrrrrnssaplsrMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYlvgpgldlllqhllENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPFDGLLSMSGSQEGGTSNSESSaagtavagagtaaHIDET
Disordered region (IsUnstruct)
****TVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMMTGL***********************************************************************LILVNPMNEEALIIQGENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL*********************************EVGNGRRNWIPIPWPFDGLL**********************************
Disordered Region (DISOPRED)
***ATVG*YWCYICSRMVNPRMEAGIKCPFCETGFVEQ************************************************************************************************************ILVNPM*********ENAASSLGEYLVGPGLDLLLQ******************VVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL***************************************************************************************
Disordered Region (DISEMBL)
MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMMTGLAPSRPRITAHEH******************SLLRRRRRNSSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQ**************DAGNTLRLANGEVGNGRRNWIPIPWPFDGLLSMS*******************************
Disordered Region (DISPRO)
******GSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS*********************WAPILLRMMTGLAP************************************************IRFGIAS**NDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL***************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRNSSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPFDGLLSMSGSQEGGTSNSESSAAGTAVAGAGTAAHIDET
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	347	2.2.26 [Sep-21-2011]
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.838	0.860	0.321	3e-36
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.642	0.679	0.317	8e-36
Q9D0C1	305	E3 ubiquitin-protein liga	yes	no	0.711	0.809	0.285	2e-21
Q9Y4L5	304	E3 ubiquitin-protein liga	yes	no	0.729	0.832	0.288	4e-20
Q91YL2	313	RING finger protein 126 O	no	no	0.677	0.750	0.293	7e-20
Q9BV68	326	RING finger protein 126 O	no	no	0.703	0.748	0.287	2e-19
Q6IRP0	312	RING finger protein 126-B	N/A	no	0.720	0.801	0.251	5e-19
Q0II22	313	RING finger protein 126 O	no	no	0.717	0.795	0.274	1e-18
Q8RXD3	310	E3 ubiquitin-protein liga	no	no	0.345	0.387	0.359	5e-18
Q6DIP3	311	RING finger protein 126 O	no	no	0.242	0.270	0.411	5e-16

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

 Score =  152 bits (384), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 104/323 (32%), Positives = 162/323 (50%), Gaps = 32/323 (9%)

Query: 2   GDATVG----SYWCYICSRMVNPRME---AGIKCPFCETGFVEQMSSSITDDSINNGIHV 54
           G  TVG     ++CY C+R VN  +    +   CP C  GF+E+  +     + N G   
Sbjct: 12  GANTVGVTNKPFFCYQCNRTVNVTISPPSSDPTCPICNEGFLEEYDNP----NPNQGSGF 67

Query: 55  GSDRALSL-WAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRN 113
            +    S+ +  + L +    A   P +      ++ +S               R  R +
Sbjct: 68  LNPNPNSIPFHDLFLTLSDPFASLLPLLFPSSSSTTTSSSASIDPNNPSLSGPTRSGRGD 127

Query: 114 SSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYLV 173
             A          F I +  ND  +   +   +I  NP +      QG    +++G+Y +
Sbjct: 128 PFA-----FDPFTF-IQNHLNDLRSSGAQIEFVIQNNPSD------QGFRLPANIGDYFI 175

Query: 174 GPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDL------QCAVCLEEFVMGN 227
           GPGL+ L+Q L ENDPNRYG+ PA K  ++ALP V I +        QCAVC+++F  G 
Sbjct: 176 GPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFNQCAVCMDDFEEGT 235

Query: 228 EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNT 287
           EAK+MPCKH +H +C++PWLEL +SCP+CR++LP+DD   +    G +  S GN D  N+
Sbjct: 236 EAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELPTDDPDYERRVRGAQGTSGGN-DGDNS 294

Query: 288 LRLANGEVGNGRRNW-IPIPWPF 309
            + ++G+     R++ I +PWPF
Sbjct: 295 GQRSDGDNRTVERSFRISLPWPF 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: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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

 Score =  151 bits (381), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 88/277 (31%), Positives = 136/277 (49%), Gaps = 54/277 (19%)

Query: 9   YWCYICSRMVNPRMEAGIK--CPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPI 66
           ++CY C++ V   + +     CP C  GF+E+      + S+N   +  SD    +  P 
Sbjct: 21  FFCYQCNQTVTISISSSADPFCPICNQGFLEEYEDPNPNQSLNFNPN-SSDSFFPMADPF 79

Query: 67  --LLRMMTG---LAPSR--------PRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRN 113
             LL ++ G    APS         P +      +  N + +  +     ++ L+  R +
Sbjct: 80  STLLPLIFGSSAAAPSGMDFMSLFGPSMQPQARSTQQNPQSDAFDPFTFLQNHLQTLRSS 139

Query: 114 SSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYLV 173
            +           F I + P+DP                        G     + G+Y  
Sbjct: 140 GTH--------FEFVIENHPSDP------------------------GNRMPGNFGDYFF 167

Query: 174 GPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDL------QCAVCLEEFVMGN 227
           GPGL+ L+Q L ENDPNRYG+ PA K  + ALPTV + +D+      QCAVC++EF  G+
Sbjct: 168 GPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCMDEFEDGS 227

Query: 228 EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
           + K+MPCKH FH +C++PWLEL +SCP+CR++LP+DD
Sbjct: 228 DVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPTDD 264

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: 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 =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/298 (28%), Positives = 134/298 (44%), Gaps = 51/298 (17%)

Query: 9   YWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALS-----LW 63
           ++C+ C   VNP++   I CP C++GF+E+++    D S   G    +D + +     LW
Sbjct: 20  FFCHFCKGEVNPKLPEYI-CPRCDSGFIEEVTD---DSSFLGGGGSRTDNSTATHFAELW 75

Query: 64  APILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEF---------ESLLRRRRRNS 114
             +   M   L   RP ++++     N +     +   +F             R R R S
Sbjct: 76  DHLDHTMF--LQDFRPFLSSNPLDQDNRANERGHQTHTDFWGPSRPPRLPMTRRYRSRGS 133

Query: 115 SAP-----LSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLG 169
           + P     +  ++Q I  G  +    P +    S S +L                 S+ G
Sbjct: 134 TRPDRSPAIEGIIQQIFAGFFANSAIPGSPHPFSWSGML----------------HSNPG 177

Query: 170 EYLVG-PGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----LQCAVCLEEF 223
           +Y  G  GLD ++  LL    N  G  PA KE + +LPTV + Q+     L+C VC E++
Sbjct: 178 DYAWGQTGLDAIVTQLLGQLENT-GPPPADKEKITSLPTVTVTQEQVNTGLECPVCKEDY 236

Query: 224 VMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGN 281
            +  + +++PC H FH  CI+PWLEL  +CP+CR  L  +D   Q   S   E SA N
Sbjct: 237 TVEEKVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSLNGEDSTRQTQSS---EASASN 291

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 = 99.4 bits (246), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 84/291 (28%), Positives = 128/291 (43%), Gaps = 38/291 (13%)

Query: 9   YWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDS---------INNGIHVGSDRA 59
           ++C+ C   V+P++   I CP CE+GF+E+    +TDDS         I+N     +   
Sbjct: 20  FFCHFCKGEVSPKLPEYI-CPRCESGFIEE----VTDDSSFLGGGGSRIDN---TTTTHF 71

Query: 60  LSLWAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRNSSAPLS 119
             LW  +   M       RP +++      N +     +   +F        R    PL 
Sbjct: 72  AELWGHLDHTMF--FQDFRPFLSSSPLDQDNRANERGHQTHTDFWGA-----RPPRLPLG 124

Query: 120 RMLQDIRFGIASRPNDPEALRERSGSLILVN---PMNEEALIIQGENAASSLGEYLVG-P 175
           R  +        R    E + +   +    N   P +       G    S+ G+Y  G  
Sbjct: 125 RRYRSRGSSRPDRSPAIEGILQHIFAGFFANSAIPGSPHPFSWSG-MLHSNPGDYAWGQT 183

Query: 176 GLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----LQCAVCLEEFVMGNEAK 230
           GLD ++  LL    N  G  PA KE + +LPTV + Q+     L+C VC E++ +  E +
Sbjct: 184 GLDAIVTQLLGQLENT-GPPPADKEKITSLPTVTVTQEQVDMGLECPVCKEDYTVEEEVR 242

Query: 231 EMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGN 281
           ++PC H FH  CI+PWLEL  +CP+CR  L  +D   Q   S + E SA N
Sbjct: 243 QLPCNHFFHSSCIVPWLELHDTCPVCRKSLNGEDSTRQ---SQSTEASASN 290

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 = 98.2 bits (243), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 84/286 (29%), Positives = 125/286 (43%), Gaps = 51/286 (17%)

Query: 7   GSYWCYICSRMVNPRMEAGIKCPFCETGFVEQM-------------SSSITDDSINNGIH 53
           G Y+C+ CS  + PR+   I CP CE+GF+E++             S++ TD   N    
Sbjct: 9   GRYFCHCCSVEIVPRLPDYI-CPRCESGFIEELPEETRNTENGSAPSTAPTDQ--NRQPF 65

Query: 54  VGSDRALSLWAPILLRMMTGLAPSRPRI-TAHEHISSNNSRIEEAEQEGEFESLLRRRRR 112
              D+ L        +   G+      I T      +++ R  E+ +E E +S   R R 
Sbjct: 66  ENVDQHLFTLPQGYSQFAFGIFDDSFEIPTFPPGAQADDGRDPESRREREHQS---RHRY 122

Query: 113 NSSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLG--- 169
            +  P +R+        A R     A     G   L   + +    I    A  SLG   
Sbjct: 123 GARQPRARL-------TARR-----ATGRHEGVPTLEGIIQQLVNGIISPAAVPSLGLGP 170

Query: 170 ---------EYLVGP-GLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----L 214
                    +Y  G  GLD ++  LL N     G  PA KE ++ALPTV + ++     L
Sbjct: 171 WGVLHSNPMDYAWGANGLDTIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGL 229

Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
           +C VC E++ +G   +++PC H FH  CI+PWLE   SCP+CR  L
Sbjct: 230 ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 275

Mus musculus (taxid: 10090)

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

 Score = 97.1 bits (240), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 79/275 (28%), Positives = 125/275 (45%), Gaps = 31/275 (11%)

Query: 7   GSYWCYICSRMVNPRMEAGIKCPFCETGFVEQM-------------SSSITDDSINNGIH 53
           G Y+C+ CS  + PR+   I CP CE+GF+E++             S++ TD S     H
Sbjct: 9   GRYFCHCCSVEIVPRLPDYI-CPRCESGFIEELPEETRSTENGSAPSTAPTDQSRPPLEH 67

Query: 54  VGSDRALSLWAPILLRMMTGLAPSRPRI-TAHEHISSNNSRIEEAEQEGEFESLLRRRRR 112
           V  D+ L        +   G+      I T      +++ R  E+ +E +  S   R R 
Sbjct: 68  V--DQHLFTLPQGYGQFAFGIFDDSFEIPTFPPGAQADDGRDPESRRERDHPS---RHRY 122

Query: 113 NSSAPLSRMLQDIRFGIASRPNDPEALRERSGSLI--LVNPMNEEALIIQGENAASSLGE 170
            +  P +R+      G   R      L      L+  ++ P    +L   G   ++ +  
Sbjct: 123 GARQPRARLTTRRATG---RHEGVPTLEGIIQQLVNGIITPATIPSLGPWGVLHSNPMDY 179

Query: 171 YLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----LQCAVCLEEFVM 225
                GLD ++  LL N     G  PA KE ++ALPTV + ++     L+C VC +++ +
Sbjct: 180 AWGANGLDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECPVCKDDYAL 238

Query: 226 GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
           G   +++PC H FH  CI+PWLE   SCP+CR  L
Sbjct: 239 GERVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSL 273

Homo sapiens (taxid: 9606)

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

 Score = 95.5 bits (236), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 68/270 (25%), Positives = 121/270 (44%), Gaps = 20/270 (7%)

Query: 6   VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAP 65
            G Y+C+ C+  + PR+     CP C++GF+E++  +  +   N+  + G+D+    +  
Sbjct: 8   AGRYFCHSCTAEITPRLPE-YTCPRCDSGFIEELPETSRNSESNSSNNSGTDQNRPSFEN 66

Query: 66  ILLRMMTGLAPSRPRITA-------HEHISSNNSRIEEAEQEGEFESLLRRRRRNSSAPL 118
           I     T L     ++T           +   +  +EE            R+R  +  P 
Sbjct: 67  IESAQFT-LPSGYGQVTFGIFNEGLDFPMFGTSGPVEETRDGESRREHQSRQRYGARQPR 125

Query: 119 SRMLQDIRFGIASRPNDPE---ALRERSGSLILVNPMNEEALIIQGENAASSLGEYLVGP 175
           +RM    R G       P     +++    +I    M+   +   G   ++ +       
Sbjct: 126 ARM--STRRGAGRNEGVPTLEGIIQQLVNGIIAPTAMSNLGVGPWGVLHSNPMDYAWGAN 183

Query: 176 GLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----LQCAVCLEEFVMGNEAK 230
           GLD ++  LL N     G  PA  + ++ALPT+ I ++     L+C VC E++ +G   +
Sbjct: 184 GLDTIITQLL-NQFENTGPPPADTDKIQALPTIQITEEHVGFGLECPVCKEDYTVGESVR 242

Query: 231 EMPCKHKFHGECIMPWLELQSSCPICRYQL 260
           ++PC H FH +CI+PWLE   +CP+CR  L
Sbjct: 243 QLPCNHLFHNDCIIPWLEQHDTCPVCRKSL 272

Xenopus laevis (taxid: 8355)

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

 Score = 94.0 bits (232), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/273 (27%), Positives = 120/273 (43%), Gaps = 24/273 (8%)

Query: 7   GSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMS------------SSITDDSINNGIHV 54
           G Y+C+ CS  + PR+   I CP CE+GF+E++             S+ + D        
Sbjct: 9   GRYFCHCCSVEIVPRLPDYI-CPRCESGFIEELPEETRSAENGSAPSTASADQSRQQPFE 67

Query: 55  GSDRALSLWAPILLRMMTGLAPSRPRI-TAHEHISSNNSRIEEAEQEGEFESLLRRRRRN 113
             D+ L            G+      I T      +++SR  E+ +E E  S   R R  
Sbjct: 68  NVDQPLFTLPQGYGHFAFGIFDDSFEIPTFPPGAQADDSRDPESRREREQHS---RHRYG 124

Query: 114 SSAPLSRMLQDIRFG-IASRPNDPEALRERSGSLILVNPMNEEALIIQGENAASSLGEYL 172
           +  P +R+      G     P     +++    +I    +    L   G   ++ +    
Sbjct: 125 ARQPRARLTARRATGRHEGVPTLEGIIQQLVNGIITPATIPNLGLGPWGVLHSNPMDYAW 184

Query: 173 VGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----LQCAVCLEEFVMGN 227
              GLD ++  LL N     G  PA KE ++ALPTV + ++     L+C VC +++ +G 
Sbjct: 185 GANGLDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECPVCKDDYGLGE 243

Query: 228 EAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
             +++PC H FH  CI+PWLE   SCP+CR  L
Sbjct: 244 HVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSL 276

Bos taurus (taxid: 9913)

>sp|Q8RXD3|AIP2_ARATH E3 ubiquitin-protein ligase AIP2 OS=Arabidopsis thaliana GN=AIP2 PE=1 SV=1

 Score = 92.4 bits (228), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 51/142 (35%), Positives = 85/142 (59%), Gaps = 22/142 (15%)

Query: 146 LILVNPMNEEALIIQGENA----------ASSLGEYLVGPGLDLLLQHLLEND-PNRYGS 194
           L+  N M+  A I+ GE++           ++L + L+  GLD+++  +L++  P R  +
Sbjct: 144 LVQQNLMSAFASIVGGESSNGPTENTIGETANLMQELIN-GLDMIIPDILDDGGPPR--A 200

Query: 195 LPAQKEVVKALPTVAIDQDL--------QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPW 246
            PA KEVV+ LP +   ++L        +C +C E  V+G++ +E+PCKH FH  C+ PW
Sbjct: 201 PPASKEVVEKLPVIIFTEELLKKFGAEAECCICKENLVIGDKMQELPCKHTFHPPCLKPW 260

Query: 247 LELQSSCPICRYQLPSDDLKVQ 268
           L+  +SCPICR++LP+DD K +
Sbjct: 261 LDEHNSCPICRHELPTDDQKYE 282

E3 ubiquitin-protein ligase that acts as a negative regulator of abscisic acid (ABA) signaling. Mediates ubiquitination and subsequent proteasomal degradation of the transcription factor ABI3.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6DIP3|RN126_XENTR RING finger protein 126 OS=Xenopus tropicalis GN=rnf126 PE=2 SV=1

 Score = 85.5 bits (210), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 37/90 (41%), Positives = 55/90 (61%), Gaps = 6/90 (6%)

Query: 176 GLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQD-----LQCAVCLEEFVMGNEAK 230
           GLD ++  LL N     G  PA  E ++ALPT+ I ++     L+C VC E++ +G   +
Sbjct: 183 GLDTIITQLL-NQFENTGPPPADTEKIQALPTIQITEEHVGSGLECPVCKEDYTVGESVR 241

Query: 231 EMPCKHKFHGECIMPWLELQSSCPICRYQL 260
           ++PC H FH +CI+PWLE   +CP+CR  L
Sbjct: 242 QLPCNHLFHNDCIIPWLEQHDTCPVCRKSL 271

Xenopus tropicalis (taxid: 8364)

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	347
255568972	348	zinc finger protein, putative [Ricinus c	0.959	0.956	0.530	2e-93
224125900	344	predicted protein [Populus trichocarpa]	0.942	0.950	0.502	1e-85
356567978	344	PREDICTED: E3 ubiquitin-protein ligase R	0.864	0.872	0.451	5e-71
224073116	356	predicted protein [Populus trichocarpa]	0.864	0.842	0.469	2e-68
449463838	362	PREDICTED: E3 ubiquitin-protein ligase R	0.936	0.897	0.443	2e-67
15241188	396	RING/U-box domain-containing protein [Ar	0.873	0.765	0.449	1e-65
297793133	395	zinc finger family protein [Arabidopsis	0.887	0.779	0.437	1e-64
224052857	340	predicted protein [Populus trichocarpa]	0.835	0.852	0.450	8e-64
18405411	351	RING/U-box domain-containing protein [Ar	0.893	0.883	0.397	1e-63
357462645	352	RING finger protein [Medicago truncatula	0.913	0.900	0.452	3e-63

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

 Score =  348 bits (894), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 192/362 (53%), Positives = 239/362 (66%), Gaps = 29/362 (8%)

Query: 1   MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRAL 60
           MGD  V  YWC++CSRMV P MEA IKCP CE GFVE++ S  T D  NNGI   S+RA 
Sbjct: 1   MGDEMVDRYWCHMCSRMVTPVMEAEIKCPLCENGFVEEIGS--TRDLNNNGIDFVSERAF 58

Query: 61  SLWAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRNSSAPLSR 120
           S+WAPILL +M GL P R RITA EH SSNN++ E  E E EFESL RRRRRN ++ LS 
Sbjct: 59  SMWAPILLGLMGGLGPVRARITAQEHDSSNNAQEEREELEREFESLFRRRRRNPASILSM 118

Query: 121 MLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQG-----------ENAASSLG 169
           +     F               + ++ILVNP N+EALI+QG            N  SS  
Sbjct: 119 LQGSENFENNGES---NGNNNNNNNVILVNPFNQEALILQGSFDASQPENPIRNMRSSFR 175

Query: 170 EYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEA 229
           +YL+GPGLDLLLQHL ENDPNRYG+LPAQK+ VKA+PT+A++Q+ +C+VCLEEF +G EA
Sbjct: 176 DYLIGPGLDLLLQHLAENDPNRYGTLPAQKKAVKAMPTIAVEQNAECSVCLEEFEIGGEA 235

Query: 230 KEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTLR 289
           KEMPCKHKFH  CI+PWLEL SSCP+CR+Q+P D+ K++ N S    D    E+    + 
Sbjct: 236 KEMPCKHKFHSACILPWLELHSSCPVCRFQMPCDNSKIEAN-SLRSNDGRTIENNAARMN 294

Query: 290 LANGEVG----NGRRNWIPIPWPFDGLLSMSGSQEGGTSNSESSAAGTAVAGAGTAAHID 345
            + G+VG    NGRR W+P+PWPFDGL S+S SQ  G S        T+    G+++H D
Sbjct: 295 DSWGDVGEQTDNGRRFWVPVPWPFDGLFSLSASQSDGNS--------TSATLTGSSSHTD 346

Query: 346 ET 347
           ET
Sbjct: 347 ET 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 =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 183/364 (50%), Positives = 237/364 (65%), Gaps = 37/364 (10%)

Query: 1   MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRAL 60
           M D  V  YWC++CS+MVNP  EA IKCPFCE+GF+E+M S    +  NN   +GS+ A 
Sbjct: 1   MEDEMVDQYWCHMCSQMVNPVTEAEIKCPFCESGFLEEMGS--VREVNNNIFDLGSEHAF 58

Query: 61  SLWAPILLRMMTGLAPSRPRITAHEHISSNNSRIEEAEQEGEFESLLRRRRRNSSAPLSR 120
           SLW   LL +M GL  S  R  A EHISS +S+ E+   E +FESLLRRR R S++ + R
Sbjct: 59  SLWDTFLLDLMGGLGTSGSRRIAQEHISSTSSQDED--DELDFESLLRRRGRLSTSSVQR 116

Query: 121 MLQDIRFGIASRPNDPEALRERSGS------LILVNPMNEEALIIQG-----------EN 163
           +LQD+      R  +PE  RE SG       +ILVNP NEEA+I+             +N
Sbjct: 117 LLQDLHL----RSENPENDRESSGGSSSSSSVILVNPFNEEAIILHSPDNMNQPENPSQN 172

Query: 164 AASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEF 223
            + S  +YL+GP +DLLL HL E+ PNRYG+ PA+KE VKA+PTV+I Q+LQC+VCLEEF
Sbjct: 173 VSISFQDYLIGPDVDLLLHHLAESGPNRYGTPPAEKEAVKAMPTVSITQNLQCSVCLEEF 232

Query: 224 VMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNED 283
            +G EAKEMPCKHKFHGECI+PWLEL SSCP+CR+ +PSDD     + S + E+   + D
Sbjct: 233 DIGCEAKEMPCKHKFHGECIVPWLELHSSCPVCRFLMPSDDSTTGVSQSRSDEERTESND 292

Query: 284 AGNTLRLANGEVGNGRRNWIPIPWPFDGLLSMSGSQEGGTSNSESSAAGTAVAGAGTAAH 343
           A    R+ N    NGRR W+PIPWPFDGL  +SGS     +   SS+A ++    G+A++
Sbjct: 293 A----RIIN----NGRRYWVPIPWPFDGLFPLSGS----QNGGSSSSAPSSTTMRGSASY 340

Query: 344 IDET 347
            DET
Sbjct: 341 SDET 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 =  274 bits (700), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 152/337 (45%), Positives = 204/337 (60%), Gaps = 37/337 (10%)

Query: 9   YWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIH--VGSDRALSLWAPI 66
           YWC++CS+MVNP M+  I+CPFC++GFVE+M ++ +  SI N       SDRALSLWAPI
Sbjct: 5   YWCHMCSQMVNPIMDMEIRCPFCQSGFVEEMGNTPSSSSIPNTSESDFESDRALSLWAPI 64

Query: 67  LLRMMTG-LAPSRPRITAHE-----HISSNNSRIEEAEQEGEFESLLRRRRRNSSAPLSR 120
           LL MM     P R R  A++     ++        E E + EFES+LRRRR  +SA + +
Sbjct: 65  LLGMMGNPRHPRRLRQIANDNGNRDYVDGVADHGRETEYDQEFESILRRRR--NSATILQ 122

Query: 121 MLQDIRFGIASRPNDPEALRERSGS---------LILVNPMNEEALIIQG---------- 161
           +LQ IR G+AS   +     +             +IL+NP+N+  +I+QG          
Sbjct: 123 LLQGIRTGLASESYENTDGHDHDREREREREREHMILINPLNQ-TIIVQGSYESNRDQSD 181

Query: 162 -ENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCL 220
             ++  SLG+Y  GPG D+LLQHL ENDPNRYG+ PAQKE ++ALPTV I+++ QC+VCL
Sbjct: 182 NHSSVGSLGDYFTGPGFDILLQHLAENDPNRYGTPPAQKEAIEALPTVIINENSQCSVCL 241

Query: 221 EEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGS----GNRE 276
           ++F +G+EAKEMPCKH+FH  CI+PWLEL SSCP+CR QLP D+ K   + S      RE
Sbjct: 242 DDFEVGSEAKEMPCKHRFHSGCILPWLELHSSCPVCRLQLPLDESKQDSDLSRDSRSQRE 301

Query: 277 DSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPFDGLL 313
           D +   D              GRR     PWPF+GL 
Sbjct: 302 DESIEHDNDEERDGEGRNASGGRR--FSFPWPFNGLF 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 =  265 bits (678), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 162/345 (46%), Positives = 209/345 (60%), Gaps = 45/345 (13%)

Query: 9   YWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILL 68
           YWC++CS+MVNP M   IKCPFC+ GF+E M  S  D+ + +    GSDRALSLWAPILL
Sbjct: 5   YWCHMCSQMVNPIMGVEIKCPFCQNGFIEDMIDSTGDNQVPDS-EFGSDRALSLWAPILL 63

Query: 69  RMM-TGLAPSRPRITAHEHISSNNSRIE-----EAEQEGEFESLLRRRRRN--SSAPLSR 120
            M+       R R   +E     N   E     E E E E ES +RRRRR+  +SA + +
Sbjct: 64  GMVGNSHRRRRLRRVEYEEDEDGNDDGEANHAGEPEFEREIESFMRRRRRSRRNSATILQ 123

Query: 121 MLQDIRFGI-ASRPNDPEAL----------RERSGSLILVNPMNEEALIIQGE------- 162
           +LQ IR GI  S   + E            RER   +IL+NP N+ ++I+QG        
Sbjct: 124 LLQGIRAGILVSESENLEGDRDRDRVRDMNRERE-RVILINPFNQ-SIIVQGSYDSNNVQ 181

Query: 163 ----NAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAV 218
               NA  SLG+Y++GPGLDLLLQHL ENDPNRYG+ PAQKE ++ALPTV + + LQC+V
Sbjct: 182 NQNQNAIGSLGDYVIGPGLDLLLQHLAENDPNRYGTPPAQKEAIEALPTVTVKEPLQCSV 241

Query: 219 CLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDS 278
           CL++F +G EA+EMPCKHKFH  CI+PWLEL SSCP+CR+QLP+D+ K+    S N  D 
Sbjct: 242 CLDDFEIGAEAREMPCKHKFHSGCILPWLELHSSCPVCRHQLPADESKLDSERSRNTFDQ 301

Query: 279 AGNEDAGNTLRLANG----------EVGNGRRNWIPIPWPFDGLL 313
             +E   +   ++NG            GNGRR     PWPF+ L 
Sbjct: 302 RDSESTNSESNISNGINVEEGDGEGRSGNGRR--FSFPWPFNSLF 344

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  262 bits (669), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 165/372 (44%), Positives = 221/372 (59%), Gaps = 47/372 (12%)

Query: 1   MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGI-------- 52
           M +     YWC++CS+MVNP ++  IKCPFC +GFVE++ + I+ D+ +N          
Sbjct: 1   MDELIATRYWCHMCSQMVNPIVDVEIKCPFCRSGFVEEIGNGISSDNNDNNNNNNNNNEL 60

Query: 53  --HVGSDRALSLWAPILLRMMTGLAPSRPRI---------TAHEHISSNNSRIEEAEQEG 101
               GS+RALSLWAPILL MM G    R R            +EH     +R+  + +  
Sbjct: 61  ESDFGSERALSLWAPILLGMM-GNPRGRRRFRHLEFDDDDDDNEHEDGEGNRV--SSETT 117

Query: 102 EFESLLRRRRRNSSAPLSRMLQDIRFGIASRPND---PEALRERSGSLILVNPMNEEALI 158
           E +S++RRRR  SSA + ++LQ IR GIA+  ++             +IL+NP N+  ++
Sbjct: 118 ELDSVIRRRR--SSATILQLLQGIRAGIATAESENSYEGERSRERERVILINPFNQ-TIV 174

Query: 159 IQG-------ENAASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAI- 210
           +QG       +N+  SLG+Y VGPGLDLLLQH+ ENDPNRYG+ PAQKE V ALPTV + 
Sbjct: 175 VQGGENQNQNQNSIGSLGDYFVGPGLDLLLQHIAENDPNRYGTPPAQKEAVDALPTVRVE 234

Query: 211 ---DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK- 266
              D  LQC+VCL+EF +  EAKEMPCKHKFH  CI+PWLEL SSCP+CR+QLP D+ K 
Sbjct: 235 LEEDSCLQCSVCLDEFEVDEEAKEMPCKHKFHTGCILPWLELHSSCPVCRHQLPGDESKR 294

Query: 267 -VQGNGSGNREDSAGNEDAGNTLRLANGEVG--NGRRNWIPIPWPFDGLLSMSGSQEGGT 323
            V G GS  R  S  N   GN      G     +GRR     PWPF+GL +  G+   G+
Sbjct: 295 DVDG-GSAARFMSDLNNGNGNGSGEIEGRNSSESGRR--FSFPWPFNGLFTSQGNSSAGS 351

Query: 324 SNSESSAAGTAV 335
           + S+S    T++
Sbjct: 352 A-SDSQRDHTSI 362

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 =  256 bits (653), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 166/369 (44%), Positives = 214/369 (57%), Gaps = 66/369 (17%)

Query: 1   MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITD-------DSINNGIH 53
           M +     YWC++CS+MVNP ME+ IKCPFC++GF+E+MS +          D  ++   
Sbjct: 1   MEETMAARYWCHMCSQMVNPVMESEIKCPFCQSGFIEEMSGNGGGGGGRGIRDVQDSETD 60

Query: 54  VGSDRALSLWAPILLRMMTGLAPSRPRITAHEHISSNNS--------------------- 92
            G+DRALSLWAPILL MM+  +P R R          N                      
Sbjct: 61  FGTDRALSLWAPILLGMMS--SPRRRRRFRRSEFGEENDDNGDDLTTNADGNGNDSNNSN 118

Query: 93  ----RIEEAEQEG-------EFESLLRRRRRNSSAPLSRMLQDIRFGIASR----PNDPE 137
               R   A + G       EFES+LRRRRR+S   L ++LQ IR GIAS      N+ +
Sbjct: 119 NNVYRHHRARRHGGEIDLDREFESILRRRRRSSGNIL-QLLQGIRAGIASEYESSDNNWD 177

Query: 138 ALRERSGSLILVNPMNEEALIIQGEN----AASSLGEYLVGPGLDLLLQHLLENDPNRYG 193
             RER   +I++NP N+  ++   +N    + +SLG+Y +GPGLDLLLQHL ENDPNR G
Sbjct: 178 NSRERD-RVIMINPYNQSLVVPSDQNQNHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQG 236

Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
           + PA+KE V+ALPTV I + LQC+VCL++F  G EAKEMPCKHKFH  CI+PWLEL SSC
Sbjct: 237 TPPARKEAVEALPTVKIMEPLQCSVCLDDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSC 296

Query: 254 PICRYQLPS---DDLKVQGNGS------GNREDSAGN--EDAGNTLRLANGEV--GNGRR 300
           P+CR++LPS   DD + + +          RE S GN  E+ GN  R    EV  GNGRR
Sbjct: 297 PVCRFELPSSADDDDETKTDSERVLRTRNVRETSNGNVVENVGNADRGREDEVRSGNGRR 356

Query: 301 NWIPIPWPF 309
                PWPF
Sbjct: 357 --FSFPWPF 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 =  253 bits (645), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 162/370 (43%), Positives = 214/370 (57%), Gaps = 62/370 (16%)

Query: 1   MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITD-------DSINNGIH 53
           M +     YWC++CS+MVNP ME+ IKCPFC++GF+E+MS +          D  ++   
Sbjct: 1   MEETMASRYWCHMCSQMVNPIMESEIKCPFCQSGFIEEMSGNSGGGGGRGIRDVQDSETD 60

Query: 54  VGSDRALSLWAPILLRMMTGLAPSRPRITAH--EHISSNNSRIE---------------- 95
            G+DRALSLWAPILL MM+     R    +   E    N   +                 
Sbjct: 61  FGTDRALSLWAPILLGMMSSPRRRRRFRRSEFGEENDDNGDELSNADGNDNNNNSNVYYH 120

Query: 96  --------EAEQEGEFESLLRRRRRNSSAPLSRMLQDIRFGIASR----PNDPEALRERS 143
                   E + + EFES+LRRRRR+S   L ++LQ IR GIAS      ND +  RER 
Sbjct: 121 HRARRHGGEIDLDREFESILRRRRRSSGNIL-QLLQGIRAGIASEYESSDNDWDNSRERD 179

Query: 144 GSLILVNPMNEEALIIQGEN-------AASSLGEYLVGPGLDLLLQHLLENDPNRYGSLP 196
             +I++NP N+ +L++QG +       + +SLG+Y +GPGLDLLLQHL ENDPNR G+ P
Sbjct: 180 -RVIMINPYNQ-SLVVQGSSDQNPNHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQGTPP 237

Query: 197 AQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPIC 256
           A+KE V+ALPTV I + LQC+VCL++F  G EAKE+PCKHKFH  CI+PWLEL SSCP+C
Sbjct: 238 ARKEAVEALPTVKIMEPLQCSVCLDDFEKGTEAKELPCKHKFHIRCIVPWLELHSSCPVC 297

Query: 257 RYQLPS-----DDLKV------QGNGSGNREDSAGNEDAGNTLRLANGEV--GNGRRNWI 303
           R++LPS     D+ K+      +    G   +    E+ GN  R    E   GNGRR   
Sbjct: 298 RFELPSSADDDDETKIDSERPPRTRNVGESNNRNIVENVGNAERGRQDEARSGNGRR--F 355

Query: 304 PIPWPFDGLL 313
             PWPF GL 
Sbjct: 356 SFPWPFSGLF 365

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224052857|ref|XP_002297615.1| predicted protein [Populus trichocarpa] gi|222844873|gb|EEE82420.1| predicted protein [Populus trichocarpa]

 Score =  250 bits (638), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 150/333 (45%), Positives = 198/333 (59%), Gaps = 43/333 (12%)

Query: 17  MVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRALSLWAPILLRMM-TGLA 75
           MVNP ME  IKCPFC++GF+E+MSSS  D  + +    GSDRALSLWAPILL MM     
Sbjct: 1   MVNPVMEVEIKCPFCQSGFIEEMSSSTGDTQVPDS-EFGSDRALSLWAPILLGMMGNSRR 59

Query: 76  PSRPRITAHEHISSNNSRIE-----EAEQEGEFESLLRRRRRNSS--APLSRMLQDIRFG 128
             R R   +E    +N   E     E E E E ES +RRRRR+    A + ++LQ IR G
Sbjct: 60  RRRLRRMEYEEGEDDNDDGEANLGGETEFEHEIESFIRRRRRSRRSSATILQLLQGIRAG 119

Query: 129 IASRPND----------PEALRERSGSLILVNPMNEEALIIQG-----------ENAASS 167
           I +  ++                    +IL+NP N+  +I+QG           +N   S
Sbjct: 120 ILASESENSEGDRDGERDRDRDRDRERVILINPFNQN-IIVQGSYDSNNDENQNQNPVGS 178

Query: 168 LGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGN 227
            G+Y +GPGLDLLLQHL +NDPNRYG+LPAQKE V+ALPTV I + LQC+VCL++F +G+
Sbjct: 179 FGDYFIGPGLDLLLQHLADNDPNRYGTLPAQKEAVEALPTVIIKEPLQCSVCLDDFEIGS 238

Query: 228 EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNT 287
           +A+EMPCKHKFH  CI+PWLEL SSCP+CR+QLP+D+ K+    + N  D    E+  + 
Sbjct: 239 KAREMPCKHKFHSGCILPWLELHSSCPVCRHQLPADESKLDSERARNSSDRREFENTNSE 298

Query: 288 LRLANG----------EVGNGRRNWIPIPWPFD 310
             +++G            GNGR      PWPF+
Sbjct: 299 SNISHGISVEEGDSEERSGNGRS--FSFPWPFN 329

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18405411|ref|NP_564693.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|15983408|gb|AAL11572.1|AF424578_1 At1g55530/T5A14_7 [Arabidopsis thaliana] gi|4204263|gb|AAD10644.1| Unknown protein [Arabidopsis thaliana] gi|14517546|gb|AAK62663.1| At1g55530/T5A14_7 [Arabidopsis thaliana] gi|23308203|gb|AAN18071.1| At1g55530/T5A14_7 [Arabidopsis thaliana] gi|332195138|gb|AEE33259.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 146/367 (39%), Positives = 195/367 (53%), Gaps = 57/367 (15%)

Query: 1   MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSI-------TDDSINNGIH 53
           M +A V  YWC++CS+ VNP MEA IKCPFC++GFVE+M            D   NN   
Sbjct: 1   MEEAVVTRYWCHMCSQTVNPVMEAEIKCPFCQSGFVEEMEDDDDHDSSDPADVRANN--- 57

Query: 54  VGSDRALSLWAPILLRMMTGLAPSRPRITAHEHISSNNSRI--EEAEQEGE------FES 105
                  SLWAPIL+ +M      R R  + E +  N + +  E  E +GE       + 
Sbjct: 58  -------SLWAPILMELMNDPVRRR-RNQSVESVEDNQNEVQTENNEDDGENDLDWQLQE 109

Query: 106 LLRRRRRNSSAPLSRMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENA- 164
           +LRRRRR+S+A L ++LQ IR G++             G +IL+N  N+   +    +  
Sbjct: 110 ILRRRRRHSAAVL-QLLQGIRAGLSVESESTGNGGNNPGRVILINTSNQTITVQNSADMD 168

Query: 165 ---ASSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLE 221
              A SLG+Y +GPG ++LLQ L ENDPNRYG+ PA+KE V+AL TV I++ LQC+VCL+
Sbjct: 169 SVPAGSLGDYFIGPGFEMLLQRLAENDPNRYGTPPAKKEAVEALATVKIEETLQCSVCLD 228

Query: 222 EFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQG------------ 269
           +F +G EAK MPC HKFH +C++PWLEL SSCP+CRYQLP+D+ K               
Sbjct: 229 DFEIGTEAKLMPCTHKFHSDCLLPWLELHSSCPVCRYQLPADEAKTDSVTTTSDNNGSSS 288

Query: 270 ----------NGSGNREDSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPFDGLLSMSGSQ 319
                     N  GNR      E+            G+G      IPWPF  L S S   
Sbjct: 289 ASATTSHGAENSDGNRRQEEEEEEEEEEEEENENNDGSG----FSIPWPFSTLFSSSQDS 344

Query: 320 EGGTSNS 326
              T +S
Sbjct: 345 NAPTDSS 351

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  248 bits (633), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 158/349 (45%), Positives = 209/349 (59%), Gaps = 32/349 (9%)

Query: 9   YWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSS--ITDDSINNGIHVGSDRALSLWAPI 66
           YWC+ CS++V+P M   IKCP C++GF+E+MSS+  I+D         G DR+ SLWAPI
Sbjct: 5   YWCHACSQIVSPVMGMEIKCPLCQSGFIEEMSSATGISDLQNTPETDFGVDRSPSLWAPI 64

Query: 67  LLRMMTG--LAPSRPRITAHEHISSNNSRIEEA---EQEGEFESLLRRRRRNSSAPLSRM 121
           LL MM    L     RI   +   S N   +       + E ES+LRRRRR SSA + ++
Sbjct: 65  LLGMMGNPRLRRRLRRIELEDDYESGNRDDDHGGVGHYDRELESILRRRRR-SSATIQQL 123

Query: 122 LQDIRFGIASRPND----PEALRERSGS-LILVNPMNEEALIIQG-----------ENAA 165
           LQ IR G+ S  ++     + +RER    +IL+NP N+  +I+QG            N  
Sbjct: 124 LQGIRAGLTSESHENTDSDDRVREREREHVILINPFNQ-TIIVQGSYDSNRDQSDNHNPI 182

Query: 166 SSLGEYLVGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVM 225
            +LG+Y VGPGLDLLLQHL ENDPNRYG+ PA KE V++LPTV I+++LQC+VCL++F +
Sbjct: 183 GALGDYFVGPGLDLLLQHLSENDPNRYGTPPAPKEAVESLPTVKINENLQCSVCLDDFEV 242

Query: 226 GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAG 285
           G+EAKEMPCKH+FH  CI+PWLEL SSCP+CR QL  D+ K   + S N  +   +E  G
Sbjct: 243 GSEAKEMPCKHRFHSACILPWLELHSSCPVCRSQLRVDEPKQDSDVSRNHRNQRDDEIIG 302

Query: 286 NTLRLANGEV-----GNGRRNWIPIPWPFDGLLSMSGSQEGGTSNSESS 329
           +    A G+        GRR     PWPF+GL S S S      N   S
Sbjct: 303 HANANAEGDSEGRSPSGGRR--FSFPWPFNGLFSSSSSSSNANGNGTQS 349

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	347
TAIR|locus:2161058	396	ATCRT1 [Arabidopsis thaliana (	0.590	0.517	0.467	8.8e-63
TAIR|locus:2193874	351	AT1G55530 [Arabidopsis thalian	0.847	0.837	0.387	3.8e-56
TAIR|locus:2131463	356	AT4G26400 [Arabidopsis thalian	0.680	0.662	0.382	6.1e-56
TAIR|locus:2092895	315	AT3G13430 [Arabidopsis thalian	0.829	0.914	0.365	2.2e-43
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.458	0.484	0.401	9.2e-36
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.305	0.268	0.429	6.9e-29
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.389	0.411	0.416	7.6e-29
TAIR|locus:2148318	407	RDUF2 "RING and Domain of Unkn	0.299	0.255	0.435	9.7e-28
TAIR|locus:2063912	401	RHC2A "RING-H2 finger C2A" [Ar	0.311	0.269	0.424	4e-27
TAIR|locus:2102569	320	RZF1 "AT3G56580" [Arabidopsis	0.354	0.384	0.377	7.1e-25

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

 Score = 457 (165.9 bits), Expect = 8.8e-63, Sum P(2) = 8.8e-63
 Identities = 107/229 (46%), Positives = 135/229 (58%)

Query:   121 MLQDIRFGIASR----PNDPEALRERSGSLILVNPMNEEALIIQGEN----AASSLGEYX 172
             +LQ IR GIAS      N+ +  RER   +I++NP N+  ++   +N    + +SLG+Y 
Sbjct:   157 LLQGIRAGIASEYESSDNNWDNSRERD-RVIMINPYNQSLVVPSDQNQNHPSLTSLGDYF 215

Query:   173 XXXXXXXXXXXXXENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEM 232
                          ENDPNR G+ PA+KE V+ALPTV I + LQC+VCL++F  G EAKEM
Sbjct:   216 IGPGLDLLLQHLAENDPNRQGTPPARKEAVEALPTVKIMEPLQCSVCLDDFEKGTEAKEM 275

Query:   233 PCKHKFHGECIMPWLELQSSCPICRYQLPS-----DDLKVQGNG---SGN-REDSAGN-- 281
             PCKHKFH  CI+PWLEL SSCP+CR++LPS     D+ K        + N RE S GN  
Sbjct:   276 PCKHKFHVRCIVPWLELHSSCPVCRFELPSSADDDDETKTDSERVLRTRNVRETSNGNVV 335

Query:   282 EDAGNTLRLANGEV--GNGRRNWIPIPWPFDGLLSMSGSQEGGTSNSES 328
             E+ GN  R    EV  GNGRR     PWPF GL S S S    TS S+S
Sbjct:   336 ENVGNADRGREDEVRSGNGRR--FSFPWPFSGLFSSSSSSSSSTSGSQS 382

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

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

 Score = 537 (194.1 bits), Expect = 3.8e-56, Sum P(2) = 3.8e-56
 Identities = 121/312 (38%), Positives = 168/312 (53%)

Query:     1 MGDATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSSITDDSINNGIHVGSDRAL 60
             M +A V  YWC++CS+ VNP MEA IKCPFC++GFVE+M      DS ++   V ++   
Sbjct:     1 MEEAVVTRYWCHMCSQTVNPVMEAEIKCPFCQSGFVEEMEDDDDHDS-SDPADVRANN-- 57

Query:    61 SLWAPILLRMMTGLAPSRPRITAHEHISSNNSRI--EEAEQEGEFEXX-----XXXXXXX 113
             SLWAPIL+ +M      R R  + E +  N + +  E  E +GE +              
Sbjct:    58 SLWAPILMELMNDPVRRR-RNQSVESVEDNQNEVQTENNEDDGENDLDWQLQEILRRRRR 116

Query:   114 XXXXXXXMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGENA----ASSLG 169
                    +LQ IR G++             G +IL+N  N+   +    +     A SLG
Sbjct:   117 HSAAVLQLLQGIRAGLSVESESTGNGGNNPGRVILINTSNQTITVQNSADMDSVPAGSLG 176

Query:   170 EYXXXXXXXXXXXXXXENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEA 229
             +Y              ENDPNRYG+ PA+KE V+AL TV I++ LQC+VCL++F +G EA
Sbjct:   177 DYFIGPGFEMLLQRLAENDPNRYGTPPAKKEAVEALATVKIEETLQCSVCLDDFEIGTEA 236

Query:   230 KEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAG-NTL 288
             K MPC HKFH +C++PWLEL SSCP+CRYQLP+D+ K   +      D+ G+  A   T 
Sbjct:   237 KLMPCTHKFHSDCLLPWLELHSSCPVCRYQLPADEAKT--DSVTTTSDNNGSSSASATTS 294

Query:   289 RLANGEVGNGRR 300
               A    GN R+
Sbjct:   295 HGAENSDGNRRQ 306

GO:0005737 "cytoplasm" evidence=ISM

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

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

 Score = 393 (143.4 bits), Expect = 6.1e-56, Sum P(2) = 6.1e-56
 Identities = 96/251 (38%), Positives = 128/251 (50%)

Query:    81 ITAHEHISSNNSRI-EEAEQEGEFEXXXXXXXXXXXXXXXXMLQDIRFGIASRPNDPEA- 138
             I  H H    + +   E + + EFE                +LQ IR GIAS     +  
Sbjct:   109 IDRHHHRRHRHRQQGREIDLDREFESILRRRRRSSATILQ-LLQGIRAGIASEYESSDRD 167

Query:   139 LRERSGSLILVNPMNEEALIIQGENAASSLGEYXXXXXXXXXXXXXXENDPNRYGSLPAQ 198
             L  +S  +     +N+     +   + S++G+Y              +ND  R+GSLPA+
Sbjct:   168 LLNQSAVVQGSTSLNQN----RNNTSLSAIGDYFVGSSLDHLLEHLADNDSIRHGSLPAR 223

Query:   199 KEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258
             KEVV  LPTV I + LQC++CL++F  G+EAKEMPCKHKFH  CI+PWLEL SSCP+CRY
Sbjct:   224 KEVVDNLPTVKISESLQCSICLDDFDKGSEAKEMPCKHKFHIRCIVPWLELHSSCPVCRY 283

Query:   259 QLPSDD-LKVQGNGSGNR--EDSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPFDGLLSM 315
             +LP DD  KV       R  E +  NE+  +  R  N  V   R ++   PWPF GL S 
Sbjct:   284 ELPPDDETKVNPVRPRTRTLEINVSNENVEDDAR--NSNVSERRFSF---PWPFSGLFSS 338

Query:   316 SGSQEGGTSNS 326
             S S     S S
Sbjct:   339 SSSSSASASGS 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 = 458 (166.3 bits), Expect = 2.2e-43, P = 2.2e-43
 Identities = 118/323 (36%), Positives = 162/323 (50%)

Query:     1 MGDATVGSYWCYICSRMVNPRMEAGI-KCPFCETGFVEQMSSSITDDSINNGIHVGSDRA 59
             M DA+  SYWC++CSR V P ++  I KC FC++GFVE+M         NN  H  +D  
Sbjct:     1 MEDASETSYWCHMCSRSVIPLIQDEIIKCNFCQSGFVEEMD--------NNDDHQAAD-- 50

Query:    60 LSLWAPILLRMM--------TGLAPSRPRITAHEHISSNNSRIEEAEQEGEFEXXXXXXX 111
              SLW PIL+ MM        T    S   I   E    ++    +   +GE +       
Sbjct:    51 -SLWTPILMEMMNNNHDQHSTNQEDSES-ILEDEDEDEDDGDDGDQNNDGEIDITHQLEE 108

Query:   112 -----XXXXXXXXXMLQDIRFGIASRPNDPEALRERSGSLILVNPMNEEALIIQGE-NAA 165
                           +LQ IR G+     + E   + S  ++L+N  N+   + Q   +  
Sbjct:   109 IRRIRTRHSTAIVNLLQGIRAGLLIESENNEDNPDNSELVVLINSFNQRIRVHQDSVDTT 168

Query:   166 S----SLGEYXXXXXXXXXXXXXXEND-PNRYGSLPAQKEVVKALPTVAIDQDL-QCAVC 219
             S    SLG+Y              END  NRYG+ PA KE V+AL  V I+  L QC+VC
Sbjct:   169 SVPSGSLGDYFIGPGFETLLQRLAENDLNNRYGTPPATKEAVEALAMVKIEDSLLQCSVC 228

Query:   220 LEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS-DDLKVQGNGSGNREDS 278
             L++F +G EAKEMPCKHKFH +C++PWLEL SSCP+CRY LP+ DD + + +   +R D 
Sbjct:   229 LDDFEIGMEAKEMPCKHKFHSDCLLPWLELHSSCPVCRYLLPTGDDDEPKTDAETSRNDD 288

Query:   279 AGNEDAGNTLRLANGEVGNGRRN 301
               NED  N    +NG   +   N
Sbjct:   289 -NNEDISNASMASNGSSPDSSSN 310

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 = 332 (121.9 bits), Expect = 9.2e-36, Sum P(2) = 9.2e-36
 Identities = 71/177 (40%), Positives = 100/177 (56%)

Query:   161 GENAASSLGEYXXXXXXXXXXXXXXENDPNRYGSLPAQKEVVKALPTVAIDQDL------ 214
             G     + G+Y              ENDPNRYG+ PA K  + ALPTV + +D+      
Sbjct:   155 GNRMPGNFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMN 214

Query:   215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGN 274
             QCAVC++EF  G++ K+MPCKH FH +C++PWLEL +SCP+CR++LP+DD   +     N
Sbjct:   215 QCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPTDDPDYE-----N 269

Query:   275 REDSAGNEDAGNTLRLANGEVGNGRRNWIPIPWPF---DGLLSMSGSQEGGTSNSES 328
             R  S G++ +G+      G+     R  I +PWPF   DG  S SG+   G  N E+
Sbjct:   270 R--SQGSQGSGDGQGSVEGQ--QTPRFSIQLPWPFRRQDGSGSGSGAPGTGGGNLET 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 = 6.9e-29, Sum P(2) = 6.9e-29
 Identities = 52/121 (42%), Positives = 70/121 (57%)

Query:   187 NDPNRYGSLPAQKEVVKALPTVAIDQ-----DLQCAVCLEEFVMGNEAKEMPCKHKFHGE 241
             N   R G+ PA K  +++LP V I       +  CAVC E F  G E +EMPCKH FHG+
Sbjct:   181 NGIGRSGNPPASKSAIESLPRVEISDCHTKAEANCAVCTEVFEAGIEGREMPCKHIFHGD 240

Query:   242 CIMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTL-RLANGEVGNGRR 300
             CI+PWL +++SCP+CR++LPSD ++       N E+ A     G T+ RL  G    GR 
Sbjct:   241 CIVPWLSIRNSCPVCRFELPSDPIQ-----RSNEEEHA----VGMTIWRLPGGGFAVGRF 291

Query:   301 N 301
             N
Sbjct:   292 N 292

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 = 272 (100.8 bits), Expect = 7.6e-29, Sum P(2) = 7.6e-29
 Identities = 62/149 (41%), Positives = 82/149 (55%)

Query:   191 RYGSLPAQKEVVKALPTVAIDQ------DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIM 244
             R G  PA +  + ALPT+ I Q      D  C VC +EF +G+EAK+MPC H +H +CI+
Sbjct:   159 RRGPPPAPRSAIDALPTIKIAQRHLRSSDSNCPVCKDEFELGSEAKQMPCNHIYHSDCIV 218

Query:   245 PWLELQSSCPICRYQLPSDDLKVQG-NGSGNREDSAGNEDAGNTLRLANG-EVGNGRRNW 302
             PWL   +SCP+CR +LPS      G + S NR     N  + ++   +N  E GN RRN 
Sbjct:   219 PWLVQHNSCPVCRQELPS----ASGPSSSQNRTTPTRNYRSSSSSSSSNSRENGNERRNP 274

Query:   303 IPIPWPF--DGLLSMSGSQEGGTSNSESS 329
                 WPF   G  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 = 238 (88.8 bits), Expect = 9.7e-28, Sum P(2) = 9.7e-28
 Identities = 51/117 (43%), Positives = 69/117 (58%)

Query:   191 RYGSLPAQKEVVKALPTVAIDQ-----DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMP 245
             R G+ PA K  +++LP V I       +  CAVC E F    EA+EMPCKH FH +CI+P
Sbjct:   169 RSGNPPASKSAIESLPRVEISDCHIGSEANCAVCTEIFETETEAREMPCKHLFHDDCIVP 228

Query:   246 WLELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTL-RLANGEVGNGRRN 301
             WL +++SCP+CR++LPS+  +   N   N ED+A     G T+ RL  G    GR N
Sbjct:   229 WLSIRNSCPVCRFELPSEPNRRSNN---NEEDNA----VGMTIWRLPGGGFAVGRFN 278

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

TAIR|locus:2063912 RHC2A "RING-H2 finger C2A" [Arabidopsis thaliana (taxid:3702)]

 Score = 234 (87.4 bits), Expect = 4.0e-27, Sum P(2) = 4.0e-27
 Identities = 53/125 (42%), Positives = 74/125 (59%)

Query:   196 PAQKEVVKALPTVAID-----QDLQ--CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE 248
             PA K  ++ALP + ID      D Q  CAVC E FV+ + A+EMPC H +H +CI+PWL 
Sbjct:   174 PASKSAIEALPLIEIDPTHLLSDSQSHCAVCKENFVLKSSAREMPCNHIYHPDCILPWLA 233

Query:   249 LQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNED-----AGNTL-RLANGEVGNGRRNW 302
             +++SCP+CR++LP++DL   G G+     +A  E+     AG T+ RL  G    GR   
Sbjct:   234 IRNSCPVCRHELPAEDL-TDGTGAALTAVTATAEEEEDSAAGLTIWRLPGGGFAVGR--- 289

Query:   303 IPIPW 307
             IP  W
Sbjct:   290 IPGGW 294

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

TAIR|locus:2102569 RZF1 "AT3G56580" [Arabidopsis thaliana (taxid:3702)]

 Score = 230 (86.0 bits), Expect = 7.1e-25, Sum P(2) = 7.1e-25
 Identities = 54/143 (37%), Positives = 73/143 (51%)

Query:   193 GSLPAQKEVVKALPTVAIDQ------DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPW 246
             G  PA K  + ALPT+ I Q      D  C VC +EF + +EAK+MPC H +H +CI+PW
Sbjct:   157 GPPPAPKSSIDALPTIKITQKHLKSSDSHCPVCKDEFELKSEAKQMPCHHIYHSDCIVPW 216

Query:   247 LELQSSCPICRYQLPSDDLKVQGNGSGNREDSAGNEDAGNTLRLANGEVGNGRRNWIPIP 306
             L   +SCP+CR +LPS        GS +   S+ N       R  NG   + RRN     
Sbjct:   217 LVQHNSCPVCRKELPS-------RGSSSSTQSSQN-------RSTNGRENSRRRNIFSNL 262

Query:   307 WPFDGLLSMSGSQEGGTSNSESS 329
             WPF    S S      T+N+ ++
Sbjct:   263 WPFRSSSSSSTQNRRDTNNTATA 285

GO:0005575 "cellular_component" evidence=ND

GO:0008270 "zinc ion binding" evidence=ISS

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

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

GO:1902006 "negative regulation of proline biosynthetic process" evidence=IMP

---

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	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00130596 hypothetical protein (344 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	347
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	9e-17
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-11
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	9e-11
pfam14369	34	pfam14369, zf-RING_3, zinc-finger	2e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	2e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-09
smart00184	40	smart00184, RING, Ring finger	2e-08
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-07
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	7e-06
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	2e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	3e-04

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

 Score = 72.8 bits (179), Expect = 9e-17
 Identities = 20/43 (46%), Positives = 28/43 (65%)

Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257
           +C +CL+EF  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 = 58.2 bits (141), Expect = 2e-11
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 3/44 (6%)

Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICR 257
           +C +CLEEF        +PC H F   CI  WL+  +++CP+CR
Sbjct: 1   ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCR 42

Length = 45

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

 Score = 56.0 bits (135), Expect = 9e-11
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258
           ++L+C +CL+     +     PC H F  ECI+ +L+ +S CPICR 
Sbjct: 1   EELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 1/33 (3%)

Query: 8  SYWCYICSRMVNP-RMEAGIKCPFCETGFVEQM 39
           YWCY C R V          CP C  GFVE++
Sbjct: 2  RYWCYQCDRFVRIAPSGDSDVCPRCGGGFVEEI 34

Length = 34

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

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 10/52 (19%)

Query: 216 CAVCLEEFVM-----GNEAKEMP-----CKHKFHGECIMPWLELQSSCPICR 257
           CA+C   F        +   + P     C H FH  CI  WL+ +++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 = 58.4 bits (141), Expect = 2e-09
 Identities = 30/103 (29%), Positives = 41/103 (39%), Gaps = 23/103 (22%)

Query: 197 AQKEVVKALPTVAIDQ----DLQCAVCLEE-FVMGNEA---------KEMPCKHKFHGEC 242
           A K++    PT   +Q    D  C +C++E F   +E          K +PC H  H  C
Sbjct: 267 ATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHC 326

Query: 243 IMPWLELQSSCPICRYQLPSDDLKVQGNGSGNREDS--AGNED 283
           +  WLE Q +CPICR         V  + S     S    N  
Sbjct: 327 LKNWLERQQTCPICR-------RPVIFDQSSPTPASPNVRNTQ 362

Length = 491

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

 Score = 57.3 bits (138), Expect = 3e-09
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 197 AQKEVVKALPTVAI---DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-S 252
             K  +K L        D+ ++CA+C+  F+  +  + +PC H+FH  C+  WL   S  
Sbjct: 304 TTKGSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNK 363

Query: 253 CPICRYQLP 261
           CP+CR  +P
Sbjct: 364 CPVCRTAIP 372

Length = 374

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

 Score = 49.8 bits (119), Expect = 2e-08
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 3/42 (7%)

Query: 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPIC 256
           C +CLEE++   +   +PC H F   CI  WLE  + +CPIC
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 = 46.7 bits (111), Expect = 2e-07
 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 3/42 (7%)

Query: 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPIC 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 = 47.7 bits (113), Expect = 7e-06
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 10/56 (17%)

Query: 215  QCAVCLEEFVMGNEAKEMP------CKHKFHGECIMPWLEL--QSSCPICRYQLPS 262
            +CA+C    V+    + +P      CK+KFH  C+  W     +S+CP+CR ++  
Sbjct: 1471 ECAICY--SVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524

Length = 1525

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

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 3/27 (11%)

Query: 234 CKHKFHGECIMPWLELQSS---CPICR 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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 15/73 (20%)

Query: 199 KEVVKALPTVAID--------QDLQCAVCLEEFVMGNEAKEM------PCKHKFHGECIM 244
           K+ +K +P+V  +        +D +CA+C+E+ V   E K M       C H F  ECI 
Sbjct: 152 KKFLKTIPSVLSEYEKLYNRSKDKECAICMEK-VYDKEIKNMYFGILSNCNHVFCIECID 210

Query: 245 PWLELQSSCPICR 257
            W + +++CP+CR
Sbjct: 211 IWKKEKNTCPVCR 223

Length = 238

>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 CKHKFHGECIMPWLELQSSCPICR 257
           C H FH  CI  WL+ +  CP+ R
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	347
PF14369	35	zf-RING_3: zinc-finger	99.57
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.49
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.42
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.17
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.14
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.11
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.08
PHA02929	238	N1R/p28-like protein; Provisional	99.07
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.04
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.88
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.86
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.82
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.78
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.77
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.74
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.65
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.61
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.6
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.59
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.57
PF14634	44	zf-RING_5: zinc-RING finger domain	98.55
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.5
PHA02926	242	zinc finger-like protein; Provisional	98.45
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.4
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.4
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.32
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.28
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.25
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.25
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.18
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.09
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.08
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.03
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.02
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.99
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.97
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.96
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	97.92
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.79
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.77
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.67
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.64
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.52
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.42
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.41
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.26
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.22
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.14
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.12
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.05
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.91
KOG2660	331	consensus Locus-specific chromosome binding protei	96.76
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.65
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.46
COG5152	259	Uncharacterized conserved protein, contains RING a	96.27
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.23
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.96
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.82
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.61
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.6
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.5
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.47
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.36
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.35
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.16
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	95.14
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.14
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.11
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.09
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	94.89
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.39
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	94.23
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	94.14
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	93.74
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	93.42
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.41
KOG4739	233	consensus Uncharacterized protein involved in syna	93.39
PHA02862	156	5L protein; Provisional	93.33
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	92.96
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.89
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.71
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	92.35
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	92.19
COG5236	493	Uncharacterized conserved protein, contains RING Z	92.07
KOG1940	276	consensus Zn-finger protein [General function pred	92.01
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	91.56
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	91.32
PHA03096	284	p28-like protein; Provisional	91.22
PHA02825	162	LAP/PHD finger-like protein; Provisional	90.91
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	90.9
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	90.43
KOG1001	674	consensus Helicase-like transcription factor HLTF/	90.25
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	90.22
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.96
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	89.67
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	89.5
PF04641	260	Rtf2: Rtf2 RING-finger	89.37
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	89.35
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	89.01
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	88.22
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	88.12
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	87.86
KOG4367	699	consensus Predicted Zn-finger protein [Function un	87.31
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	86.91
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	86.81
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	86.75
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	86.15
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	86.14
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	85.93
KOG3002	299	consensus Zn finger protein [General function pred	85.64
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	85.26
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	84.68
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	83.41
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	82.29
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	81.88
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	81.82
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	81.56

>PF14369 zf-RING_3: zinc-finger

Probab=99.57  E-value=1.3e-15  Score=100.41  Aligned_cols=33  Identities=39%  Similarity=1.040  Sum_probs=28.0

Q ss_pred             CcEeeecCCceeeecC--CCCccCCCCCCCceEec
Q 036250            7 GSYWCYICSRMVNPRM--EAGIKCPFCETGFVEQM   39 (347)
Q Consensus         7 ~rywCh~C~~~V~p~~--~~e~~CP~C~sGFiEE~   39 (347)
                      ++||||+|++.|++..  .++++||+|++||||||
T Consensus         1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence            5899999999999753  33455999999999997

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

Probab=99.49  E-value=3.3e-14  Score=137.79  Aligned_cols=71  Identities=35%  Similarity=0.852  Sum_probs=61.2

Q ss_pred             CCCcchHHHHHcCCcccccc---c---ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC-CCCCCCcccCCC
Q 036250          193 GSLPAQKEVVKALPTVAIDQ---D---LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSD  263 (347)
Q Consensus       193 ~~~p~~~~~i~~lp~~~~~~---~---~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (347)
                      ......|..++++|...+..   .   ..|+||+|+|+.|++++.|||+|.||..||++||..+. .||+||+.+...
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            44567799999999987754   1   28999999999999999999999999999999998775 599999977654

>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=4.2e-14  Score=98.00  Aligned_cols=43  Identities=49%  Similarity=1.239  Sum_probs=40.4

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCC
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR  257 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR  257 (347)
                      +|+||++.|..++.++.++|+|.||..||..|++.+.+||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            6999999999889999999999999999999999999999997

...

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

Probab=99.17  E-value=3.8e-11  Score=115.75  Aligned_cols=66  Identities=35%  Similarity=0.786  Sum_probs=51.9

Q ss_pred             hHHHHHcCCccccc----ccccchhhhhhh-ccC---------CceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          198 QKEVVKALPTVAID----QDLQCAVCLEEF-VMG---------NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       198 ~~~~i~~lp~~~~~----~~~~C~ICl~~~-~~~---------~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .|+.-+.+|++..+    ++..|.||+|++ +.+         .++++|||||++|.+|++-|++++.+||+||.++.-+
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            34444555655544    367999999994 332         3689999999999999999999999999999996444

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.14  E-value=4.6e-11  Score=107.26  Aligned_cols=55  Identities=25%  Similarity=0.690  Sum_probs=45.6

Q ss_pred             cccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc----------------CCCCCCCCcccCCCCCc
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL----------------QSSCPICRYQLPSDDLK  266 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~----------------~~~CP~CR~~l~~~~~~  266 (347)
                      ...++.+|+||++.+   .+++.++|+|+||+.||.+|+..                ...||+||..+...+..
T Consensus        14 ~~~~~~~CpICld~~---~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv   84 (193)
T PLN03208         14 DSGGDFDCNICLDQV---RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV   84 (193)
T ss_pred             cCCCccCCccCCCcC---CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence            334567999999999   77889999999999999999852                24699999999776554

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

Probab=99.11  E-value=2.9e-11  Score=113.88  Aligned_cols=50  Identities=34%  Similarity=1.079  Sum_probs=46.4

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~  262 (347)
                      ..+|+||++.|..+++.+.|||.|.||..||.+|+. .+..||+||.+++.
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            469999999999999999999999999999999997 67789999999875

>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=5.1e-11  Score=91.63  Aligned_cols=45  Identities=40%  Similarity=0.870  Sum_probs=36.1

Q ss_pred             cccchhhhhhhcc----------CCceEEecCCCcccccchHHHHhcCCCCCCCC
Q 036250          213 DLQCAVCLEEFVM----------GNEAKEMPCKHKFHGECIMPWLELQSSCPICR  257 (347)
Q Consensus       213 ~~~C~ICl~~~~~----------~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR  257 (347)
                      +..|+||++.|..          ...+...+|+|.||..||.+||+.+.+||+||
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            3469999999932          22345667999999999999999999999998

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=99.07  E-value=7.1e-11  Score=109.91  Aligned_cols=64  Identities=31%  Similarity=0.687  Sum_probs=50.4

Q ss_pred             hHHHHHcCCccccc--------ccccchhhhhhhccCC-----ceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          198 QKEVVKALPTVAID--------QDLQCAVCLEEFVMGN-----EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       198 ~~~~i~~lp~~~~~--------~~~~C~ICl~~~~~~~-----~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      .+..++.+|.+..+        .+.+|+||++.+....     -++.++|+|.||..||.+|+..+.+||+||..+.
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            56777788876422        3578999999985432     1345579999999999999999999999999875

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

Probab=99.04  E-value=1.2e-10  Score=106.43  Aligned_cols=53  Identities=25%  Similarity=0.699  Sum_probs=45.3

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC---CCCCCCCcccCCCCCcc
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQLPSDDLKV  267 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~~~~~  267 (347)
                      ...+|.||||.-   ++++++.|||+||+.||.+||..+   ..||+||..+..++...
T Consensus        46 ~~FdCNICLd~a---kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP  101 (230)
T KOG0823|consen   46 GFFDCNICLDLA---KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP  101 (230)
T ss_pred             Cceeeeeecccc---CCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence            356999999998   889999999999999999999754   35999999998776543

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

Probab=98.88  E-value=4.8e-10  Score=105.39  Aligned_cols=50  Identities=30%  Similarity=0.856  Sum_probs=45.4

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      ...|.+||+..   .++.-+||||+||+.||..|+..+..||+||..+...+.
T Consensus       239 ~~kC~LCLe~~---~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  239 TRKCSLCLENR---SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCceEEEecCC---CCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            46999999998   789999999999999999999999999999998876543

>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=98.86  E-value=9.4e-10  Score=78.19  Aligned_cols=46  Identities=35%  Similarity=0.840  Sum_probs=40.6

Q ss_pred             cccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      +..|.||++..   ..+..+||+|. ||..|+..|+.....||+||+++.
T Consensus         2 ~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            45799999998   77999999999 999999999999999999999874

...

>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=98.82  E-value=1.5e-09  Score=73.22  Aligned_cols=38  Identities=42%  Similarity=1.117  Sum_probs=32.8

Q ss_pred             chhhhhhhccCCce-EEecCCCcccccchHHHHhcCCCCCCC
Q 036250          216 CAVCLEEFVMGNEA-KEMPCKHKFHGECIMPWLELQSSCPIC  256 (347)
Q Consensus       216 C~ICl~~~~~~~~~-~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C  256 (347)
                      |+||++.+   .++ +.++|||+||..||.+|++.+..||+|
T Consensus         1 C~iC~~~~---~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDEL---RDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB----SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcc---cCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999999   556 688999999999999999988899998

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

Probab=98.78  E-value=2.6e-09  Score=73.43  Aligned_cols=38  Identities=34%  Similarity=0.937  Sum_probs=30.6

Q ss_pred             chhhhhhhccCCceEEecCCCcccccchHHHHhcC----CCCCCC
Q 036250          216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ----SSCPIC  256 (347)
Q Consensus       216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~~CP~C  256 (347)
                      |+||++.|   .+++.|+|||.||..||..|++..    ..||+|
T Consensus         1 CpiC~~~~---~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLF---KDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB----SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhh---CCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999   899999999999999999999654    359987

>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=3.8e-09  Score=71.60  Aligned_cols=43  Identities=44%  Similarity=1.152  Sum_probs=35.8

Q ss_pred             cchhhhhhhccCCceEEe-cCCCcccccchHHHHhc-CCCCCCCCccc
Q 036250          215 QCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLEL-QSSCPICRYQL  260 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l  260 (347)
                      .|+||++.+   ..+..+ +|+|.||..|+..|+.. ...||+||..+
T Consensus         1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998   444444 49999999999999987 67899999764

>smart00504 Ubox Modified RING finger domain

Probab=98.74  E-value=4.7e-09  Score=77.52  Aligned_cols=49  Identities=22%  Similarity=0.514  Sum_probs=43.7

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      ..|+||++.+   .+++.++|||+|+..||..|+..+.+||+|+..+...+.
T Consensus         2 ~~Cpi~~~~~---~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l   50 (63)
T smart00504        2 FLCPISLEVM---KDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDL   50 (63)
T ss_pred             cCCcCCCCcC---CCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhc
Confidence            4799999999   678999999999999999999888899999998865543

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

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

Probab=98.65  E-value=8e-09  Score=107.41  Aligned_cols=50  Identities=44%  Similarity=1.024  Sum_probs=44.0

Q ss_pred             cccchhhhhhhccCCc--eEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFVMGNE--AKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      +..|+||+|.+..+..  +++|+|+|+||..|+..|+++.++||+||..+..
T Consensus       291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             CCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            5789999999965543  8999999999999999999999999999995533

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

Probab=98.61  E-value=1.1e-08  Score=90.11  Aligned_cols=50  Identities=26%  Similarity=0.681  Sum_probs=42.3

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      ..|+|||+.+.. ..++-+.|||+||+.||+.-|.....||+|++.|..++
T Consensus       132 ~~CPiCl~~~se-k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  132 YKCPICLDSVSE-KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cCCCceecchhh-ccccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            589999999953 22345679999999999999999999999999886654

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.60  E-value=1.8e-08  Score=100.18  Aligned_cols=51  Identities=31%  Similarity=0.718  Sum_probs=45.1

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +...+.|+||++.|   ..++.++|+|.||..||..||.....||+||..+...
T Consensus        23 Le~~l~C~IC~d~~---~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFF---DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhh---hCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            34567999999999   6788899999999999999998888999999988654

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

>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=98.59  E-value=1.8e-08  Score=68.31  Aligned_cols=38  Identities=42%  Similarity=1.194  Sum_probs=33.2

Q ss_pred             chhhhhhhccCCceE-EecCCCcccccchHHHHh--cCCCCCCC
Q 036250          216 CAVCLEEFVMGNEAK-EMPCKHKFHGECIMPWLE--LQSSCPIC  256 (347)
Q Consensus       216 C~ICl~~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~--~~~~CP~C  256 (347)
                      |+||++.+   ..+. .++|+|.||..||..|++  ....||+|
T Consensus         1 C~iC~~~~---~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPF---EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBC---SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccc---cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999999   5566 889999999999999998  45579998

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

>smart00184 RING Ring finger

Probab=98.57  E-value=2.6e-08  Score=65.07  Aligned_cols=38  Identities=45%  Similarity=1.205  Sum_probs=34.0

Q ss_pred             chhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCC
Q 036250          216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPIC  256 (347)
Q Consensus       216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~C  256 (347)
                      |+||++..   ..++.++|+|.||..|+..|+. ....||+|
T Consensus         1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999985   7889999999999999999998 56679987

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)

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.55  E-value=3.1e-08  Score=68.56  Aligned_cols=44  Identities=27%  Similarity=0.752  Sum_probs=38.5

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY  258 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~  258 (347)
                      .|.||++.|.....++.++|+|+||..||..+......||+||+
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            49999999965567899999999999999999866678999985

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

Probab=98.50  E-value=4.7e-08  Score=76.77  Aligned_cols=50  Identities=34%  Similarity=0.788  Sum_probs=38.0

Q ss_pred             ccccchhhhhhhcc--------CC-ce-EEecCCCcccccchHHHHhc---CCCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVM--------GN-EA-KEMPCKHKFHGECIMPWLEL---QSSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~--------~~-~~-~~lpC~H~Fh~~Ci~~Wl~~---~~~CP~CR~~l~  261 (347)
                      ++..|.||...|+.        |+ .+ +.-.|+|.||..||.+||+.   +..||+||++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            46789999999852        22 23 33349999999999999975   467999999764

>PHA02926 zinc finger-like protein; Provisional

Probab=98.45  E-value=6e-08  Score=88.50  Aligned_cols=50  Identities=28%  Similarity=0.669  Sum_probs=37.9

Q ss_pred             ccccchhhhhhhccCC------ceEEecCCCcccccchHHHHhcC------CCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGN------EAKEMPCKHKFHGECIMPWLELQ------SSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~------~~~~lpC~H~Fh~~Ci~~Wl~~~------~~CP~CR~~l~  261 (347)
                      .+.+|+||++......      -....+|+|.||..||..|...+      .+||+||..+.
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            4679999999874321      12344699999999999999753      35999999764

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

Probab=98.40  E-value=8.5e-08  Score=91.94  Aligned_cols=53  Identities=36%  Similarity=0.834  Sum_probs=47.1

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      +.-+.|-||.++|   ..+.++||+|.||..||...|..+..||.|+.++....+.
T Consensus        21 D~lLRC~IC~eyf---~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr   73 (442)
T KOG0287|consen   21 DDLLRCGICFEYF---NIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLR   73 (442)
T ss_pred             HHHHHHhHHHHHh---cCceeccccchHHHHHHHHHhccCCCCCceecccchhhhh
Confidence            3456899999999   7889999999999999999999999999999988766544

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

Probab=98.40  E-value=7.8e-08  Score=96.79  Aligned_cols=55  Identities=36%  Similarity=0.753  Sum_probs=46.1

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-----CCCCCCCcccCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-----SSCPICRYQLPSDDLKVQG  269 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-----~~CP~CR~~l~~~~~~~~~  269 (347)
                      .+..|+|||+..   ..+..+.|||+||..||.++|...     ..||+||..+..+++....
T Consensus       185 t~~~CPICL~~~---~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  185 TDMQCPICLEPP---SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF  244 (513)
T ss_pred             cCCcCCcccCCC---CcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence            367999999998   778888899999999999998653     4699999999887765443

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

Probab=98.32  E-value=1.4e-07  Score=88.03  Aligned_cols=50  Identities=32%  Similarity=0.792  Sum_probs=43.2

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHH-HHhcCCC-CCCCCcccCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMP-WLELQSS-CPICRYQLPSDD  264 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~-Wl~~~~~-CP~CR~~l~~~~  264 (347)
                      .+..|.||++..   ..+..++|+|+||+.||.. |-..+.- ||+||+.+..++
T Consensus       214 ~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         214 ADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             cccceeeeeccc---CCcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            367899999999   8899999999999999999 8766654 999999876654

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

Probab=98.28  E-value=3e-07  Score=70.60  Aligned_cols=51  Identities=25%  Similarity=0.522  Sum_probs=41.0

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDL  265 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~  265 (347)
                      +.+.|+|+.+.|   .+++++||||.|...||..||.. +.+||+|+..+...+.
T Consensus         3 ~~f~CpIt~~lM---~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l   54 (73)
T PF04564_consen    3 DEFLCPITGELM---RDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDL   54 (73)
T ss_dssp             GGGB-TTTSSB----SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGS
T ss_pred             cccCCcCcCcHh---hCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccc
Confidence            456899999999   89999999999999999999988 7899999998876544

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=98.25  E-value=2.3e-07  Score=86.65  Aligned_cols=64  Identities=28%  Similarity=0.656  Sum_probs=48.6

Q ss_pred             cCCcccccccccchhhhhhhccCC-------ceEEecCCCcccccchHHHH--hcCCCCCCCCcccCCCCCccc
Q 036250          204 ALPTVAIDQDLQCAVCLEEFVMGN-------EAKEMPCKHKFHGECIMPWL--ELQSSCPICRYQLPSDDLKVQ  268 (347)
Q Consensus       204 ~lp~~~~~~~~~C~ICl~~~~~~~-------~~~~lpC~H~Fh~~Ci~~Wl--~~~~~CP~CR~~l~~~~~~~~  268 (347)
                      .+|+..++ +..|+||-..+....       +..+|.|+|+||..||+-|-  .++.+||.|+..+..+..-.+
T Consensus       216 glPtkhl~-d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsn  288 (328)
T KOG1734|consen  216 GLPTKHLS-DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSN  288 (328)
T ss_pred             CCCCCCCC-cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccC
Confidence            34555443 457999999886544       67899999999999999997  467899999998865544333

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

Probab=98.25  E-value=4e-07  Score=62.88  Aligned_cols=38  Identities=32%  Similarity=0.796  Sum_probs=22.6

Q ss_pred             chhhhhhhcc-CCceEEecCCCcccccchHHHHhcC----CCCC
Q 036250          216 CAVCLEEFVM-GNEAKEMPCKHKFHGECIMPWLELQ----SSCP  254 (347)
Q Consensus       216 C~ICl~~~~~-~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~~CP  254 (347)
                      |+||++ |.. ...++.|+|||+|+.+||.+|+...    ..||
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 733 3348999999999999999999743    2476

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

Probab=98.18  E-value=7.4e-07  Score=68.63  Aligned_cols=49  Identities=31%  Similarity=0.700  Sum_probs=36.7

Q ss_pred             ccchhhhhhhc-----------cCC-ceEE-ecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          214 LQCAVCLEEFV-----------MGN-EAKE-MPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       214 ~~C~ICl~~~~-----------~~~-~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ..|+||...+.           .+. .++. =-|.|.||..||.+||..++.||++|++...
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            46777777663           222 2222 2399999999999999999999999997643

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

Probab=98.09  E-value=1.2e-06  Score=82.58  Aligned_cols=48  Identities=31%  Similarity=0.604  Sum_probs=43.0

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      .-+.|-||.+.|   ..+..++|+|.||+-||...|..+.-||+||.+...
T Consensus        24 s~lrC~IC~~~i---~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          24 SMLRCRICDCRI---SIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             hHHHhhhhhhee---ecceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            346899999999   778899999999999999999999999999987543

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

Probab=98.08  E-value=1.6e-06  Score=61.55  Aligned_cols=42  Identities=26%  Similarity=0.777  Sum_probs=33.9

Q ss_pred             cchhhhhhhccCCceEEecCC-----CcccccchHHHHhcC--CCCCCCC
Q 036250          215 QCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLELQ--SSCPICR  257 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~--~~CP~CR  257 (347)
                      .|-||++ ...+..+.++||.     |.+|..||.+|+..+  .+||+|+
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            4889998 4445677889985     899999999999654  4799995

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

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

Probab=98.03  E-value=2.7e-06  Score=68.65  Aligned_cols=48  Identities=27%  Similarity=0.601  Sum_probs=36.0

Q ss_pred             cccchhhhhhhc-------------cCCc-eEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250          213 DLQCAVCLEEFV-------------MGNE-AKEMPCKHKFHGECIMPWLELQSSCPICRYQL  260 (347)
Q Consensus       213 ~~~C~ICl~~~~-------------~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l  260 (347)
                      ...|+||..-+.             .++. +.-=-|.|.||..||.+||+.++.||+|.++-
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            357999887652             1121 23334999999999999999999999997753

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

Probab=98.02  E-value=1.9e-06  Score=79.89  Aligned_cols=46  Identities=39%  Similarity=0.909  Sum_probs=39.5

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY  258 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~  258 (347)
                      +.+...|+||++.|   ..++.+||+|.||..||..++.....||.||.
T Consensus        10 ~~~~~~C~iC~~~~---~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYF---REPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHh---hcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            34567999999999   66699999999999999999885567999993

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

Probab=97.99  E-value=3e-06  Score=84.16  Aligned_cols=54  Identities=37%  Similarity=0.897  Sum_probs=42.0

Q ss_pred             CcccccccccchhhhhhhccCCc-eEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          206 PTVAIDQDLQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       206 p~~~~~~~~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      +...+.+-.+|+|||+.+..... ++.+.|.|.||..|+.+|.  ..+||+||+...
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            44445566799999999965432 3455599999999999994  578999999775

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

Probab=97.97  E-value=1.7e-06  Score=86.71  Aligned_cols=50  Identities=30%  Similarity=0.947  Sum_probs=39.5

Q ss_pred             cccchhhhhhhccC---C-----------ceEEecCCCcccccchHHHHh-cCCCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFVMG---N-----------EAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~---~-----------~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~  262 (347)
                      ...|+||+..+..-   .           .-..+||.|+||..|+.+|.+ .+-.||+||.+|+.
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            46899999987421   1           123559999999999999998 45589999999874

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

Probab=97.97  E-value=2.1e-06  Score=63.80  Aligned_cols=52  Identities=27%  Similarity=0.737  Sum_probs=26.4

Q ss_pred             cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCCCCcc
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKV  267 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  267 (347)
                      ++.+.|++|.+.+   .+++.| .|.|+||+.||..-+.  ..||+|+.+-...+.+.
T Consensus         5 e~lLrCs~C~~~l---~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~   57 (65)
T PF14835_consen    5 EELLRCSICFDIL---KEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQI   57 (65)
T ss_dssp             HHTTS-SSS-S-----SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS---
T ss_pred             HHhcCCcHHHHHh---cCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHh
Confidence            3456899999999   677655 4999999999988654  34999999887766554

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

Probab=97.96  E-value=3e-06  Score=90.22  Aligned_cols=53  Identities=30%  Similarity=0.844  Sum_probs=40.1

Q ss_pred             cccccccccchhhhhhhccCCceEEe------cCCCcccccchHHHHhc--CCCCCCCCcccC
Q 036250          207 TVAIDQDLQCAVCLEEFVMGNEAKEM------PCKHKFHGECIMPWLEL--QSSCPICRYQLP  261 (347)
Q Consensus       207 ~~~~~~~~~C~ICl~~~~~~~~~~~l------pC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~  261 (347)
                      ..++..-.+|+||...+..-  -+.+      .|+|.||..||.+|+..  +++||+||.+++
T Consensus      1463 ~~~fsG~eECaICYsvL~~v--dr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1463 DEKFSGHEECAICYSVLDMV--DRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hhhcCCcchhhHHHHHHHHH--hccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            34555667999999988511  1233      29999999999999965  467999998775

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

Probab=97.92  E-value=1.2e-06  Score=66.93  Aligned_cols=49  Identities=37%  Similarity=0.862  Sum_probs=36.2

Q ss_pred             cccchhhhhhhcc--------C-CceEEec-CCCcccccchHHHHhc---CCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVM--------G-NEAKEMP-CKHKFHGECIMPWLEL---QSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~--------~-~~~~~lp-C~H~Fh~~Ci~~Wl~~---~~~CP~CR~~l~  261 (347)
                      +..|-||.-.|..        | +.+.++- |.|.||..||.+||..   +..||+||++..
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            4578899888842        2 2333333 9999999999999964   346999998764

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

Probab=97.79  E-value=4.3e-06  Score=63.76  Aligned_cols=50  Identities=26%  Similarity=0.714  Sum_probs=23.4

Q ss_pred             cccchhhhhhhc-cCCceEEe----cCCCcccccchHHHHhc----C-------CCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFV-MGNEAKEM----PCKHKFHGECIMPWLEL----Q-------SSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~-~~~~~~~l----pC~H~Fh~~Ci~~Wl~~----~-------~~CP~CR~~l~~  262 (347)
                      +.+|.||+..+. .+..+.++    .|++.||..||..||..    +       ..||.|+.+|..
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            458999999875 33332222    38999999999999953    1       139999998753

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.77  E-value=1.2e-05  Score=77.40  Aligned_cols=54  Identities=20%  Similarity=0.433  Sum_probs=39.2

Q ss_pred             cccchhhhhhhccCCce--EEecCCCcccccchHHHH-hcCCCCCCCCcccCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNEA--KEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~--~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~  266 (347)
                      +..|+||+..-......  ...+|||.||..||...+ .....||.|+..+....+.
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            35799999953333332  233799999999999966 4456899999988776543

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).

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

Probab=97.68  E-value=1.5e-05  Score=77.48  Aligned_cols=47  Identities=28%  Similarity=0.737  Sum_probs=41.5

Q ss_pred             cccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ..+|.||+.+-   .+..+|||.|. .|..|.+.---+++.||+||+++..
T Consensus       290 gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  290 GKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             CCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            46899999998   78899999999 8999988766678999999998854

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

Probab=97.67  E-value=7.8e-06  Score=79.17  Aligned_cols=51  Identities=31%  Similarity=0.712  Sum_probs=40.3

Q ss_pred             ccccccchhhhhhhccCCceEEec-CCCcccccchHHHHhc-CCCCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLEL-QSSCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~  263 (347)
                      +..+..|+|||+.+   ...+..+ |.|.||..||..-+.. .+.||.||+.+.+.
T Consensus        40 ~~~~v~c~icl~ll---k~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   40 FDIQVICPICLSLL---KKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhhhccHHHHHHH---HhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            34467899999999   4344444 9999999999998855 56899999988654

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

Probab=97.64  E-value=1.6e-05  Score=75.51  Aligned_cols=48  Identities=27%  Similarity=0.580  Sum_probs=41.2

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDD  264 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (347)
                      .+|+||+...   ..++.|+|+|.||..||+--..+ ..+|++||+++++.-
T Consensus         8 ~eC~IC~nt~---n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    8 KECLICYNTG---NCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             CcceeeeccC---CcCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence            4799999998   78899999999999999877654 456999999997753

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

Probab=97.52  E-value=2.2e-05  Score=74.57  Aligned_cols=91  Identities=19%  Similarity=0.448  Sum_probs=58.1

Q ss_pred             chHHHHHHHHhcCCCCCCCCcchHHHHHcCCcc---cccccccchhhhhhhccCCceEEecCCCcccccchHHHHh----
Q 036250          176 GLDLLLQHLLENDPNRYGSLPAQKEVVKALPTV---AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE----  248 (347)
Q Consensus       176 ~ld~l~~~l~~~~~~~~~~~p~~~~~i~~lp~~---~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~----  248 (347)
                      .|..|.+++...-....| .|.--+.|+.....   .-.....|.|||.-|..+....+++|-|+||..|+-.+|.    
T Consensus        76 ~~~~i~~~~~~iikq~~g-~pii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~  154 (368)
T KOG4445|consen   76 EFREIQRQIQEIIKQNSG-MPIICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLT  154 (368)
T ss_pred             HHHHHHHHHHHHHHhcCC-CchhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHH
Confidence            455666665443322344 33334444432211   1123468999999999888899999999999999955542    


Q ss_pred             --------------c-----CCCCCCCCcccCCCCCcc
Q 036250          249 --------------L-----QSSCPICRYQLPSDDLKV  267 (347)
Q Consensus       249 --------------~-----~~~CP~CR~~l~~~~~~~  267 (347)
                                    .     ...||+||..|..+....
T Consensus       155 ~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~sl  192 (368)
T KOG4445|consen  155 GLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENSL  192 (368)
T ss_pred             HHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccce
Confidence                          1     124999999886654443

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

Probab=97.42  E-value=4.1e-05  Score=80.52  Aligned_cols=54  Identities=26%  Similarity=0.485  Sum_probs=46.0

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      ...|++|+..+..+......+|.|+||..||..|-...++||+||..+......
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V~  176 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKVL  176 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeeee
Confidence            357999999998766667778999999999999999999999999987655433

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

Probab=97.41  E-value=0.00011  Score=72.38  Aligned_cols=50  Identities=26%  Similarity=0.776  Sum_probs=42.5

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhc--CCCCCCCCcccCCCCCcc
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL--QSSCPICRYQLPSDDLKV  267 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~~~~~~  267 (347)
                      .|.||-+.-   .++++-||||+.|..|+-.|-..  .++||.||.++...+..+
T Consensus       371 LCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vi  422 (563)
T KOG1785|consen  371 LCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVI  422 (563)
T ss_pred             HHHHhhccC---CCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccccee
Confidence            699999876   78899999999999999999843  578999999997766543

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

Probab=97.26  E-value=7.6e-05  Score=73.14  Aligned_cols=49  Identities=31%  Similarity=0.838  Sum_probs=36.1

Q ss_pred             ccchhhhhhhccCCceEEec-CCCcccccchHHHHhcC---CCCCCCCcccCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQ---SSCPICRYQLPS  262 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~  262 (347)
                      ..|.||-+.+-...++.-+. |||+||..|+.+|++..   ..||+|+-.++.
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~   57 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQE   57 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccc
Confidence            37999966664444444444 99999999999999864   369999944433

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

Probab=97.22  E-value=3.9e-05  Score=55.09  Aligned_cols=45  Identities=27%  Similarity=0.621  Sum_probs=35.8

Q ss_pred             ccchhhhhhhccCCceEEecCCCc-ccccchHHHH-hcCCCCCCCCcccC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWL-ELQSSCPICRYQLP  261 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl-~~~~~CP~CR~~l~  261 (347)
                      .+|.||++.-   .+-+.-.|+|. .|..|-..-+ ..+..||+||.++.
T Consensus         8 dECTICye~p---vdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHP---VDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCc---chHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            5899999886   45556679998 7888876555 47889999999874

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

Probab=97.14  E-value=8.6e-05  Score=78.34  Aligned_cols=51  Identities=31%  Similarity=0.705  Sum_probs=42.8

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCCCcccCCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPSDDL  265 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~~  265 (347)
                      +-+.|++|-..+   .+++++.|+|+||..||.+.+. ++..||.|...+...|.
T Consensus       642 ~~LkCs~Cn~R~---Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  642 ELLKCSVCNTRW---KDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             hceeCCCccCch---hhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            457999999888   6777888999999999999996 45789999998866554

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

Probab=97.12  E-value=0.00021  Score=71.47  Aligned_cols=49  Identities=31%  Similarity=0.760  Sum_probs=43.7

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ..+..|.||+..+   -.++.+||+|.||..||.+-+.....||+||..+..
T Consensus        82 ~sef~c~vc~~~l---~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRAL---YPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhc---CCCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            3467999999999   778899999999999999988877889999999875

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

Probab=97.05  E-value=0.00032  Score=68.93  Aligned_cols=54  Identities=28%  Similarity=0.712  Sum_probs=38.9

Q ss_pred             ccccccccchhhhhhhccCC----ceEEec-CCCcccccchHHHH--hc-----CCCCCCCCcccC
Q 036250          208 VAIDQDLQCAVCLEEFVMGN----EAKEMP-CKHKFHGECIMPWL--EL-----QSSCPICRYQLP  261 (347)
Q Consensus       208 ~~~~~~~~C~ICl~~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl--~~-----~~~CP~CR~~l~  261 (347)
                      .....+..|.||++......    .-.+|| |.|.||..||..|-  .+     ...||.||....
T Consensus       156 ~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  156 LQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            33356779999999985322    012335 99999999999998  33     357999998653

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

Probab=96.91  E-value=0.00036  Score=70.03  Aligned_cols=52  Identities=27%  Similarity=0.844  Sum_probs=44.6

Q ss_pred             ccccccchhhhhhhccCCceEE-ecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKE-MPCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      +++++.|+||...+   .++.. ..|+|.||..||..|+..+..||.|+..+....
T Consensus        18 ~~~~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            45668999999999   66666 589999999999999999999999988775543

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

Probab=96.76  E-value=0.00033  Score=67.61  Aligned_cols=50  Identities=26%  Similarity=0.679  Sum_probs=42.1

Q ss_pred             cccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .....|.+|...|   .++..+. |-|.||..||...|+...+||.|...+-..
T Consensus        13 n~~itC~LC~GYl---iDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYL---IDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhcccee---ecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            3456899999999   5666665 999999999999999999999998877544

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

Probab=96.65  E-value=0.00073  Score=66.82  Aligned_cols=48  Identities=27%  Similarity=0.826  Sum_probs=36.6

Q ss_pred             cccchhhhhhhccC--CceEEecCCCcccccchHHHHhc--CCCCCCCCccc
Q 036250          213 DLQCAVCLEEFVMG--NEAKEMPCKHKFHGECIMPWLEL--QSSCPICRYQL  260 (347)
Q Consensus       213 ~~~C~ICl~~~~~~--~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l  260 (347)
                      ..+|+||++.+.-.  ...+.+.|+|.|...||.+||.+  ...||.|...-
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            35899999998532  24556679999999999999953  23599997643

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

Probab=96.46  E-value=0.0015  Score=47.83  Aligned_cols=40  Identities=28%  Similarity=0.806  Sum_probs=27.9

Q ss_pred             cccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcC--CCCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQ--SSCPI  255 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~--~~CP~  255 (347)
                      ...|+|.+..|   .++++- .|+|+|-...|..||..+  ..||+
T Consensus        11 ~~~CPiT~~~~---~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPF---EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChh---hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            46899999999   677665 699999999999999443  35998

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

Probab=96.27  E-value=0.0012  Score=59.69  Aligned_cols=44  Identities=18%  Similarity=0.594  Sum_probs=39.6

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL  260 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l  260 (347)
                      ..|.||..+|   ..++...|+|.||..|...-......|-+|-+..
T Consensus       197 F~C~iCKkdy---~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDY---ESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhc---cchhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence            5799999999   7888999999999999999888888999997654

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

Probab=96.23  E-value=0.0014  Score=64.55  Aligned_cols=48  Identities=35%  Similarity=0.767  Sum_probs=38.9

Q ss_pred             cccchhhhhhhccC-CceEEecCCCcccccchHHHHhcC--CCCCCCCccc
Q 036250          213 DLQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQ--SSCPICRYQL  260 (347)
Q Consensus       213 ~~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l  260 (347)
                      ++.|..|-+.+... +..--|||.|+||..|+...|+++  .+||.||+-.
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            46899999998543 456778999999999999999765  4799999533

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

Probab=95.96  E-value=0.0036  Score=57.59  Aligned_cols=52  Identities=21%  Similarity=0.530  Sum_probs=40.9

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcC--C------CCCCCCcccCCCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ--S------SCPICRYQLPSDDL  265 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~------~CP~CR~~l~~~~~  265 (347)
                      ..-|..|...+..|+.+ +|-|-|+||+.|+..|-..-  +      .||.|..+|.....
T Consensus        50 ~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~N  109 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPIN  109 (299)
T ss_pred             CCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcc
Confidence            34799999999887755 66699999999999997542  2      39999998866533

>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=95.82  E-value=0.0037  Score=53.30  Aligned_cols=35  Identities=14%  Similarity=0.485  Sum_probs=29.9

Q ss_pred             cccchhhhhhhccCCceEEecCC------CcccccchHHHH
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCK------HKFHGECIMPWL  247 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~------H~Fh~~Ci~~Wl  247 (347)
                      ..+|.||++.+....-++.++|+      |.||..|+.+|-
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            45899999999775567888886      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.

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

Probab=95.61  E-value=0.0026  Score=55.75  Aligned_cols=28  Identities=29%  Similarity=0.809  Sum_probs=26.2

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHG  240 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~  240 (347)
                      .-+|.||||+++.|+++.+|||-.+||+
T Consensus       177 kGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  177 KGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             CCcEEEEhhhccCCCceeccceEEEeec
Confidence            4699999999999999999999999996

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

Probab=95.60  E-value=0.0045  Score=60.56  Aligned_cols=45  Identities=33%  Similarity=0.672  Sum_probs=33.9

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      .....|.||++..   ...+.+||||+-|  |..-.. .-..||+||..+.
T Consensus       303 ~~p~lcVVcl~e~---~~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  303 PQPDLCVVCLDEP---KSAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIR  347 (355)
T ss_pred             CCCCceEEecCCc---cceeeecCCcEEE--chHHHh-hCCCCchhHHHHH
Confidence            3456899999999   6689999999866  664432 2345999998764

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

Probab=95.50  E-value=0.0036  Score=63.85  Aligned_cols=50  Identities=30%  Similarity=0.745  Sum_probs=41.5

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-----CCCCCCCCcccCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-----QSSCPICRYQLPSDD  264 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-----~~~CP~CR~~l~~~~  264 (347)
                      +..+|-+|-+.-   ++.+...|.|.||..||..++..     .-+||+|...|..+.
T Consensus       535 ~~~~C~lc~d~a---ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl  589 (791)
T KOG1002|consen  535 GEVECGLCHDPA---EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL  589 (791)
T ss_pred             CceeecccCChh---hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence            346899999998   77889999999999999888853     347999999887663

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

Probab=95.47  E-value=0.0041  Score=59.37  Aligned_cols=46  Identities=22%  Similarity=0.515  Sum_probs=40.8

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ..|-||...|   ..+++..|+|.||..|...-+.....|.+|-+....
T Consensus       242 f~c~icr~~f---~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYF---YRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             cccccccccc---ccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            4699999999   788999999999999999988888999999876643

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

Probab=95.36  E-value=0.0074  Score=57.68  Aligned_cols=46  Identities=30%  Similarity=0.685  Sum_probs=37.6

Q ss_pred             ccchhhhhhhccCCceEEec-CCCcccccchHHHH-hcCCCCCCCCc-ccCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWL-ELQSSCPICRY-QLPS  262 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl-~~~~~CP~CR~-~l~~  262 (347)
                      +.|+.|...+   ..+.++| |+|.||..||..-| +....||.|.. .+..
T Consensus       275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvll  323 (427)
T COG5222         275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLL  323 (427)
T ss_pred             ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCcccccchh
Confidence            6899999998   7788887 89999999998776 56678999944 4433

>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=95.35  E-value=0.0062  Score=49.16  Aligned_cols=37  Identities=30%  Similarity=0.587  Sum_probs=30.6

Q ss_pred             cccccccccchhhhhhhccCCceEEecCCCcccccchH
Q 036250          207 TVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIM  244 (347)
Q Consensus       207 ~~~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~  244 (347)
                      .+.+++...|+||...+.. ......||+|+||..|+.
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            3456677889999999965 567788999999999974

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 [].

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

Probab=95.16  E-value=0.009  Score=66.90  Aligned_cols=50  Identities=34%  Similarity=0.717  Sum_probs=40.4

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC----------CCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS----------SCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----------~CP~CR~~l~  261 (347)
                      .+..|-||..+-......++|.|+|+||..|...-|+++-          +||+|+.++.
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            3678999998876666788999999999999977766532          4999998774

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

Probab=95.14  E-value=0.014  Score=48.64  Aligned_cols=36  Identities=19%  Similarity=0.518  Sum_probs=30.2

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCceEecCCC
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSS   42 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~~   42 (347)
                      ....||..|..++.+... ++.||.|+|..+.-+...
T Consensus        68 p~~~~C~~C~~~~~~e~~-~~~CP~C~s~~~~i~~G~  103 (115)
T COG0375          68 PAECWCLDCGQEVELEEL-DYRCPKCGSINLRIIGGD  103 (115)
T ss_pred             ccEEEeccCCCeecchhh-eeECCCCCCCceEEecCC
Confidence            467899999999987766 688999999999877654

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

Probab=95.14  E-value=0.013  Score=41.07  Aligned_cols=40  Identities=30%  Similarity=0.802  Sum_probs=26.7

Q ss_pred             chhhhhhhccCCceEEecCC--C---cccccchHHHHhc--CCCCCCC
Q 036250          216 CAVCLEEFVMGNEAKEMPCK--H---KFHGECIMPWLEL--QSSCPIC  256 (347)
Q Consensus       216 C~ICl~~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~--~~~CP~C  256 (347)
                      |-||++.-.... +.+.||.  -   ..|..||..|+..  ..+|++|
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            678998875533 5677864  3   7899999999964  4569887

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

Probab=95.11  E-value=0.01  Score=57.97  Aligned_cols=49  Identities=24%  Similarity=0.466  Sum_probs=43.3

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      .++..|+||...-   ..++..||+|.-|+.||.+-|.+.+.|=.|+..+..
T Consensus       420 sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            3567899998876   778899999999999999999999999999998764

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

Probab=95.09  E-value=0.012  Score=55.67  Aligned_cols=47  Identities=26%  Similarity=0.522  Sum_probs=36.8

Q ss_pred             ccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhc--CCCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLEL--QSSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~  261 (347)
                      .+.+|++|-+.-   .-+.++ +|+|+||..||..-+..  ..+||.|-.++.
T Consensus       238 ~~~~C~~Cg~~P---tiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  238 SDTECPVCGEPP---TIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             CCceeeccCCCC---CCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            457999999887   445554 49999999999887653  468999987665

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

Probab=94.89  E-value=0.0096  Score=59.22  Aligned_cols=46  Identities=28%  Similarity=0.666  Sum_probs=37.1

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC--------CCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS--------SCPICRY  258 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--------~CP~CR~  258 (347)
                      ...|.||+++..-....+.+||+|+||..|+..++..+-        .||-+..
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            358999999986557899999999999999999985421        3776654

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

Probab=94.39  E-value=0.011  Score=56.35  Aligned_cols=42  Identities=26%  Similarity=0.632  Sum_probs=33.0

Q ss_pred             cccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ...|+||++.-   .+-+.|+|||. -|..|-..    -+.||+||+.+.
T Consensus       300 ~~LC~ICmDaP---~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAP---RDCVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCC---cceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            35799999998   78899999997 56667533    247999998763

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

Probab=94.23  E-value=0.017  Score=40.73  Aligned_cols=44  Identities=30%  Similarity=0.589  Sum_probs=21.8

Q ss_pred             chhhhhhhccCCceEEec--CCCcccccchHHHHh-cCCCCCCCCccc
Q 036250          216 CAVCLEEFVMGNEAKEMP--CKHKFHGECIMPWLE-LQSSCPICRYQL  260 (347)
Q Consensus       216 C~ICl~~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l  260 (347)
                      |++|.+++.. .....+|  |++.+|..|...-++ ....||-||.+.
T Consensus         1 cp~C~e~~d~-~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDE-TDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--C-CCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCccccccc-CCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999833 3334555  889999999888775 467899999864

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

Probab=94.14  E-value=0.037  Score=53.65  Aligned_cols=47  Identities=21%  Similarity=0.480  Sum_probs=37.9

Q ss_pred             cccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ...|+||+...   ..+..+. -|-+||+.||...+..++.||+=-.+...
T Consensus       300 ~~~CpvClk~r---~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v  347 (357)
T KOG0826|consen  300 REVCPVCLKKR---QNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASV  347 (357)
T ss_pred             cccChhHHhcc---CCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchH
Confidence            46899999998   4444444 69999999999999999999997666543

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=93.74  E-value=0.033  Score=40.34  Aligned_cols=45  Identities=24%  Similarity=0.531  Sum_probs=32.9

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      .|-.|...-   .+...+||+|+.+..|..-+  +-+.||+|-+++...+
T Consensus         9 ~~~~~~~~~---~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    9 PCVFCGFVG---TKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eEEEccccc---cccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence            344454443   56789999999999997553  6678999988886543

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

Probab=93.42  E-value=0.027  Score=60.46  Aligned_cols=48  Identities=27%  Similarity=0.668  Sum_probs=33.9

Q ss_pred             ccccchhhhhhhccCCceE-EecCCCcccccchHHHHhcCC-------CCCCCCcc
Q 036250          212 QDLQCAVCLEEFVMGNEAK-EMPCKHKFHGECIMPWLELQS-------SCPICRYQ  259 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~~~~-------~CP~CR~~  259 (347)
                      ...+|.||++.+.....+- --.|-|+||..||..|-....       .||.|...
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            3468999999995422211 113889999999999985421       39999843

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

Probab=93.41  E-value=0.0069  Score=59.78  Aligned_cols=50  Identities=24%  Similarity=0.618  Sum_probs=42.6

Q ss_pred             ccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          214 LQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       214 ~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      ..|+||.+.+... +....+-|+|.+|..||.+||.....||.|+.+|+..
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            4799999988644 4567778999999999999999999999999988654

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

Probab=93.39  E-value=0.027  Score=52.44  Aligned_cols=47  Identities=19%  Similarity=0.492  Sum_probs=34.3

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      .|..|..--. +.....+.|.|+||..|...-  ....||+|++.+....
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRIIQ   51 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhcccC--Cccccccccceeeeee
Confidence            5777765544 566778889999999998552  2228999999875543

>PHA02862 5L protein; Provisional

Probab=93.33  E-value=0.029  Score=48.38  Aligned_cols=45  Identities=18%  Similarity=0.548  Sum_probs=33.6

Q ss_pred             ccchhhhhhhccCCceEEecCC-----CcccccchHHHHhc--CCCCCCCCcccCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLEL--QSSCPICRYQLPS  262 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~  262 (347)
                      ..|=||++.-+  +.  .-||.     ..-|..|+..|+..  +..|++|+.+..-
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            46999999853  22  46764     46899999999954  4569999998743

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

Probab=92.96  E-value=0.038  Score=49.28  Aligned_cols=50  Identities=24%  Similarity=0.673  Sum_probs=35.9

Q ss_pred             ccchhhhhhhccCCceE----EecCCCcccccchHHHHhc----CC-------CCCCCCcccCCC
Q 036250          214 LQCAVCLEEFVMGNEAK----EMPCKHKFHGECIMPWLEL----QS-------SCPICRYQLPSD  263 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~----~lpC~H~Fh~~Ci~~Wl~~----~~-------~CP~CR~~l~~~  263 (347)
                      ..|-||...-..|..+-    -..|+..||.-|+..||..    +.       .||+|-.++..+
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            46888877665554332    3359999999999999964    11       399999887654

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

Probab=92.89  E-value=0.076  Score=59.53  Aligned_cols=82  Identities=24%  Similarity=0.462  Sum_probs=51.5

Q ss_pred             cCCchHHHHHHHHhcCCCCCCCCcchHHHHHcCCcccccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCC
Q 036250          173 VGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS  252 (347)
Q Consensus       173 ~g~~ld~l~~~l~~~~~~~~~~~p~~~~~i~~lp~~~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~  252 (347)
                      .-+|+-.++..|.+.........+-.+..+.-  ...+.....|.||++.+..  .-.+.-|+|.+|..|+..|+..+..
T Consensus      1115 s~~G~~r~lk~l~e~~~~~~~~i~~~es~~~y--~~~~~~~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~ 1190 (1394)
T KOG0298|consen 1115 SIPGLLRYLKGLKESKADTPCKIAQTESDVRY--LMNLSGHFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSR 1190 (1394)
T ss_pred             ccchHHHHHHHHHHHhccCccccCCccchHHH--HHHhhcccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhcc
Confidence            33566666666665443322222111111111  1122234589999999952  3345569999999999999999999


Q ss_pred             CCCCCc
Q 036250          253 CPICRY  258 (347)
Q Consensus       253 CP~CR~  258 (347)
                      ||.|+.
T Consensus      1191 ~~~~ks 1196 (1394)
T KOG0298|consen 1191 CPICKS 1196 (1394)
T ss_pred             Ccchhh
Confidence            999984

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.71  E-value=0.084  Score=49.41  Aligned_cols=54  Identities=19%  Similarity=0.247  Sum_probs=45.1

Q ss_pred             ccchhhhhhhccCC-ceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCcc
Q 036250          214 LQCAVCLEEFVMGN-EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKV  267 (347)
Q Consensus       214 ~~C~ICl~~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  267 (347)
                      ..|+||.+.+.... .++.-||+|+|+..|+.+.+..-..||+|-.++...+...
T Consensus       222 yiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~  276 (303)
T KOG3039|consen  222 YICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIG  276 (303)
T ss_pred             eecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEe
Confidence            57999999996544 3555579999999999999988899999999998876554

>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=92.35  E-value=0.033  Score=38.38  Aligned_cols=41  Identities=27%  Similarity=0.799  Sum_probs=22.7

Q ss_pred             chhhhhhhccCCceEEecCCCcccccchHHHHhcCC--CCCCC
Q 036250          216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS--SCPIC  256 (347)
Q Consensus       216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~C  256 (347)
                      |.+|.+.+..|..-....|.=.+|..|+..++....  .||.|
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            678888885443222223888999999999997665  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=92.19  E-value=0.12  Score=51.16  Aligned_cols=31  Identities=29%  Similarity=0.763  Sum_probs=23.5

Q ss_pred             CCCcccccchHHHHhcC-------------CCCCCCCcccCCCC
Q 036250          234 CKHKFHGECIMPWLELQ-------------SSCPICRYQLPSDD  264 (347)
Q Consensus       234 C~H~Fh~~Ci~~Wl~~~-------------~~CP~CR~~l~~~~  264 (347)
                      |...+|.+|+-+|+..+             -.||+||+.+..-|
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence            56778999998888442             35999999876554

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

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

Probab=92.07  E-value=0.07  Score=52.16  Aligned_cols=47  Identities=26%  Similarity=0.753  Sum_probs=38.5

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHH--HHhcCCCCCCCCccc
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMP--WLELQSSCPICRYQL  260 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~--Wl~~~~~CP~CR~~l  260 (347)
                      ++...|.||.+.+   .-..++||+|..|-.|...  -|.....||+||.+-
T Consensus        59 Een~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          59 EENMNCQICAGST---TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccceeEEecCCc---eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            3456899999998   6678999999999999854  456788999999864

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

Probab=92.01  E-value=0.084  Score=50.51  Aligned_cols=45  Identities=27%  Similarity=0.696  Sum_probs=38.0

Q ss_pred             ccchhhhhhhccCC-ceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250          214 LQCAVCLEEFVMGN-EAKEMPCKHKFHGECIMPWLELQSSCPICRY  258 (347)
Q Consensus       214 ~~C~ICl~~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~  258 (347)
                      ..|+||.+.+.... .+..++|+|..|..|+......+-+||+|.+
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            45999999986554 5778899999999999888866788999988

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=91.56  E-value=0.17  Score=42.24  Aligned_cols=35  Identities=23%  Similarity=0.458  Sum_probs=27.3

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS   41 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~   41 (347)
                      ..+.||+.|...+.+... .+.||.|++..++-+..
T Consensus        68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~G  102 (115)
T TIGR00100        68 PVECECEDCSEEVSPEID-LYRCPKCHGIMLQVRAG  102 (115)
T ss_pred             CcEEEcccCCCEEecCCc-CccCcCCcCCCcEEecC
Confidence            578999999988875433 57899999987665543

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.

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

Probab=91.32  E-value=0.11  Score=31.39  Aligned_cols=22  Identities=36%  Similarity=0.919  Sum_probs=18.7

Q ss_pred             eecCCceeeecC-CCCccCCCCC
Q 036250           11 CYICSRMVNPRM-EAGIKCPFCE   32 (347)
Q Consensus        11 Ch~C~~~V~p~~-~~e~~CP~C~   32 (347)
                      |..|.+.|.|.- ...++||.|+
T Consensus         1 C~sC~~~i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    1 CTSCGRPIAPREQAVPFPCPNCG   23 (24)
T ss_pred             CccCCCcccCcccCceEeCCCCC
Confidence            789999998875 5579999996

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

>PHA03096 p28-like protein; Provisional

Probab=91.22  E-value=0.088  Score=50.73  Aligned_cols=45  Identities=27%  Similarity=0.455  Sum_probs=31.2

Q ss_pred             ccchhhhhhhccCC----ceEEec-CCCcccccchHHHHhcC---CCCCCCCc
Q 036250          214 LQCAVCLEEFVMGN----EAKEMP-CKHKFHGECIMPWLELQ---SSCPICRY  258 (347)
Q Consensus       214 ~~C~ICl~~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl~~~---~~CP~CR~  258 (347)
                      ..|.||++......    .--.|+ |.|.||..||..|-...   .+||.||.
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            57999999885421    223455 99999999999998432   23555543

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=90.91  E-value=0.1  Score=45.79  Aligned_cols=47  Identities=28%  Similarity=0.662  Sum_probs=34.0

Q ss_pred             cccchhhhhhhccCCceEEecCC--C---cccccchHHHHhcC--CCCCCCCcccCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCK--H---KFHGECIMPWLELQ--SSCPICRYQLPSD  263 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~  263 (347)
                      +..|=||.+.-.    .-.-||.  .   .-|.+|+..|+...  .+|++|+.+....
T Consensus         8 ~~~CRIC~~~~~----~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          8 DKCCWICKDEYD----VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCeeEecCCCCC----CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            458999998852    2235754  4   56999999999654  4699998876443

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

Probab=90.90  E-value=0.099  Score=50.16  Aligned_cols=47  Identities=23%  Similarity=0.615  Sum_probs=38.3

Q ss_pred             ccchhhhhhhccC---CceEEecCCCcccccchHHHHhc-CCCCCCCCccc
Q 036250          214 LQCAVCLEEFVMG---NEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQL  260 (347)
Q Consensus       214 ~~C~ICl~~~~~~---~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l  260 (347)
                      ..|-||-++|..+   ..++.|.|+|.||..|+.+-+.. ...||.||.+.
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            4799999999765   24778889999999999877754 34699999985

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=90.43  E-value=0.21  Score=41.59  Aligned_cols=36  Identities=19%  Similarity=0.585  Sum_probs=26.3

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS   41 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~   41 (347)
                      ..++||..|...+......-..||.|+|.-++=+..
T Consensus        68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G  103 (114)
T PRK03681         68 EAECWCETCQQYVTLLTQRVRRCPQCHGDMLRIVAD  103 (114)
T ss_pred             CcEEEcccCCCeeecCCccCCcCcCcCCCCcEEccC
Confidence            678999999988864433126699999887665543

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

Probab=90.25  E-value=0.082  Score=56.69  Aligned_cols=50  Identities=26%  Similarity=0.625  Sum_probs=41.2

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhcC--CCCCCCCcccCCCCCcc
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ--SSCPICRYQLPSDDLKV  267 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~~~~  267 (347)
                      ..|.||++ .   +.+...+|+|.||..|+..-+...  ..||+||..+..+....
T Consensus       455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence            78999999 4   788999999999999999988653  25999999886665443

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=90.22  E-value=0.22  Score=41.36  Aligned_cols=34  Identities=24%  Similarity=0.657  Sum_probs=26.1

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCceEecC
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMS   40 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~   40 (347)
                      ..++||..|.....+... .+.||.|++.-++-+.
T Consensus        68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~  101 (113)
T PRK12380         68 PAQAWCWDCSQVVEIHQH-DAQCPHCHGERLRVDT  101 (113)
T ss_pred             CcEEEcccCCCEEecCCc-CccCcCCCCCCcEEcc
Confidence            678999999988865432 5779999987666554

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

Probab=89.96  E-value=0.12  Score=55.84  Aligned_cols=43  Identities=23%  Similarity=0.616  Sum_probs=34.0

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL  260 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l  260 (347)
                      ...|.+|--.++  -..+..-|+|.||.+|+.   .....||.|+.++
T Consensus       840 ~skCs~C~~~Ld--lP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLD--LPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccc--cceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            358999998884  345666799999999997   4566899998844

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

Probab=89.67  E-value=0.22  Score=43.71  Aligned_cols=32  Identities=25%  Similarity=0.649  Sum_probs=22.9

Q ss_pred             cccchhhhhhhccCCceEEecCC------------C-cccccchHHHH
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCK------------H-KFHGECIMPWL  247 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~------------H-~Fh~~Ci~~Wl  247 (347)
                      +..|+||+|.-   -.++.|-|.            . .-|..||+++-
T Consensus         2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence            46899999987   566676553            2 24788998774

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.

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=89.50  E-value=0.3  Score=40.87  Aligned_cols=36  Identities=19%  Similarity=0.214  Sum_probs=26.1

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS   41 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~   41 (347)
                      ..++||..|.....+.-.....||.|+|-.++=+..
T Consensus        69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G  104 (117)
T PRK00564         69 KVELECKDCSHVFKPNALDYGVCEKCHSKNVIITQG  104 (117)
T ss_pred             CCEEEhhhCCCccccCCccCCcCcCCCCCceEEecC
Confidence            678999999988764422234599999988775543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=89.37  E-value=0.22  Score=47.26  Aligned_cols=53  Identities=21%  Similarity=0.447  Sum_probs=40.2

Q ss_pred             cccchhhhhhhccCCc-eEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      ...|+|...+|..... +...||||+|...+|..-- ....||+|-.++...+..
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            3589999999944334 4455899999999998862 355799999998766544

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

Probab=89.35  E-value=0.12  Score=49.79  Aligned_cols=42  Identities=29%  Similarity=0.661  Sum_probs=29.2

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL  260 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l  260 (347)
                      .|.-|--.+.  .--+.+||+|+||.+|...  ..-+.||+|-..|
T Consensus        92 fCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   92 FCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             eecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            5666655543  3347889999999999743  3456799996654

>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=89.01  E-value=0.2  Score=41.62  Aligned_cols=34  Identities=26%  Similarity=0.457  Sum_probs=23.9

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCceEecC
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMS   40 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~   40 (347)
                      ..++||..|.....+... .+.||.|++..++=+.
T Consensus        68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~  101 (113)
T PF01155_consen   68 PARARCRDCGHEFEPDEF-DFSCPRCGSPDVEIIS  101 (113)
T ss_dssp             --EEEETTTS-EEECHHC-CHH-SSSSSS-EEEEE
T ss_pred             CCcEECCCCCCEEecCCC-CCCCcCCcCCCcEEcc
Confidence            578999999999987655 5889999999876544

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.

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

Probab=88.22  E-value=0.15  Score=43.46  Aligned_cols=47  Identities=26%  Similarity=0.687  Sum_probs=36.0

Q ss_pred             ccchhhhhhhccCCceEEe-c---CCCcccccchHHHHh---cCCCCCCCCcccCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEM-P---CKHKFHGECIMPWLE---LQSSCPICRYQLPSD  263 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~l-p---C~H~Fh~~Ci~~Wl~---~~~~CP~CR~~l~~~  263 (347)
                      -+|.||.|...   +.+-| |   ||-..|..|....|+   .+..||+|+..+.+.
T Consensus        81 YeCnIC~etS~---ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   81 YECNICKETSA---EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             eeccCcccccc---hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            58999999983   33333 3   999999999877664   467899999987654

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

Probab=88.12  E-value=0.23  Score=36.86  Aligned_cols=28  Identities=29%  Similarity=0.624  Sum_probs=21.1

Q ss_pred             eeecCCceeeecCCCCccCCCCCCC-ceEecC
Q 036250           10 WCYICSRMVNPRMEAGIKCPFCETG-FVEQMS   40 (347)
Q Consensus        10 wCh~C~~~V~p~~~~e~~CP~C~sG-FiEE~~   40 (347)
                      =|+.|.+.+.   ++.-+||.|+|- |.||-.
T Consensus         6 AC~~Ck~l~~---~d~e~CP~Cgs~~~te~W~   34 (64)
T COG2093           6 ACKNCKRLTP---EDTEICPVCGSTDLTEEWF   34 (64)
T ss_pred             HHhhccccCC---CCCccCCCCCCcccchhhc
Confidence            3999999875   224579999996 877754

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

Probab=87.86  E-value=0.34  Score=48.28  Aligned_cols=48  Identities=19%  Similarity=0.323  Sum_probs=39.8

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC---CCCCCCCcc
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQ  259 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~  259 (347)
                      ....|+|=.+.-.....|..|.|||+...+-|.+.....   ..||+|-.+
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            346899999988877889999999999999998877553   469999543

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

Probab=87.31  E-value=0.23  Score=49.96  Aligned_cols=36  Identities=28%  Similarity=0.658  Sum_probs=31.2

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhc
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL  249 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~  249 (347)
                      ++++.|+||-..|   .++++|||+|..|..|...-+..
T Consensus         2 eeelkc~vc~~f~---~epiil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFY---REPIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhc---cCceEeecccHHHHHHHHhhccc
Confidence            4678999999999   88999999999999998766543

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

Probab=86.91  E-value=0.43  Score=33.85  Aligned_cols=29  Identities=34%  Similarity=0.864  Sum_probs=22.9

Q ss_pred             CCcEeeecCCceee-ecCCCCccCCCCCCC
Q 036250            6 VGSYWCYICSRMVN-PRMEAGIKCPFCETG   34 (347)
Q Consensus         6 ~~rywCh~C~~~V~-p~~~~e~~CP~C~sG   34 (347)
                      ...|-|-.|.+.|. ......+.||+|++-
T Consensus         4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           4 MMEYKCARCGREVELDQETRGIRCPYCGSR   33 (49)
T ss_pred             eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence            45799999999996 333447999999984

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

Probab=86.81  E-value=0.28  Score=53.33  Aligned_cols=37  Identities=22%  Similarity=0.661  Sum_probs=29.1

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHH
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWL  247 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl  247 (347)
                      ++....|.+|...+.. ..-.+-||+|.||+.||.+-.
T Consensus       814 ~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             ecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence            4456799999998854 455677899999999996543

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

Probab=86.75  E-value=0.31  Score=44.87  Aligned_cols=39  Identities=33%  Similarity=0.701  Sum_probs=29.8

Q ss_pred             chhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250          216 CAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       216 C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      |-+|.+.=   ..+..+||.|+ +|..|-..    ...||+|+....
T Consensus       161 Cr~C~~~~---~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGERE---ATVLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcCC---ceEEeecccceEeccccccc----CccCCCCcChhh
Confidence            88887765   77999999987 78888533    456999987653

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=86.15  E-value=0.62  Score=32.22  Aligned_cols=29  Identities=21%  Similarity=0.480  Sum_probs=24.1

Q ss_pred             cEeeecCCceeeecCCCCccCCCCCCCce
Q 036250            8 SYWCYICSRMVNPRMEAGIKCPFCETGFV   36 (347)
Q Consensus         8 rywCh~C~~~V~p~~~~e~~CP~C~sGFi   36 (347)
                      .|-|-.|..+|.....+.+.||.|++--+
T Consensus         2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIl   30 (44)
T smart00659        2 IYICGECGRENEIKSKDVVRCRECGYRIL   30 (44)
T ss_pred             EEECCCCCCEeecCCCCceECCCCCceEE
Confidence            48999999999877666799999997533

present in RNA polymerase I, II and III

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=86.14  E-value=0.57  Score=40.19  Aligned_cols=35  Identities=23%  Similarity=0.358  Sum_probs=25.5

Q ss_pred             CCcEeeecCCceeeecC--------------------CCCccCCCCCCCceEecC
Q 036250            6 VGSYWCYICSRMVNPRM--------------------EAGIKCPFCETGFVEQMS   40 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~--------------------~~e~~CP~C~sGFiEE~~   40 (347)
                      ..+|||..|.....+.-                    ...+.||.|++.-++-+.
T Consensus        68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~  122 (135)
T PRK03824         68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK  122 (135)
T ss_pred             ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence            57899999998876541                    224779999987766444

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=85.93  E-value=0.47  Score=34.33  Aligned_cols=38  Identities=26%  Similarity=0.670  Sum_probs=31.0

Q ss_pred             ccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPI  255 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~  255 (347)
                      ..|.+|-+.|..++++++-| |+-.+|+.|..+    ...|-+
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            47999999998888888888 999999999643    455544

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

Probab=85.64  E-value=0.53  Score=45.73  Aligned_cols=45  Identities=24%  Similarity=0.609  Sum_probs=34.6

Q ss_pred             ccccccchhhhhhhccCCceEEecC--CCcccccchHHHHhcCCCCCCCCcccC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPC--KHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC--~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      +.+-++|+||.+.+.    +-.+.|  ||+-|..|-.   +..+.||.||.++.
T Consensus        45 ~~~lleCPvC~~~l~----~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLS----PPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCc----ccceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            344579999999983    335556  6999999975   36778999999886

>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=85.26  E-value=0.26  Score=34.65  Aligned_cols=33  Identities=30%  Similarity=0.703  Sum_probs=23.1

Q ss_pred             EecCC-CcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          231 EMPCK-HKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       231 ~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .+.|. |..|..|+...|.....||+|.++|+..
T Consensus        15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            44575 9999999999999999999999999764

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.

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

Probab=84.68  E-value=0.38  Score=50.66  Aligned_cols=44  Identities=32%  Similarity=0.739  Sum_probs=33.0

Q ss_pred             cccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcc
Q 036250          213 DLQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQ  259 (347)
Q Consensus       213 ~~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~  259 (347)
                      -+.|.||+..|... -.++-|-|+|..|..|+..-  .+.+|| |++.
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~D   55 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRD   55 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCcc
Confidence            35799998888532 36777889999999998664  456788 6553

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=83.41  E-value=0.88  Score=38.44  Aligned_cols=35  Identities=17%  Similarity=0.290  Sum_probs=24.5

Q ss_pred             CCcEeeecCCceeeecCCC------CccCCCCCCCceEecCC
Q 036250            6 VGSYWCYICSRMVNPRMEA------GIKCPFCETGFVEQMSS   41 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~------e~~CP~C~sGFiEE~~~   41 (347)
                      ..++|| .|.....+....      -+.||.|++..++-+..
T Consensus        68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G  108 (124)
T PRK00762         68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG  108 (124)
T ss_pred             CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence            578999 999886543110      15699999988775543

>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=82.29  E-value=1.1  Score=28.98  Aligned_cols=25  Identities=32%  Similarity=0.693  Sum_probs=20.0

Q ss_pred             EeeecCCceeeecCCCCccCCCCCC
Q 036250            9 YWCYICSRMVNPRMEAGIKCPFCET   33 (347)
Q Consensus         9 ywCh~C~~~V~p~~~~e~~CP~C~s   33 (347)
                      |-|-.|..+|.....+.+.||.|+.
T Consensus         1 Y~C~~Cg~~~~~~~~~~irC~~CG~   25 (32)
T PF03604_consen    1 YICGECGAEVELKPGDPIRCPECGH   25 (32)
T ss_dssp             EBESSSSSSE-BSTSSTSSBSSSS-
T ss_pred             CCCCcCCCeeEcCCCCcEECCcCCC
Confidence            7799999999877666799999985

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 ....

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

Probab=81.88  E-value=1.4  Score=30.39  Aligned_cols=32  Identities=28%  Similarity=0.717  Sum_probs=24.4

Q ss_pred             CcEeeecCCceeeecCCC-CccCCCCCCCceEe
Q 036250            7 GSYWCYICSRMVNPRMEA-GIKCPFCETGFVEQ   38 (347)
Q Consensus         7 ~rywCh~C~~~V~p~~~~-e~~CP~C~sGFiEE   38 (347)
                      ..|-|-.|-..+...... .+.||+|++-++-.
T Consensus         2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~   34 (46)
T PRK00398          2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFK   34 (46)
T ss_pred             CEEECCCCCCEEEECCCCCceECCCCCCeEEEc
Confidence            368899999998654332 58999999888743

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

Probab=81.82  E-value=0.47  Score=50.78  Aligned_cols=30  Identities=30%  Similarity=0.680  Sum_probs=25.1

Q ss_pred             CCceEEecCCCcccccchHHHHhcCCCCCC
Q 036250          226 GNEAKEMPCKHKFHGECIMPWLELQSSCPI  255 (347)
Q Consensus       226 ~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~  255 (347)
                      |...+...|+|+.|.+|...|++....||.
T Consensus      1040 gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1040 GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            344555679999999999999999999985

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

Probab=81.56  E-value=1.1  Score=47.03  Aligned_cols=47  Identities=36%  Similarity=0.923  Sum_probs=39.5

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      ...|.||+...    ..+..+|.   |..|+.+|+..+..||+|+..+..++..
T Consensus       479 ~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~  525 (543)
T KOG0802|consen  479 NDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFL  525 (543)
T ss_pred             cCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccccc
Confidence            46899999998    45677788   8999999999999999999988666433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	347
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-12
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		5e-11
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		5e-09
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		5e-08
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		1e-06
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		1e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-06
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		2e-06
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		9e-06

>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 = 68.9 bits (167), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 7/73 (9%)
Query: 196 PAQKEVVKALPTV-------AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE 248
           PA KE + ALP +       A+ Q++ C +C  E+V G+ A E+PC H FH  C+  WL+
Sbjct: 16  PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQ 75
Query: 249 LQSSCPICRYQLP 261
              +CP+CR   P
Sbjct: 76  KSGTCPVCRCMFP 88

>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 = 65.5 bits (158), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260
           +   L+C VC E++ +G   +++PC H FH  CI+PWLE   SCP+CR  L
Sbjct: 12  VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 25/50 (50%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 209 AIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICR 257
           A+D  ++CAVCL E   G EA+ +P C H FH EC+  WL   S+CP+CR
Sbjct: 1   AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 21/41 (51%), Positives = 29/41 (70%)
Query: 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPIC 256
           CAVCLE+F   +E    PCKH FH +C++ WLE++  CP+C
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
            + AQKE V +     ++ +LQC +C E F+   EA  + C H F   CI  W++ +  C
Sbjct: 34  KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 90
Query: 254 PICRYQLPS 262
           PICR  + S
Sbjct: 91  PICRKDIKS 99

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
            + AQKE V +     ++ +LQC +C E F+   EA  + C H F   CI  W++ +  C
Sbjct: 34  KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 90
Query: 254 PICRYQLPS 262
           PICR  + S
Sbjct: 91  PICRKDIKS 99

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY----QLPSD 263
           +C +CL     G + + +PC H FH  C+  WL     CPICR     QLPS+
Sbjct: 16  KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSE 68

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSC 253
            + AQKE V +     ++ +LQC +C E F+   EA  + C H F   CI  W++ +  C
Sbjct: 45  KMQAQKEEVLSHMNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIEC 101
Query: 254 PICRYQLPSDDLKVQGNGSGNR 275
           PICR  + S    +  +   N+
Sbjct: 102 PICRKDIKSKTYSLVLDNCINK 123

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257
           C VC+ +F      + +PC H+FH +C+  WL+   +CPICR
Sbjct: 26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	347
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-40
2ect_A	78	Ring finger protein 126; metal binding protein, st	8e-28
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-24
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	4e-23
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-22
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-19
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-18
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-16
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-14
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	1e-13
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	8e-12
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-11
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-10
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	6e-10
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	1e-09
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-09
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-09
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	6e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-05
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-08
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-08
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-08
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	2e-08
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-08
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-08
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	6e-08
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	1e-07
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-07
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	7e-07
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-06
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	1e-06
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	1e-06
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	3e-06
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	5e-06
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	1e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	1e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	5e-05
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	9e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	2e-04
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	3e-04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	6e-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 =  136 bits (344), Expect = 2e-40
 Identities = 29/88 (32%), Positives = 46/88 (52%), Gaps = 7/88 (7%)

Query: 181 LQHLLENDPNRYGSLPAQKEVVKALPTVAI-------DQDLQCAVCLEEFVMGNEAKEMP 233
           + H   +  +   + PA KE + ALP + +        Q++ C +C  E+V G+ A E+P
Sbjct: 1   MGHHHHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP 60

Query: 234 CKHKFHGECIMPWLELQSSCPICRYQLP 261
           C H FH  C+  WL+   +CP+CR   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 =  102 bits (257), Expect = 8e-28
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
           +   L+C VC E++ +G   +++PC H FH  CI+PWLE   SCP+CR  L   +
Sbjct: 12  VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN 66

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

 Score = 93.2 bits (232), Expect = 4e-24
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 6/70 (8%)

Query: 197 AQKEVVKALPTVAI------DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ 250
                   LP+          +   C VC+ +F      + +PC H+FH +C+  WL+  
Sbjct: 1   GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 251 SSCPICRYQL 260
            +CPICR   
Sbjct: 61  RTCPICRADS 70

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

 Score = 90.2 bits (224), Expect = 4e-23
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGN 270
           +    CAVCLE+F   +E    PCKH FH +C++ WLE++  CP+C   +     ++ G 
Sbjct: 13  NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA-QLSGP 71

Query: 271 GSG 273
            SG
Sbjct: 72  SSG 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 = 89.0 bits (221), Expect = 1e-22
 Identities = 18/54 (33%), Positives = 27/54 (50%)

Query: 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
           D + +C +CL     G + + +PC H FH  C+  WL     CPICR  + +  
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 = 79.2 bits (196), Expect = 3e-19
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 209 AIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQL 260
           A+D  ++CAVCL E   G EA+ +P C H FH EC+  WL   S+CP+CR  +
Sbjct: 1   AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 78.2 bits (193), Expect = 1e-18
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
           +  + +C +C++          +PC H F  +CI  W +   +CPICR Q+   +
Sbjct: 12  LTDEEECCICMDGR----ADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN 62

>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 = 76.2 bits (188), Expect = 4e-18
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 215 QCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQSSCPICR 257
            C +CLE+       A  +PC H  H  C    L+    CP+C 
Sbjct: 7   GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 72.1 bits (177), Expect = 2e-16
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257
               +C +CLE+    N +  +PC H F   CI  W+    +CP+C+
Sbjct: 3   TVAERCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCK 47

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

 Score = 66.1 bits (161), Expect = 3e-14
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 211 DQDLQCAVCLEEFV----MGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 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 = 64.5 bits (157), Expect = 1e-13
 Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 4/63 (6%)

Query: 207 TVAIDQDLQCAVCLEEFV----MGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262
            +     + C +C++ +      G       C H F  +C+   L+  ++CP CR ++  
Sbjct: 4   GLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 63

Query: 263 DDL 265
              
Sbjct: 64  KRY 66

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

 Score = 64.4 bits (157), Expect = 1e-13
 Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 212 QDLQCAVCLEEFVMGNEAKEM----PCKHKFHGECIMPWLELQSSCPICRYQLPSDDL 265
             + C +C++ +    +   +     C H F  +C+   L+  ++CP CR ++     
Sbjct: 2   AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 59

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

 Score = 61.0 bits (148), Expect = 2e-12
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 207 TVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL 265
           T       +CA+CL+  V       +PCKH F   C+     L   C +CR ++P D L
Sbjct: 9   TAPSLTVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFL 64

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

 Score = 60.2 bits (146), Expect = 3e-12
 Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 2/55 (3%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
           +   + C++C    +  +      C H F   CI+      + CP C   +    
Sbjct: 12  LTPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ 64

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

 Score = 59.5 bits (144), Expect = 8e-12
 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

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

>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 = 58.0 bits (140), Expect = 4e-11
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 5/59 (8%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQ-SSCPICRYQLPSDDLK 266
           I +  +C +C+E+     +A+  P C       CI  WL  Q + CP CR  L   +L 
Sbjct: 19  IAEVFRCFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELV 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 = 56.0 bits (135), Expect = 2e-10
 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
           ++  L C +C   F+  +    + C H F   CI+ +LE    CPIC  Q+    
Sbjct: 12  LNPHLMCVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64

>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 = 54.2 bits (130), Expect = 6e-10
 Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 4/55 (7%)

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

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

 Score = 53.3 bits (128), Expect = 1e-09
 Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 3/47 (6%)

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

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

 Score = 53.9 bits (129), Expect = 3e-09
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 181 LQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHG 240
            + L +    +      ++EV+  +  V ++ +LQC +C E F    EA  + C H F  
Sbjct: 33  NKELEQTKEEKEKMQAQKEEVLSHMNDV-LENELQCIICSEYF---IEAVTLNCAHSFCS 88

Query: 241 ECIMPWLELQSSCPICRYQLPSDD 264
            CI  W++ +  CPICR  + S  
Sbjct: 89  YCINEWMKRKIECPICRKDIKSKT 112

>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 = 56.3 bits (135), Expect = 4e-09
 Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 7/88 (7%)

Query: 181 LQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHG 240
           L  L E  P  +  +  ++  +             C +C E      + K  PC H    
Sbjct: 303 LTGLCEPTPQDHIKVTQEQYELYC---EMGSTFQLCKICAENDK---DVKIEPCGHLMCT 356

Query: 241 ECIMPWLELQS-SCPICRYQLPSDDLKV 267
            C+  W E +   CP CR ++   +  V
Sbjct: 357 SCLTSWQESEGQGCPFCRCEIKGTEPIV 384

>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 = 52.6 bits (126), Expect = 6e-09
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS-CPICRYQLPSDDLK 266
              + + C +C        +  E  CKH F   CI+  L++  S CP CRY     DL+
Sbjct: 19  HFVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 74

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

 Score = 52.1 bits (124), Expect = 1e-08
 Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 211 DQDLQCAVCLEEFVMGNEAKE----MPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264
              + C +C++ +    +         C H F  +C+   L+  ++CP CR ++    
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 62

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

 Score = 42.5 bits (99), Expect = 2e-05
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 4/59 (6%)

Query: 211 DQDLQCAVCLEEF----VMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL 265
              + C +C++ +      G       C H F  +C+   L+  ++CP CR ++     
Sbjct: 70  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 128

>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 = 51.4 bits (122), Expect = 1e-08
 Identities = 11/44 (25%), Positives = 15/44 (34%), Gaps = 1/44 (2%)

Query: 215 QCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICR 257
           +C                  C H FH  CI  WL+ +  CP+  
Sbjct: 53  ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 51.4 bits (123), Expect = 1e-08
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDL 265
           ++   +C +CL       EA + PC H+F   CI+  + +    CP+    L  + L
Sbjct: 15  LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQL 68

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

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPSDDLK 266
           ID  L+C +C E F   N A  +P C H +   CI  +L  ++ CP C   +   DLK
Sbjct: 19  IDDLLRCGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73

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

 Score = 54.9 bits (131), Expect = 2e-08
 Identities = 15/83 (18%), Positives = 26/83 (31%), Gaps = 16/83 (19%)

Query: 194 SLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEM-----PCKHKFHGECIMPWLE 248
             P              +++L+C +C    + G E   +      C  K H  C+  W +
Sbjct: 289 YFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFK 348

Query: 249 -----------LQSSCPICRYQL 260
                          CP C+ +L
Sbjct: 349 TLMDGKTFLEVSFGQCPFCKAKL 371

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

 Score = 49.8 bits (119), Expect = 2e-08
 Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 4/57 (7%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDL 265
           ++   +C  C          K+  C H+F   C+   L      C  C+  +  D +
Sbjct: 12  VEDKYKCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV 65

>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 = 51.0 bits (121), Expect = 2e-08
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 21/86 (24%)

Query: 193 GSLPAQKEVV-KALPTVAIDQDLQCAVCLEEFVMGNEAKEM---------------PCKH 236
           GS    ++V+ K    + +  +  C +C+E+  + +   +M                C H
Sbjct: 4   GSSGEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSH 63

Query: 237 KFHGECIMPWLELQS-----SCPICR 257
            FH  C++      +      CP C+
Sbjct: 64  AFHLLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 51.0 bits (121), Expect = 2e-08
 Identities = 11/44 (25%), Positives = 15/44 (34%), Gaps = 1/44 (2%)

Query: 215 QCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICR 257
           +C                  C H FH  CI  WL+ +  CP+  
Sbjct: 64  ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

>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 = 50.9 bits (121), Expect = 6e-08
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS-CPICRYQLPSDDLK 266
           ++   +C +CL       EA + PC H+F   CI+  +      CP+    L  + L 
Sbjct: 15  LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLF 69

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

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 6/50 (12%)

Query: 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP 261
           Q L+C  C  E       K +PC H     C+         CPIC+   P
Sbjct: 5   QFLRCQQCQAEA---KCPKLLPCLHTLCSGCLE---ASGMQCPICQAPWP 48

>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 = 48.0 bits (114), Expect = 2e-07
 Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 204 ALPTVAIDQ--DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQL 260
           ALP  AI    + QC +C+E  V   E   +PC H     C    +E  S  CP CR ++
Sbjct: 4   ALPKDAIPSLSECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV 60

Query: 261 PS 262
            S
Sbjct: 61  SS 62

>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 = 48.9 bits (116), Expect = 2e-07
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 4/56 (7%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSDD 264
           ++Q   C  C E      +     C H    +C+    + Q  SCP CR+ L  + 
Sbjct: 75  LEQSFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNY 127

>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 = 46.9 bits (111), Expect = 7e-07
 Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPS 262
           +++  QC  C E            C+H    +C+      Q  SCP CRY L  
Sbjct: 49  VEETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR 99

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

 Score = 48.2 bits (114), Expect = 1e-06
 Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 5/93 (5%)

Query: 178 DLLLQHLLENDPNRYGSLP-AQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKH 236
             +    L      +     A  E+ + +     D    C +C    + G   +   C  
Sbjct: 144 KFVQNKWLIEKEGEFTLHGRAILEMEQYIRETYPDAVKICNICHSLLIQGQSCET--CGI 201

Query: 237 KFHGECIMPWLELQSS--CPICRYQLPSDDLKV 267
           + H  C+  + +  +   CP C    P +  KV
Sbjct: 202 RMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPKV 234

>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 = 46.1 bits (109), Expect = 1e-06
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 11/81 (13%)

Query: 188 DPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPW 246
           +P+  G+    +  +  L     ++ L+C+ C        E   +  C+H F   C+   
Sbjct: 2   EPDGRGAWAHSRAALDRL-----EKLLRCSRCTNIL---REPVCLGGCEHIFCSNCVSDC 53

Query: 247 LELQSSCPICRYQLPSDDLKV 267
           +   + CP+C       DLK+
Sbjct: 54  IG--TGCPVCYTPAWIQDLKI 72

>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 = 44.7 bits (106), Expect = 1e-06
 Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 7/66 (10%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQS--SCPICRYQLPS-DDL 265
           I  +L C +C +      +A  +P C + +  ECI   L      +CP C     S D L
Sbjct: 12  IPDELLCLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDAL 68

Query: 266 KVQGNG 271
               +G
Sbjct: 69  SGPSSG 74

>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 = 45.1 bits (106), Expect = 3e-06
 Identities = 11/71 (15%), Positives = 24/71 (33%), Gaps = 4/71 (5%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDLKVQ 268
           ++    C+ C           +  C H++   C+   L     +C  C ++   ++    
Sbjct: 28  LEAKYLCSACRNVL---RRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISI 84

Query: 269 GNGSGNREDSA 279
              S    D+A
Sbjct: 85  LESSSAFPDNA 95

>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 = 42.6 bits (100), Expect = 5e-06
 Identities = 14/59 (23%), Positives = 18/59 (30%), Gaps = 3/59 (5%)

Query: 213 DLQCAVCLEEFVMGNEAKEM--PCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDLKVQ 268
           D  C  C          K M   C H     C+         +CP C   L   + +VQ
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ 61

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 6/58 (10%)

Query: 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQLPSDDLK 266
           +++ C +CL+      +   + C H F  +CI    E       CP+C+  +  + ++
Sbjct: 19  EEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAIR 73

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 7/62 (11%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLE--LQSSCPICRYQLPS-DDL 265
           I  +L C +C +      +A  +P C + +  ECI   L    + +CP C     S D L
Sbjct: 10  IPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDAL 66

Query: 266 KV 267
             
Sbjct: 67  IA 68

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

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 2/58 (3%)

Query: 211 DQDLQCAVCLEEF-VMGNEAKEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDLK 266
           +  ++C +C+E   +         C ++    C      +    CP CR   P D   
Sbjct: 9   EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV 66

>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 = 42.3 bits (99), Expect = 5e-05
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 184 LLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGEC 242
           L E       ++    E+V +  +  +  +L C +CL+             C H+F  +C
Sbjct: 27  LYELQRTPQEAITDGLEIVVSPRS--LHSELMCPICLDMLK---NTMTTKECLHRFCADC 81

Query: 243 IMPWLEL-QSSCPICRYQLPSDD 264
           I+  L      CP CR +L S  
Sbjct: 82  IITALRSGNKECPTCRKKLVSKR 104

>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 = 18/61 (29%), Positives = 25/61 (40%), Gaps = 9/61 (14%)

Query: 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ------SSCPICRYQLPSDDL 265
           +++ C +CLE      E     C H F   CI    E         +CP+CR   P  +L
Sbjct: 18  EEVTCPICLELLK---EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNL 74

Query: 266 K 266
           K
Sbjct: 75  K 75

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 12/61 (19%)

Query: 212 QDLQCAVCLEEF---VMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQLPSDDL 265
           + L+C +CLE     V         C H F   C++  L  +   S CP+C+  +    L
Sbjct: 20  KILECPICLELIKEPVS------TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL 73

Query: 266 K 266
           +
Sbjct: 74  Q 74

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 209 AIDQDLQCAVCLEEFVMGNEA-KEMPCKHKFHGECIMPWLELQS---SCPICR 257
           A+ + L+C +C+E F       K + C H    +C+   L        CP C 
Sbjct: 11  ALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

>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 = 38.4 bits (90), Expect = 2e-04
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 16/71 (22%)

Query: 206 PTVAIDQDLQCAVCLEEF---VMGNEAKEMPCKHKFHGECIMPWLELQ-------SSCPI 255
            +  + +++ C +CLE     +       + C H     CI    +         SSCP+
Sbjct: 5   SSGNVQEEVTCPICLELLTEPLS------LDCGHSLCRACITVSNKEAVTSMGGKSSCPV 58

Query: 256 CRYQLPSDDLK 266
           C      + L+
Sbjct: 59  CGISYSFEHLQ 69

>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 = 41.1 bits (95), Expect = 3e-04
 Identities = 12/67 (17%), Positives = 21/67 (31%), Gaps = 6/67 (8%)

Query: 205 LPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS--CPI--CRYQL 260
           L       +L C +  +            C H F  + I  +L+  ++  CP   C   +
Sbjct: 173 LQIEGGKIELTCPITCK--PYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV 230

Query: 261 PSDDLKV 267
              D   
Sbjct: 231 SMRDFVR 237

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 37.2 bits (86), Expect = 6e-04
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 8/52 (15%)

Query: 215 QCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLELQSS--CPICRYQ 259
            C +C  E    +     PC      H  H  C+  W++   +  C +C+Y+
Sbjct: 17  ICRICHCEGDDESPLI-TPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYE 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	347
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.59
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.46
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.46
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.44
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.4
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.4
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.31
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.31
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.31
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.3
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.29
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.29
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.25
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.24
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.24
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.23
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.22
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.22
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.21
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.21
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.21
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.2
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.2
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.18
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.18
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.17
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.17
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.16
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.12
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.12
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.11
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.11
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.09
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.09
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.03
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.03
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.02
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.01
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.0
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.0
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.99
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.99
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.99
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.98
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.98
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.94
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.93
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.92
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.92
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.87
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.84
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.81
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.8
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.8
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.76
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.74
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.71
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.7
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.65
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.56
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.48
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.44
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.44
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.44
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.44
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.35
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.34
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.18
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.79
3nw0_A	238	Non-structural maintenance of chromosomes element	97.41
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	93.58
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	91.4
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	90.94
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	86.79
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	85.16
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	84.06
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	82.95
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	81.53
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	80.75

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

Probab=99.59  E-value=7e-16  Score=121.94  Aligned_cols=72  Identities=38%  Similarity=0.942  Sum_probs=63.5

Q ss_pred             CCCCCcchHHHHHcCCcccccc-------cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          191 RYGSLPAQKEVVKALPTVAIDQ-------DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       191 ~~~~~p~~~~~i~~lp~~~~~~-------~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      .....+++++.+++||.+.+.+       +..|+||++.|..+..++.|||+|.||..||.+||..+.+||+||+.+..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            4567789999999999887643       45799999999887889999999999999999999999999999998865

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

Probab=99.46  E-value=1.5e-14  Score=109.82  Aligned_cols=52  Identities=33%  Similarity=0.896  Sum_probs=47.0

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +...|+||++.|..+..++.+||+|.||..||.+||..+.+||+||+.+...
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            3568999999998878889999999999999999999999999999988653

>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=6e-14  Score=107.03  Aligned_cols=58  Identities=40%  Similarity=1.085  Sum_probs=50.6

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCccc
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQ  268 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~  268 (347)
                      .+...|+||++.|.....++.++|+|.||..||.+|+..+.+||+||..+...+...+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            4467899999999877778889999999999999999999999999999987655443

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

Probab=99.44  E-value=3.1e-14  Score=101.34  Aligned_cols=51  Identities=47%  Similarity=1.079  Sum_probs=46.3

Q ss_pred             cccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ++...|+||++.|..++.++.++ |+|.||..||.+|+..+.+||+||+.+.
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            45678999999998878889998 9999999999999999999999999874

>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=99.40  E-value=1.1e-13  Score=103.04  Aligned_cols=52  Identities=33%  Similarity=0.932  Sum_probs=47.4

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      ....|+||++.|..+..++.++|+|.||..||.+|+..+.+||+||..+...
T Consensus        13 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           13 TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             CCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            4568999999998778899999999999999999999999999999998665

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

Probab=99.40  E-value=1.1e-13  Score=104.49  Aligned_cols=54  Identities=39%  Similarity=0.930  Sum_probs=48.1

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +.....|+||++.|.....++.++|+|.||..||.+|+..+.+||+||+.+...
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            344678999999998878888899999999999999999999999999998654

>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=7.3e-13  Score=93.99  Aligned_cols=49  Identities=29%  Similarity=0.649  Sum_probs=42.8

Q ss_pred             cccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ...|+||++.|..+ ..++.++|+|.||..||.+|+..+.+||+||+.+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            5 SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            46899999999543 34788899999999999999999999999999874

>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=99.31  E-value=1.5e-12  Score=106.37  Aligned_cols=52  Identities=21%  Similarity=0.633  Sum_probs=42.0

Q ss_pred             ccccchhhhhhhccCC---------------ceEEecCCCcccccchHHHH-----hcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGN---------------EAKEMPCKHKFHGECIMPWL-----ELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~---------------~~~~lpC~H~Fh~~Ci~~Wl-----~~~~~CP~CR~~l~~~  263 (347)
                      .+..|+||++.|....               .++.++|+|.||..||..||     ..+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4568999999996432               34478899999999999999     4567899999988544

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

Probab=99.31  E-value=1.1e-12  Score=98.70  Aligned_cols=55  Identities=20%  Similarity=0.533  Sum_probs=47.0

Q ss_pred             ccccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCCCCcc
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKV  267 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  267 (347)
                      +.+...|+||++.|   .+++.+ +|+|.||..||..|+..+..||+||..+...+...
T Consensus        12 ~~~~~~C~IC~~~~---~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   67 (72)
T 2djb_A           12 LTPYILCSICKGYL---IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLS   67 (72)
T ss_dssp             CCGGGSCTTTSSCC---SSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCC
T ss_pred             cCCCCCCCCCChHH---HCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccccc
Confidence            44567999999999   567776 99999999999999998999999999997765443

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

Probab=99.30  E-value=8.1e-13  Score=102.11  Aligned_cols=51  Identities=24%  Similarity=0.651  Sum_probs=40.3

Q ss_pred             cccchhhhhhhc-----------cCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          213 DLQCAVCLEEFV-----------MGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       213 ~~~C~ICl~~~~-----------~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +..|+||++.|.           .++.++.++ |+|.||..||.+||..+.+||+||+++...
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            345666666663           445566776 999999999999999999999999987543

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

Probab=99.29  E-value=5.5e-13  Score=99.50  Aligned_cols=55  Identities=22%  Similarity=0.648  Sum_probs=46.3

Q ss_pred             cccccchhhhhhhcc----CCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          211 DQDLQCAVCLEEFVM----GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~----~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      .++..|+||++.|..    +..++.++|+|.||..||.+|+..+.+||+||..+...+.
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   66 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhe
Confidence            456789999999953    2344889999999999999999999999999999876543

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

Probab=99.29  E-value=6.2e-13  Score=98.41  Aligned_cols=53  Identities=21%  Similarity=0.585  Sum_probs=44.6

Q ss_pred             ccccccchhhhhhhccC----CceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          210 IDQDLQCAVCLEEFVMG----NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      +.+...|+||++.|...    ..++.++|+|.||..||..|+..+.+||+||..+..
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            34567899999999542    334889999999999999999999999999998754

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

Probab=99.25  E-value=3.4e-12  Score=96.63  Aligned_cols=53  Identities=30%  Similarity=0.664  Sum_probs=45.0

Q ss_pred             cccccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcC--CCCCCCCcccCCCC
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQ--SSCPICRYQLPSDD  264 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~  264 (347)
                      .+.+...|+||++.|   .+++.++ |+|.||..||..|+..+  ..||+||..+...+
T Consensus        11 ~~~~~~~C~IC~~~~---~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           11 PIPDELLCLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CSCGGGSCSSSCCCC---TTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             cCCCCCCCcCCChHH---hCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            344567999999999   7788999 99999999999999765  68999999865544

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

Probab=99.24  E-value=1.4e-12  Score=95.09  Aligned_cols=53  Identities=23%  Similarity=0.657  Sum_probs=45.1

Q ss_pred             cccchhhhhhhcc----CCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          213 DLQCAVCLEEFVM----GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       213 ~~~C~ICl~~~~~----~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      ...|+||++.+..    +..++.++|+|.||..||.+|+..+.+||+||..+...+.
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   59 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   59 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCE
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccce
Confidence            4689999999953    2345889999999999999999999999999999876543

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

Probab=99.24  E-value=1.6e-12  Score=97.52  Aligned_cols=50  Identities=32%  Similarity=0.678  Sum_probs=44.9

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .+...|+||++.+   .+++.++|+|.||..||..|+..+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~---~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           13 LTVPECAICLQTC---VHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSCCBCSSSSSBC---SSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCCccCCccc---CCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            3456899999999   7789999999999999999999999999999998654

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

Probab=99.23  E-value=3.4e-12  Score=95.73  Aligned_cols=52  Identities=23%  Similarity=0.654  Sum_probs=44.9

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHh---cCCCCCCCCcccCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE---LQSSCPICRYQLPSDD  264 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---~~~~CP~CR~~l~~~~  264 (347)
                      +.+...|+||++.|   .+++.++|+|.||..||..|+.   ....||+||..+..++
T Consensus        17 ~~~~~~C~IC~~~~---~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           17 LQEEVICPICLDIL---QKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCBCTTTCSBC---SSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             CccCCEeccCCccc---CCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            44567999999999   6788999999999999999996   4558999999987654

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

Probab=99.22  E-value=4.3e-12  Score=96.64  Aligned_cols=53  Identities=19%  Similarity=0.480  Sum_probs=46.5

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDL  265 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~  265 (347)
                      +.+...|+||++.|   .+++.++|+|.||..||..|+.. +.+||+||..+...+.
T Consensus         5 ~~~~~~C~IC~~~~---~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l   58 (78)
T 1t1h_A            5 FPEYFRCPISLELM---KDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGL   58 (78)
T ss_dssp             CSSSSSCTTTSCCC---SSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCC
T ss_pred             CcccCCCCCccccc---cCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhC
Confidence            45567999999999   78999999999999999999986 7789999999876543

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

Probab=99.22  E-value=4.2e-12  Score=94.05  Aligned_cols=49  Identities=33%  Similarity=0.853  Sum_probs=42.6

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ....|+||++.+.  ..++.++|+|.||..||..|+..+.+||+||..+..
T Consensus         4 ~~~~C~IC~~~~~--~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCcccc--CCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            3568999999993  235889999999999999999999999999998864

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

Probab=99.21  E-value=2.5e-12  Score=108.96  Aligned_cols=50  Identities=40%  Similarity=0.929  Sum_probs=45.0

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .++..|+||++.|   .+++.+||+|.||..||..|+..+.+||+||.++...
T Consensus        51 ~~~~~C~iC~~~~---~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           51 ENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHHSBCTTTCSBC---SSEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cccCCCcccCccc---CCceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            3456899999999   7889999999999999999999999999999998654

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

Probab=99.21  E-value=3.9e-12  Score=93.95  Aligned_cols=52  Identities=21%  Similarity=0.612  Sum_probs=44.2

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCCCcccCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPSDD  264 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~  264 (347)
                      +.+...|+||++.+   .+++.++|+|.||..||..|+. ....||+||..+..++
T Consensus        12 ~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVL---CSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEE---SSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CCcCCCCCCCChHh---cCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            34567899999999   6677799999999999999994 5678999999987654

>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=99.21  E-value=3.9e-12  Score=103.55  Aligned_cols=50  Identities=26%  Similarity=0.528  Sum_probs=42.2

Q ss_pred             ccccchhhhhhhccC---------------CceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMG---------------NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~---------------~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ++..|+||++.|...               ..++.++|+|.||..||.+||..+.+||+||+.+.
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            356899999998643               12577899999999999999999999999999863

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

Probab=99.20  E-value=6.2e-12  Score=97.51  Aligned_cols=55  Identities=25%  Similarity=0.601  Sum_probs=46.0

Q ss_pred             cccccccchhhhhhhccCCc-eEEecCCCcccccchHHHHhcC---CCCCCCCcccCCC
Q 036250          209 AIDQDLQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQ---SSCPICRYQLPSD  263 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~  263 (347)
                      .+.+...|+||++.|..... ++.++|+|.||..||..|+..+   ..||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           11 ALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             hccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            44556799999999954333 8899999999999999999875   7899999988654

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

Probab=99.20  E-value=1.6e-12  Score=97.01  Aligned_cols=51  Identities=29%  Similarity=0.866  Sum_probs=44.7

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      .+...|+||++.+   .. +.++|+|.||..||.+|+..+.+||+||..+...+.
T Consensus        13 ~~~~~C~IC~~~~---~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           13 TDEEECCICMDGR---AD-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCSSSCCSC---CS-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             CCCCCCeeCCcCc---cC-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            4467899999999   44 889999999999999999999999999999876543

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

Probab=99.18  E-value=1.2e-11  Score=94.99  Aligned_cols=54  Identities=35%  Similarity=0.824  Sum_probs=46.3

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc------CCCCCCCCcccCCCCCc
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL------QSSCPICRYQLPSDDLK  266 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~~~~~  266 (347)
                      +.+...|+||++.|   .+++.++|+|.||..||..|+..      ...||+||..+...+..
T Consensus        16 ~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecw_A           16 IKEEVTCPICLELL---KEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLK   75 (85)
T ss_dssp             CCTTTSCTTTCSCC---SSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCE
T ss_pred             CccCCCCcCCChhh---CcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCC
Confidence            45567999999999   67789999999999999999987      66899999998765443

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

Probab=99.18  E-value=6e-12  Score=96.65  Aligned_cols=47  Identities=21%  Similarity=0.595  Sum_probs=43.3

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ....|+||++.|   ..++.++|+|.||..||..|+.....||+||..+.
T Consensus        14 ~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           14 IPFRCFICRQAF---QNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCSBCSSSCSBC---CSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCcCCCchh---cCeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            456899999999   77889999999999999999998899999999985

>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=99.17  E-value=3.5e-12  Score=102.30  Aligned_cols=53  Identities=32%  Similarity=0.725  Sum_probs=45.7

Q ss_pred             ccccccchhhhhhhccCCceEE-ecCCCcccccchHHHHhcC-CCCCCCCcccCCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKE-MPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDDL  265 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~~  265 (347)
                      +.+...|+||++.|   ..++. ++|+|.||..||..|+... ..||+||..+...+.
T Consensus        19 l~~~~~C~IC~~~~---~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l   73 (100)
T 3lrq_A           19 IAEVFRCFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL   73 (100)
T ss_dssp             HHHHTBCTTTCSBC---SSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCccCCccc---cCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHh
Confidence            34567999999999   67888 9999999999999999887 699999999865543

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

Probab=99.17  E-value=5.6e-12  Score=95.88  Aligned_cols=53  Identities=26%  Similarity=0.679  Sum_probs=45.5

Q ss_pred             cccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-------CCCCCCCCcccCCCC
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-------QSSCPICRYQLPSDD  264 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-------~~~CP~CR~~l~~~~  264 (347)
                      .+.+...|+||++.|   .+++.++|+|.||..||..|+..       ...||+||..+...+
T Consensus         8 ~~~~~~~C~IC~~~~---~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   67 (79)
T 2egp_A            8 NVQEEVTCPICLELL---TEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH   67 (79)
T ss_dssp             CCCCCCEETTTTEEC---SSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSG
T ss_pred             hcccCCCCcCCCccc---CCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhh
Confidence            345667999999999   66788999999999999999976       568999999987654

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

Probab=99.16  E-value=1.8e-11  Score=93.95  Aligned_cols=53  Identities=26%  Similarity=0.795  Sum_probs=45.8

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc------CCCCCCCCcccCCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL------QSSCPICRYQLPSDDL  265 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~~~~  265 (347)
                      +.+...|+||++.+   .+++.++|+|.||..||..|+..      ...||+||..+...+.
T Consensus        16 ~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecv_A           16 VKEEVTCPICLELL---TQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENI   74 (85)
T ss_dssp             CCCCCCCTTTCSCC---SSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSC
T ss_pred             ccCCCCCCCCCccc---CCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhc
Confidence            44567999999999   67788999999999999999977      7789999999876543

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

Probab=99.12  E-value=2e-11  Score=94.40  Aligned_cols=52  Identities=23%  Similarity=0.625  Sum_probs=43.2

Q ss_pred             ccccchhhhhhhccCCceEEecCC-----CcccccchHHHHhcC--CCCCCCCcccCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLELQ--SSCPICRYQLPSDD  264 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~  264 (347)
                      +...|.||+++|..++. .++||+     |.||..||.+||..+  .+||+||+.+....
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            35689999999976554 479996     999999999999765  48999999987653

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

Probab=99.12  E-value=1.1e-11  Score=98.72  Aligned_cols=50  Identities=32%  Similarity=0.782  Sum_probs=44.2

Q ss_pred             cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .+...|+||++.|   .+++.+ +|+|.||..||..|+..+..||+||..+...
T Consensus        20 ~~~~~C~IC~~~~---~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           20 DDLLRCGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HHHTBCTTTCSBC---SSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CCCCCcccCChhh---CCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChh
Confidence            3457899999999   678887 8999999999999999889999999988653

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

Probab=99.11  E-value=2.5e-11  Score=88.66  Aligned_cols=45  Identities=27%  Similarity=0.724  Sum_probs=39.2

Q ss_pred             cccccccchhhhhhhccCCceEEecCCCcccccchHHHHh---cCCCCCCC
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE---LQSSCPIC  256 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---~~~~CP~C  256 (347)
                      .+.+...|+||++.|   .+++.++|+|.||..||..|+.   ....||+|
T Consensus        16 ~~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDIL---QKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBC---SSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             hCccCCCCCcCCchh---CCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            345567999999999   6789999999999999999997   45589998

>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=99.11  E-value=2e-11  Score=101.24  Aligned_cols=49  Identities=31%  Similarity=0.690  Sum_probs=43.4

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC-CCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~  262 (347)
                      .+...|+||++.|   ..++.++|+|.||..||..|+.... .||+||..+..
T Consensus        50 ~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELV---FRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBC---SSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHH---cCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            3457899999999   7899999999999999999998554 89999999865

>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=2.9e-11  Score=97.87  Aligned_cols=51  Identities=33%  Similarity=0.772  Sum_probs=45.5

Q ss_pred             ccccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +.+...|+||++.|   .+++.+ +|+|.||..||..|+.....||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~---~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           12 LNPHLMCVLCGGYF---IDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HGGGTBCTTTSSBC---SSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCcCCCccCChHH---hCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            44567999999999   678887 9999999999999999889999999998764

>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=99.09  E-value=1e-11  Score=102.75  Aligned_cols=49  Identities=27%  Similarity=0.567  Sum_probs=0.5

Q ss_pred             cccchhhhhhhccC-------------C--ceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVMG-------------N--EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~~-------------~--~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      +..|+||++.|...             +  .++.++|+|.||..||.+||..+.+||+||+++.
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             C---------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            46899999999641             1  2334589999999999999999999999999864

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

Probab=99.09  E-value=3.5e-11  Score=94.35  Aligned_cols=49  Identities=29%  Similarity=0.674  Sum_probs=42.9

Q ss_pred             ccccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcC--CCCCCCCcccC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQ--SSCPICRYQLP  261 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~  261 (347)
                      +.+...|+||++.|   .+++.++ |+|.||..||..|+...  ..||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~---~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEEC---SSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhh---cCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            45568999999999   7889999 99999999999999654  58999999873

>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=4.4e-11  Score=96.91  Aligned_cols=51  Identities=29%  Similarity=0.768  Sum_probs=43.8

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC---CCCCCCcccCCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS---SCPICRYQLPSDDL  265 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~~~~~  265 (347)
                      +...|+||++.|   ..++.++|+|.||..||..|+..+.   .||+||..+...+.
T Consensus        20 ~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   73 (112)
T 1jm7_A           20 KILECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (112)
T ss_dssp             HHTSCSSSCCCC---SSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CCCCCcccChhh---cCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhc
Confidence            456899999999   6778899999999999999998654   89999999876543

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

Probab=99.03  E-value=5e-11  Score=98.74  Aligned_cols=55  Identities=22%  Similarity=0.649  Sum_probs=46.5

Q ss_pred             ccccchhhhhhhcc----CCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          212 QDLQCAVCLEEFVM----GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       212 ~~~~C~ICl~~~~~----~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      +...|+||++.|..    +..++.++|+|.||..||..||..+.+||+||+.+......
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            45789999999943    23348999999999999999999999999999999776543

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

Probab=99.03  E-value=4.9e-11  Score=85.26  Aligned_cols=44  Identities=36%  Similarity=0.935  Sum_probs=37.6

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHh---cCCCCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE---LQSSCPIC  256 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---~~~~CP~C  256 (347)
                      +.+...|+||++.+   .+++.++|+|.||..||..|+.   ....||+|
T Consensus        12 ~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYL---KEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBC---SSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCccc---CccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            34567999999999   6678899999999999999954   56789998

>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=99.02  E-value=7.8e-11  Score=101.43  Aligned_cols=49  Identities=29%  Similarity=0.631  Sum_probs=43.9

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC-CCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (347)
                      +...|+||++.|   .+++.++|+|.||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~---~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELV---YQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBC---SSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhh---cCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            457899999999   7889999999999999999998654 899999998765

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

Probab=99.01  E-value=1e-10  Score=85.98  Aligned_cols=53  Identities=19%  Similarity=0.430  Sum_probs=41.7

Q ss_pred             cccchhhhh-hhccCCc-eEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCCC
Q 036250          213 DLQCAVCLE-EFVMGNE-AKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDL  265 (347)
Q Consensus       213 ~~~C~ICl~-~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~  265 (347)
                      +..|+||++ .+..... ++.++|+|.||..||..|+.. ...||+||..+...+.
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            468999999 7754322 256799999999999999764 4679999999876654

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

Probab=99.00  E-value=8.9e-11  Score=91.51  Aligned_cols=52  Identities=12%  Similarity=0.135  Sum_probs=46.6

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      +.+...|+||++.|   .+++.++|||.|+..||..||..+.+||+|+..+...+
T Consensus        11 ~p~~~~CpI~~~~m---~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   62 (85)
T 2kr4_A           11 APDEFRDPLMDTLM---TDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESM   62 (85)
T ss_dssp             CCTTTBCTTTCSBC---SSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CchheECcccCchh---cCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHh
Confidence            34567999999999   88999999999999999999998899999999886553

>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=1.5e-10  Score=93.14  Aligned_cols=52  Identities=13%  Similarity=0.170  Sum_probs=47.1

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      .+...|+||++.|   .+++.++|||.|+..||..||..+.+||+||.++...++
T Consensus        27 p~~~~CpI~~~~m---~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L   78 (100)
T 2kre_A           27 PDEFRDPLMDTLM---TDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESML   78 (100)
T ss_dssp             STTTBCTTTCSBC---SSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSS
T ss_pred             cHhhCCcCccCcc---cCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhc
Confidence            4567999999999   899999999999999999999988999999999976544

>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=8.7e-11  Score=102.10  Aligned_cols=49  Identities=33%  Similarity=0.832  Sum_probs=42.8

Q ss_pred             cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhc-CCCCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLEL-QSSCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~  262 (347)
                      .+...|+||++.|   ..++.+ +|+|.||..||..||.. +..||+||..+..
T Consensus        52 ~~~~~C~IC~~~~---~~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDML---KNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBC---SSEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHh---hCcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            3456899999999   667777 89999999999999987 7789999999854

>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=98.99  E-value=4.3e-11  Score=98.02  Aligned_cols=52  Identities=33%  Similarity=0.734  Sum_probs=45.2

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDD  264 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (347)
                      +.+...|+||++.|   .+++.++|+|.||..||..|+.. ...||+||..+...+
T Consensus        20 ~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           20 FVKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHHHTBCTTTCSBC---SSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             ccCCCCCCCCCcHh---cCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            34457899999999   77889999999999999999987 678999999987654

>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=1.6e-10  Score=92.54  Aligned_cols=53  Identities=13%  Similarity=0.140  Sum_probs=47.4

Q ss_pred             ccccccchhhhhhhccCCceEEecCC-CcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCK-HKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      +.+...|+||++.|   .+++.++|+ |.|+..||..||..+.+||+||.+|...++
T Consensus        19 ~p~~~~CpI~~~~m---~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L   72 (98)
T 1wgm_A           19 ACDEFLDPIMSTLM---CDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             CCTTTBCTTTCSBC---SSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             CcHhcCCcCccccc---cCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhc
Confidence            34567999999999   899999999 999999999999988899999999976544

>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=8.7e-11  Score=96.70  Aligned_cols=51  Identities=27%  Similarity=0.704  Sum_probs=44.7

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC-CCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (347)
                      +.+...|+||++.+   ..++.++|+|.||..||..|+.... +||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           15 LESKYECPICLMAL---REAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCGGGBCTTTCSBC---SSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcCChhh---cCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            34567999999999   7789999999999999999997765 999999998654

>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=98.98  E-value=4.7e-11  Score=97.63  Aligned_cols=49  Identities=31%  Similarity=0.752  Sum_probs=43.2

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~  262 (347)
                      .++..|+||++.|   .+++.++|+|.||..||..|+.. ...||+||..+..
T Consensus        13 ~~~~~C~iC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEIL---VEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBC---SSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCccCCccc---CceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3457899999999   77899999999999999999976 6689999998853

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

Probab=98.94  E-value=1.1e-10  Score=96.56  Aligned_cols=53  Identities=23%  Similarity=0.669  Sum_probs=45.0

Q ss_pred             ccccchhhhhhhcc----CCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          212 QDLQCAVCLEEFVM----GNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       212 ~~~~C~ICl~~~~~----~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      +...|+||++.|..    +..++.++|+|.||..||.+||..+.+||+||..+..++
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            35689999999953    233488899999999999999999999999999987654

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

Probab=98.93  E-value=2.7e-10  Score=86.73  Aligned_cols=50  Identities=20%  Similarity=0.563  Sum_probs=41.2

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcC--CCCCCCCcccCCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ--SSCPICRYQLPSDD  264 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~  264 (347)
                      ...|+||++.|..+.  +-..|+|.||..||.+||+.+  .+||+||.++..+.
T Consensus        15 i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           15 VKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            468999999997543  333799999999999999877  78999999876543

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

Probab=98.92  E-value=1.7e-10  Score=82.71  Aligned_cols=46  Identities=33%  Similarity=0.689  Sum_probs=39.9

Q ss_pred             ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +...|+||++.|   .+++.|+|+|.||..||..|   ...||+||+.+...
T Consensus         5 ~~~~C~IC~~~~---~~p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            5 QFLRCQQCQAEA---KCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSC---BCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             cCCCceEeCCcc---CCeEEcCCCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            457899999999   67889999999999999884   56899999988654

>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=98.92  E-value=2.2e-10  Score=94.16  Aligned_cols=49  Identities=24%  Similarity=0.638  Sum_probs=42.9

Q ss_pred             cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSDD  264 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~  264 (347)
                      .+...|+||++.|   ..++.+ +|+|.||..||..|+.  ..||+||..+...+
T Consensus        20 ~~~~~C~IC~~~~---~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (117)
T 1jm7_B           20 EKLLRCSRCTNIL---REPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (117)
T ss_dssp             HHTTSCSSSCSCC---SSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hhCCCCCCCChHh---hCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccc
Confidence            4567999999999   778888 9999999999999998  78999999985543

>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=98.87  E-value=3.4e-10  Score=96.47  Aligned_cols=51  Identities=16%  Similarity=0.481  Sum_probs=44.2

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC-CCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~  263 (347)
                      +.+...|+||++.|   .+++.++|+|.||..||..|+.... .||+||.++..+
T Consensus        28 l~~~~~C~IC~~~~---~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           28 LEAKYLCSACRNVL---RRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CCGGGBCTTTCSBC---SSEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             CCcCcCCCCCChhh---cCcEECCCCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            45567999999999   7889999999999999999998665 899999987543

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

Probab=98.84  E-value=1.4e-09  Score=83.54  Aligned_cols=56  Identities=21%  Similarity=0.549  Sum_probs=43.4

Q ss_pred             ccccccchhhhhhhccCCceEEec--CCCcccccchHHHHhc-CCCCCCCCcccCCCCCc
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMP--CKHKFHGECIMPWLEL-QSSCPICRYQLPSDDLK  266 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~  266 (347)
                      +.++..|+||++.+.. .+++.+|  |||.||..||..|+.. ...||+||+.+......
T Consensus         8 ~~~~~~CpICle~~~~-~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEI-DDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCCBCTTTCCBCCT-TTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             cccCCcCCccCccCcc-ccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            4566799999998853 2344555  9999999999999853 56899999999776543

>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=98.81  E-value=1.3e-09  Score=80.31  Aligned_cols=47  Identities=17%  Similarity=0.354  Sum_probs=41.4

Q ss_pred             ccccchhhhhhhccCCceEEe--cCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEM--PCKHK-FHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~l--pC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ++..|.||++.+   .+++.+  ||+|. ||..|+..|+..+..||+||..+.
T Consensus         7 ~~~~C~IC~~~~---~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRP---KNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSC---SCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCC---CCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            456899999998   667766  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=98.80  E-value=1e-09  Score=101.85  Aligned_cols=53  Identities=19%  Similarity=0.201  Sum_probs=45.4

Q ss_pred             cccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-CCCCCCCcccCCCC
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDD  264 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (347)
                      .+.....|+||++.|   .+++.+||||.||..||..||... .+||+||.++...+
T Consensus       204 ~~~~~~~c~i~~~~~---~dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          204 DIPDYLCGKISFELM---REPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             CCCSTTBCTTTCSBC---SSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CCCcccCCcCcCCHh---cCCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhc
Confidence            344567999999999   899999999999999999999764 45999999986543

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

Probab=98.80  E-value=7.9e-10  Score=83.71  Aligned_cols=45  Identities=20%  Similarity=0.567  Sum_probs=40.0

Q ss_pred             cccccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      .++..|.||++.+   .+++.+||+|. ||..|+..|    ..||+||..+..
T Consensus        22 ~~~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           22 QEEKLCKICMDRN---IAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHHTBCTTTSSSB---CCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             ccCCCCCCCCCCC---CCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            3456899999999   78999999999 999999998    789999998854

>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=98.76  E-value=2.5e-09  Score=104.98  Aligned_cols=47  Identities=30%  Similarity=0.793  Sum_probs=43.0

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCCCcccCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPSD  263 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~  263 (347)
                      ..|+||++.+   .+++.+||+|.||..||..|+. .+.+||+||..+...
T Consensus       333 ~~C~ICle~~---~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          333 QLCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SBCTTTSSSB---CCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCccCcCC---CCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            6899999999   7899999999999999999998 678999999988654

>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=98.74  E-value=1.5e-09  Score=85.96  Aligned_cols=51  Identities=24%  Similarity=0.608  Sum_probs=42.8

Q ss_pred             ccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcC------CCCCC--CCcc-cCCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQ------SSCPI--CRYQ-LPSDDL  265 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~------~~CP~--CR~~-l~~~~~  265 (347)
                      +.+.|+||++.|   .+++.++ |+|.|+..||..||..+      .+||+  |+.. +...++
T Consensus         6 ~~~~CPI~~~~~---~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L   66 (94)
T 2yu4_A            6 SGFTCPITKEEM---KKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDL   66 (94)
T ss_dssp             SCCBCTTTCSBC---SSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGE
T ss_pred             cEeECcCcCchh---cCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhC
Confidence            457899999999   8899997 99999999999999754      48999  9876 655443

>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=98.71  E-value=4.1e-09  Score=77.39  Aligned_cols=46  Identities=20%  Similarity=0.428  Sum_probs=40.4

Q ss_pred             cccchhhhhhhccCCceEEe--cCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVMGNEAKEM--PCKHK-FHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~l--pC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      ...|.||++.+   .+++.+  ||+|. ||..|+..|+.....||+||.++.
T Consensus         7 ~~~C~IC~~~~---~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRP---RDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSB---SCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCCCcccCCcC---CCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            45899999988   666666  99999 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=98.70  E-value=3e-09  Score=92.70  Aligned_cols=51  Identities=27%  Similarity=0.700  Sum_probs=44.5

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-CCCCCCCcccCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSD  263 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~  263 (347)
                      +.+.+.|+||++.|   ..++.++|+|.||..||..|+... .+||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~---~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           15 LESKYECPICLMAL---REAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCGGGBCTTTCSBC---SSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCChhh---cCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            44567999999999   778999999999999999999764 4899999988664

>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=9.6e-09  Score=90.86  Aligned_cols=53  Identities=21%  Similarity=0.206  Sum_probs=45.6

Q ss_pred             cccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-CCCCCCCcccCCCC
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDD  264 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (347)
                      .+.+...|+||++.|   .+|+.+||||.|+..||..||..+ .+||+|+.++...+
T Consensus       102 ~ip~~f~CPI~~elm---~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~  155 (179)
T 2f42_A          102 EIPDYLCGKISFELM---REPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQ  155 (179)
T ss_dssp             CCCGGGBCTTTCSBC---SSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCcHhhcccCccccC---CCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhh
Confidence            344567999999999   889999999999999999999764 46999999886653

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

Probab=98.56  E-value=8.1e-09  Score=78.16  Aligned_cols=45  Identities=20%  Similarity=0.572  Sum_probs=38.3

Q ss_pred             ccccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +...|+||++.+   .+++.+||+|. ||..|+..    ...||+||..+...
T Consensus        24 ~~~~C~IC~~~~---~~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           24 EEKLCKICMDRN---IAIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHHSCSSSCSSC---CCBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCCcCCCCC---CCEEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            345899999999   77889999999 99999954    37899999988653

>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=98.48  E-value=1.9e-08  Score=77.24  Aligned_cols=45  Identities=31%  Similarity=0.694  Sum_probs=39.2

Q ss_pred             ccccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +...|.||++.+   .+++.+||+|. ||..|+..|    ..||+||..+...
T Consensus        17 ~~~~C~IC~~~~---~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           17 EAMLCMVCCEEE---INSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHTBCTTTSSSB---CCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCEeEEeCccc---CcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            346899999998   78999999999 999999887    3899999988654

>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=98.44  E-value=4.2e-08  Score=95.18  Aligned_cols=45  Identities=29%  Similarity=0.697  Sum_probs=40.2

Q ss_pred             cccccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      .++..|+||++.+   ..++.+||+|. ||..|+..|    ..||+||..+..
T Consensus       293 ~~~~~C~IC~~~~---~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKE---VSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSB---CCEEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcC---CceEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            4567999999999   78999999999 999999988    689999998854

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

Probab=98.44  E-value=2.8e-08  Score=95.55  Aligned_cols=52  Identities=25%  Similarity=0.742  Sum_probs=39.7

Q ss_pred             ccccchhhhhhhcc-CCceE----EecCCCcccccchHHHHhcC-----------CCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVM-GNEAK----EMPCKHKFHGECIMPWLELQ-----------SSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~-~~~~~----~lpC~H~Fh~~Ci~~Wl~~~-----------~~CP~CR~~l~~~  263 (347)
                      ...+|+||++.+.. +.-+.    ..+|+|.||..||.+||...           ++||+||+++...
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            34589999999976 32221    23699999999999999652           4599999988654

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

Probab=98.44  E-value=6.3e-08  Score=72.18  Aligned_cols=45  Identities=24%  Similarity=0.651  Sum_probs=38.7

Q ss_pred             ccccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      +...|.||++.+   ..++.+||+|. ||..|+..    ...||+||..+...
T Consensus        14 ~~~~C~IC~~~~---~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           14 NSKDCVVCQNGT---VNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CSSCCSSSSSSC---CCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCcCcCC---CCEEEECCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            356899999998   78899999999 99999973    57899999988653

>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=98.44  E-value=4.5e-08  Score=71.55  Aligned_cols=50  Identities=12%  Similarity=0.193  Sum_probs=45.0

Q ss_pred             ccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          214 LQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      ..|+||++.+   .+++.+ +|||+|...||.+||..+.+||+++.+|..+++.
T Consensus         4 ~~CpIs~~~m---~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Li   54 (61)
T 2bay_A            4 MLCAISGKVP---RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   54 (61)
T ss_dssp             CCCTTTCSCC---SSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             EEecCCCCCC---CCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcE
Confidence            5799999999   788999 8999999999999998888999999999776544

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.35  E-value=1.3e-07  Score=68.87  Aligned_cols=47  Identities=26%  Similarity=0.682  Sum_probs=36.9

Q ss_pred             ccccchhhhhhhccCCceEEecCC--C---cccccchHHHHhc--CCCCCCCCcccC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCK--H---KFHGECIMPWLEL--QSSCPICRYQLP  261 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~--~~~CP~CR~~l~  261 (347)
                      +...|.||++..   ....++||.  |   .||..||.+|+..  +.+||+|++.+.
T Consensus         5 ~~~~CrIC~~~~---~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEEL---GNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEEC---SCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCC---CCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            356899999974   333478954  4   9999999999964  568999999874

>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=98.34  E-value=7.8e-08  Score=89.48  Aligned_cols=53  Identities=21%  Similarity=0.498  Sum_probs=44.4

Q ss_pred             cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcC--CCCCC--CCcccCCCCCc
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQ--SSCPI--CRYQLPSDDLK  266 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~--~~CP~--CR~~l~~~~~~  266 (347)
                      .....|+||++.|   .+++.. .|||.||..||..|+..+  ..||+  |++.+...++.
T Consensus       179 ~~el~CPIcl~~f---~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~  236 (267)
T 3htk_C          179 KIELTCPITCKPY---EAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFV  236 (267)
T ss_dssp             BCCSBCTTTSSBC---SSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEE
T ss_pred             ceeeECcCccCcc---cCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCC
Confidence            3467999999999   788875 899999999999999764  46999  99988765543

>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=98.18  E-value=2.8e-07  Score=72.52  Aligned_cols=50  Identities=30%  Similarity=0.636  Sum_probs=37.7

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcC--------CCCCC--CCcc--cCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ--------SSCPI--CRYQ--LPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--------~~CP~--CR~~--l~~  262 (347)
                      ..+|+||++.+.........+|+|.||..||..++..+        -.||.  |+..  +..
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            46899999998543333334799999999999999631        26999  9987  543

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.79  E-value=6.7e-06  Score=65.41  Aligned_cols=47  Identities=23%  Similarity=0.471  Sum_probs=38.6

Q ss_pred             cchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCC
Q 036250          215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSD  263 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~  263 (347)
                      .|.+|--.+.  .-.+.+||+|+||.+|+..|.++ .++||.|+.++..-
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            4788877774  45788999999999999999854 57899999988543

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

Probab=97.41  E-value=4.1e-05  Score=70.47  Aligned_cols=51  Identities=22%  Similarity=0.591  Sum_probs=40.2

Q ss_pred             cccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCC--CCCCCCcccCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQS--SCPICRYQLPSDDLK  266 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~~~~  266 (347)
                      ...|.||.+.+..|   .+-+ |+|.||..|+..|+..+.  .||.|+...+...+.
T Consensus       180 i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~~  233 (238)
T 3nw0_A          180 VKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK  233 (238)
T ss_dssp             CCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCCC
T ss_pred             CCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCC
Confidence            35899999999654   3333 999999999999997654  899999987665433

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=91.40  E-value=0.12  Score=41.91  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=27.6

Q ss_pred             CCcEeeecCCceeeecCCCCc-cCCCCCCCceEecCC
Q 036250            6 VGSYWCYICSRMVNPRMEAGI-KCPFCETGFVEQMSS   41 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~-~CP~C~sGFiEE~~~   41 (347)
                      ...|||..|...+..... .. +||.|++..++-+..
T Consensus        71 p~~~~C~~CG~~~e~~~~-~~~~CP~Cgs~~~~i~~G  106 (119)
T 2kdx_A           71 KVELECKDCSHVFKPNAL-DYGVCEKCHSKNVIITQG  106 (119)
T ss_dssp             CCEEECSSSSCEECSCCS-TTCCCSSSSSCCCEEEES
T ss_pred             cceEEcCCCCCEEeCCCC-CCCcCccccCCCcEEecC
Confidence            678999999999875433 57 899999997775543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=90.94  E-value=0.053  Score=42.26  Aligned_cols=32  Identities=19%  Similarity=0.577  Sum_probs=25.2

Q ss_pred             cccchhhhhhhccCCceEE--ecCCCcccccchHHH
Q 036250          213 DLQCAVCLEEFVMGNEAKE--MPCKHKFHGECIMPW  246 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~--lpC~H~Fh~~Ci~~W  246 (347)
                      +..|.||++.+.  ..++.  +.|+|.||..|+..+
T Consensus         3 e~~C~~C~~~~~--~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPA--QDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSC--CBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCC--CCceEECCcCChHHhHHHCHHH
Confidence            468999997642  34455  899999999999983

>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=86.79  E-value=0.22  Score=53.80  Aligned_cols=51  Identities=16%  Similarity=0.230  Sum_probs=45.0

Q ss_pred             ccccchhhhhhhccCCceEEecCC-CcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCK-HKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      +...|+|-++.+   .+|+.+|.| +.|-..+|.+||..+.+||+=|.+|...+.
T Consensus       890 ~~F~cPIs~~lM---~DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~l  941 (968)
T 3m62_A          890 DEFLDPLMYTIM---KDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDV  941 (968)
T ss_dssp             GGGBCTTTCSBC---SSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGC
T ss_pred             HHhCCcchhhHH---hCCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccc
Confidence            356899999999   899999997 589999999999989999999999976543

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=85.16  E-value=0.31  Score=35.52  Aligned_cols=43  Identities=23%  Similarity=0.549  Sum_probs=30.7

Q ss_pred             cccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCC----CCCCCCcc
Q 036250          213 DLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQS----SCPICRYQ  259 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~  259 (347)
                      ...|.||.+.    .++..- .|...||..|+.+.|....    .||.|...
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            3579999753    333222 3899999999999886543    59999754

>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=84.06  E-value=0.4  Score=36.72  Aligned_cols=34  Identities=26%  Similarity=0.560  Sum_probs=24.0

Q ss_pred             cccccccchhhhhhhccCCceEEec---CCCcccccchHHH
Q 036250          209 AIDQDLQCAVCLEEFVMGNEAKEMP---CKHKFHGECIMPW  246 (347)
Q Consensus       209 ~~~~~~~C~ICl~~~~~~~~~~~lp---C~H~Fh~~Ci~~W  246 (347)
                      .+..+..|.||--.=    .-.++|   |+-+||..|+.+.
T Consensus        11 ~~~~D~~C~VC~~~t----~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           11 PVVNDEMCDVCEVWT----AESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTTCCCC----SSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCCcccCcccccc----ccceeccccccccccHhhcccc
Confidence            344567899996332    223455   8899999999986

>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=82.95  E-value=0.71  Score=38.53  Aligned_cols=35  Identities=17%  Similarity=0.348  Sum_probs=26.0

Q ss_pred             CCcEeeecCCceeeecC-----------CC---------CccCCCCCCCceEecC
Q 036250            6 VGSYWCYICSRMVNPRM-----------EA---------GIKCPFCETGFVEQMS   40 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~-----------~~---------e~~CP~C~sGFiEE~~   40 (347)
                      ..++||..|........           ..         ..+||.|++--++-+.
T Consensus        68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i~~  122 (139)
T 3a43_A           68 EAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVK  122 (139)
T ss_dssp             CCEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEEEE
T ss_pred             CCcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEEec
Confidence            57899999999886543           11         4779999998776433

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=81.53  E-value=0.67  Score=33.57  Aligned_cols=31  Identities=19%  Similarity=0.386  Sum_probs=25.8

Q ss_pred             CCcEeeecCCceeeecCCCCccCCCCCCCce
Q 036250            6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFV   36 (347)
Q Consensus         6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFi   36 (347)
                      ...|-|-.|..+|.....+.+.||.|+.-.+
T Consensus        19 ~v~Y~C~~Cg~~~~l~~~~~iRC~~CG~RIL   49 (63)
T 3h0g_L           19 TMIYLCADCGARNTIQAKEVIRCRECGHRVM   49 (63)
T ss_dssp             CCCCBCSSSCCBCCCCSSSCCCCSSSCCCCC
T ss_pred             CeEEECCCCCCeeecCCCCceECCCCCcEEE
Confidence            3569999999999877766799999997554

>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=80.75  E-value=0.65  Score=31.55  Aligned_cols=32  Identities=22%  Similarity=0.720  Sum_probs=22.2

Q ss_pred             CcEeeecCCceeeec----CCCCccCCCCCCCceEec
Q 036250            7 GSYWCYICSRMVNPR----MEAGIKCPFCETGFVEQM   39 (347)
Q Consensus         7 ~rywCh~C~~~V~p~----~~~e~~CP~C~sGFiEE~   39 (347)
                      ..|-|-.|-++++-.    ++ +++||.|+---|.-+
T Consensus         2 ~iY~C~rCg~~fs~~el~~lP-~IrCpyCGyrii~Kv   37 (48)
T 4ayb_P            2 AVYRCGKCWKTFTDEQLKVLP-GVRCPYCGYKIIFMV   37 (48)
T ss_dssp             ---CCCCTTTTCCCCCSCCCS-SSCCTTTCCSCEECC
T ss_pred             cEEEeeccCCCccHHHHhhCC-CcccCccCcEEEEEe
Confidence            468999999998532    35 799999987655544

---

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	347
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-19
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	4e-15
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	7e-13
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-12
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	6e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-11
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	5e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	5e-11
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	6e-10
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	8e-10
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	6e-09
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	6e-07
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-06
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	7e-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 = 78.8 bits (194), Expect = 1e-19
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 209 AIDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQL 260
           A+D  ++CAVCL E   G EA+ +P C H FH EC+  WL   S+CP+CR  +
Sbjct: 1   AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 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 = 66.9 bits (163), Expect = 4e-15
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKVQGNGSGN 274
           +C +CLE+    N +  +PC H F   CI  W+    +CP+C+  + S    ++ +    
Sbjct: 7   RCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSEFG 64

Query: 275 RE 276
            +
Sbjct: 65  DQ 66

>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 = 60.9 bits (147), Expect = 7e-13
 Identities = 14/59 (23%), Positives = 19/59 (32%), Gaps = 3/59 (5%)

Query: 213 DLQCAVCLEEFVMGNEAKEM--PCKHKFHGECIMPWLELQS-SCPICRYQLPSDDLKVQ 268
           D  C  C          K M   C H     C+       + +CP C   L   + +VQ
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ 61

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 4/56 (7%)

Query: 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS-CPICRYQLPSDDL 265
                C +C E      + K  PC H     C+  W E +   CP CR ++   + 
Sbjct: 21  STFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP 73

>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 = 58.0 bits (140), Expect = 6e-12
 Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 6/52 (11%)

Query: 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD 263
           Q L+C  C  E       K +PC H     C+         CPIC+   P  
Sbjct: 5   QFLRCQQCQAEA---KCPKLLPCLHTLCSGCLEAS---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 = 58.2 bits (140), Expect = 1e-11
 Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 15/57 (26%)

Query: 216 CAVCLEEFV---------------MGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257
           CA+C    +                        C H FH  CI  WL+ +  CP+  
Sbjct: 24  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>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 = 57.0 bits (137), Expect = 5e-11
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 6/61 (9%)

Query: 209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS---SCPICRYQLPSDDL 265
           A+ + L+C +CLE      E     C H F   C++  L  +     CP+C+  +    L
Sbjct: 17  AMQKILECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL 73

Query: 266 K 266
           +
Sbjct: 74  Q 74

>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 = 55.1 bits (132), Expect = 5e-11
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 214 LQCAVCLEEFVMGNEA-KEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSD 263
           ++C +C+E   + +       C ++    C       ++  CP CR   P D
Sbjct: 1   VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 53.6 bits (128), Expect = 6e-10
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 9/80 (11%)

Query: 188 DPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWL 247
           +P+  G+    +  +  L     ++ L+C+ C              C+H F   C+   +
Sbjct: 2   EPDGRGAWAHSRAALDRL-----EKLLRCSRCTNILREPV--CLGGCEHIFCSNCVSDCI 54

Query: 248 ELQSSCPICRYQLPSDDLKV 267
                CP+C       DLK+
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 = 52.6 bits (126), Expect = 8e-10
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS-CPICRYQLPSDDLK 266
             + + C +C        +  E  CKH F   CI+  L++  S CP CRY     DL+
Sbjct: 20  FVKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 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 = 49.5 bits (117), Expect = 6e-09
 Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 4/53 (7%)

Query: 211 DQDLQCAVCLEEFVMGNEAKEMP--CKHKFHGECIMPWLELQ--SSCPICRYQ 259
           +    C +C EE                  H  C+  WL +   ++C IC   
Sbjct: 4   EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 45.4 bits (106), Expect = 6e-07
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 21/86 (24%)

Query: 193 GSLPAQKEVV-KALPTVAIDQDLQCAVCLEEFVMGNEAKE---------------MPCKH 236
           GS    ++V+ K    + +  +  C +C+E+  + +   +                 C H
Sbjct: 4   GSSGEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSH 63

Query: 237 KFHGECIMPWLELQS-----SCPICR 257
            FH  C++      +      CP C+
Sbjct: 64  AFHLLCLLAMYCNGNKDGSLQCPSCK 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 = 43.2 bits (101), Expect = 1e-06
 Identities = 7/52 (13%), Positives = 19/52 (36%), Gaps = 2/52 (3%)

Query: 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL 265
           + CA+  +  V          +  F    +  +++   + PI    L  +++
Sbjct: 1   MLCAISGK--VPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI 50

>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 = 42.8 bits (100), Expect = 3e-06
 Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 8/56 (14%)

Query: 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS--------SCPICRY 258
                C +CL E+ +        C+  F   C+  ++EL          SCP    
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC 58

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 38.5 bits (89), Expect = 7e-05
 Identities = 10/58 (17%), Positives = 19/58 (32%), Gaps = 4/58 (6%)

Query: 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDLK 266
             +  +C + LE      +   +     +    I  WL+    +CP  +  L    L 
Sbjct: 5   FPEYFRCPISLELM---KDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLT 59

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	347
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.56
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.38
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.29
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.28
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.27
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.24
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.23
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.22
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	99.09
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	98.87
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.78
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.03
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	85.32
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	84.97
d2dkta1	74	RING finger and CHY zinc finger domain-containing	82.35

>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=99.56  E-value=3.7e-16  Score=110.94  Aligned_cols=51  Identities=47%  Similarity=1.079  Sum_probs=46.4

Q ss_pred             cccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      +++.+|+||+++|..++.++.++ |+|.||..||.+||+.+.+||+||++|.
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            45678999999999888888886 9999999999999999999999999874

>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=99.38  E-value=6e-14  Score=103.39  Aligned_cols=48  Identities=33%  Similarity=0.881  Sum_probs=41.9

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS  262 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~  262 (347)
                      ..+|+||++.|.  +.++.++|+|.||..||.+||+.+.+||+||+++..
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            357999999994  346778999999999999999999999999998753

>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=2.3e-13  Score=95.03  Aligned_cols=49  Identities=20%  Similarity=0.502  Sum_probs=40.6

Q ss_pred             ccchhhhhhhccCCc-eEEecCCCcccccchHHHHhcC-CCCCCCCcccCC
Q 036250          214 LQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPS  262 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~  262 (347)
                      ++|+||+++|..+.. ++.++|+|.||..||.+|+... ..||+||+++..
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            479999999965543 4566899999999999999864 469999998865

>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=99.28  E-value=1.8e-12  Score=104.33  Aligned_cols=68  Identities=18%  Similarity=0.509  Sum_probs=46.9

Q ss_pred             cchHHHHHcC-CcccccccccchhhhhhhccC---------------CceEEecCCCcccccchHHHHhcC-----CCCC
Q 036250          196 PAQKEVVKAL-PTVAIDQDLQCAVCLEEFVMG---------------NEAKEMPCKHKFHGECIMPWLELQ-----SSCP  254 (347)
Q Consensus       196 p~~~~~i~~l-p~~~~~~~~~C~ICl~~~~~~---------------~~~~~lpC~H~Fh~~Ci~~Wl~~~-----~~CP  254 (347)
                      ...++.++++ ..+....+..|+||++.|...               ..+.+++|+|+||..||..||...     .+||
T Consensus         7 ~~pe~v~~~~~e~~~~~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP   86 (114)
T d1v87a_           7 GEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP   86 (114)
T ss_dssp             CCHHHHHHHHEEECSSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCT
T ss_pred             CCCHHHHHHHHHHhcccccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccc
Confidence            3344444442 222333456899999998531               235678899999999999999753     3799


Q ss_pred             CCCcccCCC
Q 036250          255 ICRYQLPSD  263 (347)
Q Consensus       255 ~CR~~l~~~  263 (347)
                      +||..+..+
T Consensus        87 ~CR~~~~~~   95 (114)
T d1v87a_          87 SCKTIYGEK   95 (114)
T ss_dssp             TTCCBSSSC
T ss_pred             cccchhccC
Confidence            999877544

>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=99.27  E-value=8e-13  Score=100.15  Aligned_cols=48  Identities=29%  Similarity=0.801  Sum_probs=42.6

Q ss_pred             ccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDD  264 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (347)
                      ..|+||++.+   .+++.+||+|.||..||..||.. +++||+||..|...+
T Consensus        24 ~~C~IC~~~~---~~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          24 QLCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TBCTTTSSSB---CCEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCccCCCcC---CCeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            4699999999   78999999999999999999974 578999999997654

>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=99.24  E-value=1.3e-12  Score=95.30  Aligned_cols=54  Identities=19%  Similarity=0.402  Sum_probs=42.5

Q ss_pred             ccccchhhhhhhccCC--ceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCCC
Q 036250          212 QDLQCAVCLEEFVMGN--EAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDL  265 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~--~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~  265 (347)
                      ++..|+||++.+....  ....++|+|.||..||..||.. ...||+||+.|...+.
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~   58 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccc
Confidence            3568999999874432  3456789999999999999965 5679999999866543

>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=1.2e-12  Score=101.10  Aligned_cols=49  Identities=27%  Similarity=0.549  Sum_probs=40.8

Q ss_pred             cccchhhhhhhccCC---------------ceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250          213 DLQCAVCLEEFVMGN---------------EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP  261 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~---------------~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~  261 (347)
                      +..|+||++.+....               .++.++|+|.||..||.+||+.+++||+||++..
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            456999988774321               3677899999999999999999999999999864

>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=99.22  E-value=7.6e-13  Score=93.77  Aligned_cols=49  Identities=14%  Similarity=0.264  Sum_probs=44.2

Q ss_pred             ccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      +.|+||++.+   .+++.++ |||+||..||.+||+.+.+||+||.++..++.
T Consensus         1 l~C~Ic~~~~---~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           1 MLCAISGKVP---RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCCTTTCSCC---SSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCCccCCchH---HhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            3699999999   7888886 99999999999999999999999999977654

>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=2.5e-12  Score=101.94  Aligned_cols=52  Identities=31%  Similarity=0.773  Sum_probs=44.1

Q ss_pred             cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC---CCCCCCCcccCCCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQLPSDDL  265 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~~~  265 (347)
                      .+.+.|+||++.|   .+++.++|+|.||..||..|+...   ..||+||..+...+.
T Consensus        19 ~~~l~CpIC~~~~---~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          19 QKILECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HHHTSCSSSCCCC---SSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             ccCcCCCccCchh---CCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            3457899999999   778899999999999999999765   379999999866543

>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=2.6e-12  Score=98.87  Aligned_cols=49  Identities=35%  Similarity=0.781  Sum_probs=43.0

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-CCCCCCCcccCCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDD  264 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~  264 (347)
                      ...|+||++.|   .+++.++|+|.||..||..|++.+ .+||+||.++...+
T Consensus        23 ~l~C~IC~~~~---~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          23 SISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HTBCTTTCSBC---SSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CcCCccCCcch---hcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            46899999999   789999999999999999999754 57999999886543

>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=99.09  E-value=5.3e-12  Score=89.42  Aligned_cols=45  Identities=31%  Similarity=0.685  Sum_probs=39.5

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD  263 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~  263 (347)
                      .+.|+||++.|   .+++.+||+|.||..||..|   +.+||+||.++...
T Consensus         6 ~l~C~IC~~~~---~~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEA---KCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSC---BCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCcccCccc---CCCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            36899999999   67889999999999999876   66899999998654

>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=2.7e-11  Score=94.79  Aligned_cols=50  Identities=26%  Similarity=0.652  Sum_probs=41.2

Q ss_pred             cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSDDL  265 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~  265 (347)
                      .+.+.|+||++.|   ..++.+ +|+|.||..||..|+.  ..||+||..+...+.
T Consensus        20 ~~~l~C~IC~~~~---~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l   70 (97)
T d1jm7b_          20 EKLLRCSRCTNIL---REPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (97)
T ss_dssp             HHTTSCSSSCSCC---SSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             hhcCCCccCCchh---hcCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhC
Confidence            4457899999999   667665 7999999999999984  459999998866543

>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=3.9e-11  Score=90.61  Aligned_cols=52  Identities=19%  Similarity=0.210  Sum_probs=45.2

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCC
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDD  264 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~  264 (347)
                      +.+++.|+||++.|   .+++.++|||.||..||..||.. +.+||+||..+...+
T Consensus         4 iP~~l~CpIc~~l~---~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           4 IPDYLCGKISFELM---REPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             CCSTTBCTTTCSBC---SSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CCccccCcCcCchh---hhhcccCCcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            44678999999999   88999999999999999999965 557999999886554

>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=6.7e-11  Score=88.79  Aligned_cols=54  Identities=19%  Similarity=0.458  Sum_probs=46.8

Q ss_pred             ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-CCCCCCCcccCCCCCc
Q 036250          210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDDLK  266 (347)
Q Consensus       210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~~~  266 (347)
                      +.+++.|+||++.|   .+++.++|+|.||..||..|+..+ ..||.|+..+...+..
T Consensus         5 iP~~l~CpIc~~~m---~dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~   59 (78)
T d1t1ha_           5 FPEYFRCPISLELM---KDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLT   59 (78)
T ss_dssp             CSSSSSCTTTSCCC---SSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCE
T ss_pred             CCccCCCcCcCchh---hCceEccCCCcchHHHHHHHHHHCCCCCCcccccCCccccc
Confidence            44678999999999   889999999999999999999764 5799999998766543

>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=98.87  E-value=2.8e-10  Score=81.16  Aligned_cols=48  Identities=25%  Similarity=0.667  Sum_probs=37.4

Q ss_pred             cccccchhhhhhhccCCceEEecC-----CCcccccchHHHHhc--CCCCCCCCcccC
Q 036250          211 DQDLQCAVCLEEFVMGNEAKEMPC-----KHKFHGECIMPWLEL--QSSCPICRYQLP  261 (347)
Q Consensus       211 ~~~~~C~ICl~~~~~~~~~~~lpC-----~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~  261 (347)
                      ++...|.||++.+.   .....||     +|.||..||.+|+..  +.+||+||+++.
T Consensus         4 ed~~~C~IC~~~~~---~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELG---NERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECS---CCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCC---CceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            34568999999883   3444554     599999999999953  558999999874

>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=98.78  E-value=1.1e-09  Score=85.82  Aligned_cols=52  Identities=13%  Similarity=0.186  Sum_probs=46.2

Q ss_pred             ccccchhhhhhhccCCceEEecCC-CcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250          212 QDLQCAVCLEEFVMGNEAKEMPCK-HKFHGECIMPWLELQSSCPICRYQLPSDDLK  266 (347)
Q Consensus       212 ~~~~C~ICl~~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  266 (347)
                      +++.|+||++.|   .++++++|+ |.|+..||..||..+.+||+|+.+|..+++.
T Consensus        21 ~~f~CPI~~~lm---~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          21 DEFLDPIMSTLM---CDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             TTTBCTTTCSBC---SSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             HHhCCcCchhHH---HHHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhc
Confidence            467999999999   899999976 5899999999999999999999999776554

>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=98.03  E-value=3.2e-07  Score=70.31  Aligned_cols=46  Identities=26%  Similarity=0.575  Sum_probs=35.6

Q ss_pred             cccchhhhhhhccCCceEEecCCCcccccchHHHHhcC----C----CCCCCCc
Q 036250          213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ----S----SCPICRY  258 (347)
Q Consensus       213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~----~CP~CR~  258 (347)
                      ...|+||++++...+.++.++|+|.||..||..|++..    .    .||.|+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            45899999999654555666799999999999999531    1    4998643

>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=85.32  E-value=0.094  Score=34.28  Aligned_cols=43  Identities=28%  Similarity=0.551  Sum_probs=28.4

Q ss_pred             cchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCC----CCCCCCc
Q 036250          215 QCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQS----SCPICRY  258 (347)
Q Consensus       215 ~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~----~CP~CR~  258 (347)
                      .|.||...-..+ ..+.= .|...||..|+.+-+....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            488887654322 22222 3899999999988775432    4999974

>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=84.97  E-value=0.13  Score=37.33  Aligned_cols=36  Identities=28%  Similarity=0.655  Sum_probs=26.3

Q ss_pred             cccccccccchhhhhhhccCCceEEec---CCCcccccchHHH
Q 036250          207 TVAIDQDLQCAVCLEEFVMGNEAKEMP---CKHKFHGECIMPW  246 (347)
Q Consensus       207 ~~~~~~~~~C~ICl~~~~~~~~~~~lp---C~H~Fh~~Ci~~W  246 (347)
                      ...+..+..|.|| +.+..   -.++|   |+-+||..|+.+.
T Consensus         9 re~v~~D~mC~vC-~v~t~---~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_           9 REPVVNDEMCDVC-EVWTA---ESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCCSCCCTTT-CCCCS---SCCSSCSSSSSCCCHHHHHHH
T ss_pred             ccCCCcCcccccc-Ccccc---cceecceeecchhhHHHHHHh
Confidence            3445567789999 66633   33456   7899999999886

>d2dkta1 g.89.1.1 (A:8-81) RING finger and CHY zinc finger domain-containing protein 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CHY zinc finger-like
superfamily: CHY zinc finger-like
family: CHY zinc finger
domain: RING finger and CHY zinc finger domain-containing protein 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.35  E-value=0.43  Score=33.65  Aligned_cols=27  Identities=26%  Similarity=0.571  Sum_probs=21.4

Q ss_pred             CCCcEeeecCCceeeecCCCCccCCCCCCCc
Q 036250            5 TVGSYWCYICSRMVNPRMEAGIKCPFCETGF   35 (347)
Q Consensus         5 ~~~rywCh~C~~~V~p~~~~e~~CP~C~sGF   35 (347)
                      ...+.+||.|.....  ++  ..||.|++-|
T Consensus        48 ~~~~l~CH~Cg~~~~--~~--~~C~~Cgs~F   74 (74)
T d2dkta1          48 KVKEVQCINCEKLQH--AQ--QTCEDCSTLF   74 (74)
T ss_dssp             SCCCEEESSSCCEEC--SC--SBCSSSCCBS
T ss_pred             cCCEEEeccCCCccc--CC--CcCCCCCCCC
Confidence            468899999999763  22  4699999987