Citrus Sinensis ID: 013396

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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-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440----
Protein Sequence
MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNTSTADPVSSSPTQREGEPTPTVTVPTPSSPAAAGEESPEQSTQLLSASASGSSALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTRGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNSPNNSVPESNNQQVSETAHNNPMNDTNAQGSCGASSGTN
Secondary Structure (PSIPRED)
cccccccccccccccHHHcccccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccccccccHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHcccHHHHHHccccccccccccHcHccccccccccEcccccHccEEEEEEccccccHHHHHHccccccHHHHHHHHHHHHcccccccccEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEcccccccEEEccccHcccccccccccccEEccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccHHHHHHHHHHHHHHHHHcccccccHHHHHHcccccHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
meenkqcdarltspaafveggiqdacddacsiclepfsdsdpstvtsfdfHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCqrssqcpmcwqpislkdptrfCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFililfpsmqlpvgatdAELEERIIQHLAAAAAMGRARhigrresqrnrssaqarpqffvfsthpntstadpvsssptqregeptptvtvptpsspaaageespeqsTQLLSASasgssalassqhestlnnrrspnqpspnsqdragpsdfqSFSESLKSRFNAVSMRYKESISKSTRGWKERFFSRynttsdlgsevrreddaGIERVSGMMERLetrdnnssstasvsnspnnsvpesnnqqvsetahnnpmndtnaqgscgassgtn
Flexible Loop (DISEMBL)
meenkqcdarltspaaFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYlrrsnkrgalvlIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFfvfsthpntstadpvsssptqregeptptVTVPTPSSPAAAGEESPEQSTQLLSASASGSSALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRykesiskstrgwkerffsrynttsdlgsevrreddagieRVSGMMErletrdnnssstasvsnspnnsvpESNNQQVSETAHNnpmndtnaqgscgassgtn
Low Complexity Region (SEG)
MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVslilsggfililfPSMQLPVGATDAELEERIIQHLaaaaamgrarhigrrESQRNRSSAQARPQFFVFSTHPNTSTADPVSSSPTQREGEptptvtvptpsspAAAGEESPEqstqllsasasgssalassqHESTLnnrrspnqpspnsqDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTRGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDnnssstasvsnspnnsvpesnnqqvsETAHNNPMNDTNAQGSCGASSGTN
Disordered region (IsUnstruct)
**************AAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVGATDAELEERIIQHLAAAAA*******************************************************************************************************************************************************FF*************************************************************************************
Disordered Region (DISOPRED)
************************ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL*********************************************************************************************IIQHLA**************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
*********RLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVGATDAELEERIIQHLAA***********************ARPQFFVFSTHPN*****************************************************************************************SESLKSRFNAVSMRYKESISKSTRGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERL*********************************HNNPMNDTN************
Disordered Region (DISPRO)
***********************DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVGATDAELEERIIQHLAAAAAMGR***I*************ARPQ**********************************************************************************************************N*V***YKE*ISKSTRGWKERFF****T*SDLG***RREDDAGIERVSG***********************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNTSTADPVSSSPTQREGEPTPTVTVPTPSSPAAAGEESPEQSTQLLSASASGSSALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTRGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNSPNNSVPESNNQQVSETAHNNPMNDTNAQGSCGASSGTN
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	444	2.2.26 [Sep-21-2011]
Q9ZT42	375	E3 ubiquitin-protein liga	yes	no	0.828	0.981	0.461	3e-85
Q4TU14	371	E3 ubiquitin-protein liga	no	no	0.119	0.142	0.475	4e-16
Q5XF85	432	E3 ubiquitin-protein liga	no	no	0.153	0.157	0.279	0.0005
Q9SL78	390	Putative RING-H2 finger p	no	no	0.112	0.128	0.289	0.0008

>sp|Q9ZT42|RHF2A_ARATH E3 ubiquitin-protein ligase RHF2A OS=Arabidopsis thaliana GN=RHF2A PE=2 SV=1

 Score =  316 bits (809), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 204/442 (46%), Positives = 249/442 (56%), Gaps = 74/442 (16%)

Query: 3   ENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRD 62
           E    +  LTS AAFVEGGIQDACDDACSICLE F +SDPST                  
Sbjct: 6   ETTTSEGHLTSAAAFVEGGIQDACDDACSICLESFCESDPST------------------ 47

Query: 63  LGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRS 122
                    LTSC+HE+HLQC+LEWCQRSSQCPMCWQ ISLKDPT               
Sbjct: 48  ---------LTSCKHEYHLQCILEWCQRSSQCPMCWQSISLKDPT--------------- 83

Query: 123 NKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSM 182
                 +L  +E    F  R   T +  +F       F  Q+                  
Sbjct: 84  ---SQELLEAVEQERNF--RFNPTRNATIFRHPTLGDFELQH------------------ 120

Query: 183 QLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNTST 242
            LPVG  +AE+EERIIQHLAAAAAMGRARH  RRE  R+RSS+Q   QF VFS+ PN S+
Sbjct: 121 -LPVGVDNAEIEERIIQHLAAAAAMGRARHGVRREGHRSRSSSQGHQQFMVFSSQPNASS 179

Query: 243 ADPVSSSPTQREGEPTPTVTVPTPSSPAAAGEESPEQSTQLLSASASGSSALASSQHEST 302
             P    P+              P +  A GE S + +TQ  ++S     + ++S     
Sbjct: 180 PPPHPPMPSSPSQRDESDTVSNLPHN--ALGEGSHQSNTQPPTSSHPRQVSPSASD---- 233

Query: 303 LNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTRGWKERFFSRY 362
            +N R  NQ SP+ QDRAGPS+ QSFSESLKSR NAVS RYKESISK+TR WK+R FSR 
Sbjct: 234 -SNSRPLNQSSPSEQDRAGPSELQSFSESLKSRLNAVSTRYKESISKNTRNWKDRLFSRN 292

Query: 363 NTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNSPNNSVPESNNQQVSET 422
            + +DLGSEV+RE  AGI  VS MMERLETR+N+  STASVS+   N  PE+NN+     
Sbjct: 293 TSMADLGSEVKREVSAGIATVSRMMERLETRENSRPSTASVSDVSENHTPETNNEHNRAA 352

Query: 423 AHN-NPMNDTNAQGSCGASSGT 443
           A + + +N+   + +C   SG+
Sbjct: 353 AGDEHSVNERGVKETCATGSGS 374

Probable E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. Required for the degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophytes development. Functions in association with RHF1A.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q4TU14|RHF1A_ARATH E3 ubiquitin-protein ligase RHF1A OS=Arabidopsis thaliana GN=RHF1A PE=1 SV=1

 Score = 86.3 bits (212), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 46/80 (57%), Gaps = 27/80 (33%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
           DDACSICLEPF+  DPSTVTS                           C+HE+HLQC++E
Sbjct: 43  DDACSICLEPFTLQDPSTVTS---------------------------CKHEYHLQCIIE 75

Query: 87  WCQRSSQCPMCWQPISLKDP 106
           W QRS +CP+CWQ   L+DP
Sbjct: 76  WSQRSKECPICWQLFVLRDP 95

E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. Mediates the proteasomal degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophyte development. Functions in association with RHF2A. Possesses E3 ubiquitin ligase activity in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5XF85|ATL42_ARATH E3 ubiquitin-protein ligase ATL42 OS=Arabidopsis thaliana GN=ATL42 PE=1 SV=2

 Score = 46.2 bits (108), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 36/68 (52%)

Query: 58  VILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARN 117
           V L    +  +L  L  CRH FH+ C+ +W ++ + CP+C   +S+++ +    N  +  
Sbjct: 125 VCLSKFESVEILRLLPKCRHAFHIGCIDQWLEQHATCPLCRDRVSMEEDSSVLTNGNSFR 184

Query: 118 YLRRSNKR 125
           +L +S  R
Sbjct: 185 FLNQSEIR 192

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9SL78|ATL12_ARATH Putative RING-H2 finger protein ATL12 OS=Arabidopsis thaliana GN=ATL12 PE=3 SV=1

 Score = 45.4 bits (106), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 26/76 (34%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           CS+CL  F D                 V ILR          L  CRH FH+ C+ +W +
Sbjct: 124 CSVCLSKFED-----------------VEILR---------LLPKCRHAFHIGCIDQWLE 157

Query: 90  RSSQCPMCWQPISLKD 105
           + + CP+C   ++++D
Sbjct: 158 QHATCPLCRNRVNIED 173

Arabidopsis thaliana (taxid: 3702)

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	444
225436087	393	PREDICTED: E3 ubiquitin-protein ligase R	0.851	0.961	0.548	1e-117
224058945	386	predicted protein [Populus trichocarpa]	0.822	0.945	0.540	1e-110
356550038	398	PREDICTED: E3 ubiquitin-protein ligase R	0.849	0.947	0.541	1e-106
359481051	387	PREDICTED: E3 ubiquitin-protein ligase R	0.840	0.963	0.532	1e-105
357453313	382	RING finger protein [Medicago truncatula	0.826	0.960	0.525	1e-101
356543652	401	PREDICTED: E3 ubiquitin-protein ligase R	0.835	0.925	0.540	1e-100
357453317	383	RING finger protein [Medicago truncatula	0.826	0.958	0.524	1e-100
255637379	401	unknown [Glycine max]	0.835	0.925	0.535	6e-99
224138254	387	predicted protein [Populus trichocarpa]	0.819	0.940	0.489	5e-97
296089345	391	unnamed protein product [Vitis vinifera]	0.75	0.851	0.539	3e-96

>gi|225436087|ref|XP_002277399.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A [Vitis vinifera] gi|296084011|emb|CBI24399.3| unnamed protein product [Vitis vinifera]

 Score =  428 bits (1101), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 249/454 (54%), Positives = 290/454 (63%), Gaps = 76/454 (16%)

Query: 1   MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVIL 60
           MEE+ + +  LTS AAFVEGGIQ+ACDDACSICLE F DSDPSTVTS             
Sbjct: 6   MEESNKSECHLTSAAAFVEGGIQEACDDACSICLEAFCDSDPSTVTS------------- 52

Query: 61  RDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLR 120
                         C+HEFHLQC+LEWCQRSSQCPMCWQPISLKDPT             
Sbjct: 53  --------------CKHEFHLQCILEWCQRSSQCPMCWQPISLKDPT------------- 85

Query: 121 RSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFP 180
                   +L  +E    F  R   + +  +F       F  Q+                
Sbjct: 86  -----SQELLEAVERERTF--RFNPSRNATIFHHPTLGDFELQH---------------- 122

Query: 181 SMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNT 240
              LPVGA DAELEERIIQHLAAAAAMGRARHI RRE QR RSSAQ RPQF VFS HP+T
Sbjct: 123 ---LPVGANDAELEERIIQHLAAAAAMGRARHIARREGQRTRSSAQGRPQFLVFSAHPST 179

Query: 241 STADPVSSSPTQR-EGEPTPTVTVPTPSS-PAAAGEESPEQSTQLLS-------ASASGS 291
             A P SSSP QR E EP P +T   PSS P A GEES   +T  LS       ASASGS
Sbjct: 180 PQAGPASSSPAQRGEDEPAPAITAAMPSSLPTAVGEESSRLTTSQLSSQAEEITASASGS 239

Query: 292 SALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKST 351
               ++QH ++ NNRRSP Q  P+ QD+AGPS+FQSFSE+LKSRFNAVSMRYKESISKST
Sbjct: 240 IIHTTNQHGTSSNNRRSPGQSLPSGQDKAGPSEFQSFSETLKSRFNAVSMRYKESISKST 299

Query: 352 RGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSN-SPNNS 410
           RGWKER FSR  + +D+GS+VRRE +AGI  VS MME LETRDN+ ++ +SVS+ S + S
Sbjct: 300 RGWKERLFSRNTSMADIGSDVRREVNAGIATVSRMMEHLETRDNSRTTPSSVSDSSEDTS 359

Query: 411 VPESNNQQVSETAHNNPMNDTNAQGSCGASSGTN 444
            P   +Q+++ET+ +NP+ DTN Q SC ASSGTN
Sbjct: 360 SPSLGDQRMAETSAHNPLGDTNVQASCAASSGTN 393

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224058945|ref|XP_002299657.1| predicted protein [Populus trichocarpa] gi|222846915|gb|EEE84462.1| predicted protein [Populus trichocarpa]

 Score =  404 bits (1037), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 247/457 (54%), Positives = 284/457 (62%), Gaps = 92/457 (20%)

Query: 2   EENKQCDARLT-SPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVIL 60
           E  K+ +A LT S AAFVEGGIQ+ACDDACSICLE F DSDPSTVTS             
Sbjct: 6   ERKKKSEAHLTVSAAAFVEGGIQEACDDACSICLENFCDSDPSTVTS------------- 52

Query: 61  RDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLR 120
                         C+HEFHLQC+LEWCQRSSQCPMCWQPISLKDP              
Sbjct: 53  --------------CKHEFHLQCILEWCQRSSQCPMCWQPISLKDPM------------- 85

Query: 121 RSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFP 180
                   +L  +E    F  RL  + +  +F       F  Q+                
Sbjct: 86  -----SQELLEAVEQERSF--RLNPSRNATIFHHPALGDFELQH---------------- 122

Query: 181 SMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNT 240
              LPVGA DAELEER+IQHL AAAAMGR R I RRE QRNRSSAQ RPQF V S+ PN 
Sbjct: 123 ---LPVGANDAELEERLIQHLTAAAAMGR-RRIARREGQRNRSSAQGRPQFLVLSSQPNG 178

Query: 241 STADPVSSSPTQREGEPTPTVTVPTPSSPAAAGEESPEQSTQLL------------SASA 288
           S A  +SSSPTQREGEP   +T+ TPSS      +  E S QL+            SASA
Sbjct: 179 SPAGSISSSPTQREGEPVSAITIATPSS------QPLESSLQLITPLSSEALADPCSASA 232

Query: 289 SGSSALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESIS 348
           SGSS   ++QH ++++NR SPNQ SPNSQDRAGPSD QSFSES+KS+FNAVSMRYKESIS
Sbjct: 233 SGSSF--TNQHANSMDNR-SPNQSSPNSQDRAGPSDLQSFSESIKSKFNAVSMRYKESIS 289

Query: 349 KSTRGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNSPN 408
           KSTRGWKERFF+R  T +DLGSEVRRE +AGI  VS MME LETRD++ + T+SVSNS +
Sbjct: 290 KSTRGWKERFFTRNTTMADLGSEVRREVNAGIATVSRMMESLETRDDSRTGTSSVSNSVD 349

Query: 409 NSVPESNNQQVSETAHNNPMND--TNAQGSCGASSGT 443
            SV ESN+QQ  E    N  +D  T  Q S  ASSG+
Sbjct: 350 GSVAESNSQQ-PEVGVVNATSDPNTKVQASHAASSGS 385

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550038|ref|XP_003543397.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Glycine max]

 Score =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 249/460 (54%), Positives = 287/460 (62%), Gaps = 83/460 (18%)

Query: 1   MEENK------QCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRF 54
           MEEN       + +A LTS AAFVEGGIQDACDDACSICLE F DSDPSTVTS       
Sbjct: 6   MEENNIINDDNKSEAHLTSAAAFVEGGIQDACDDACSICLEAFCDSDPSTVTS------- 58

Query: 55  FRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFA 114
                               C+HEFHLQC+LEWCQRSSQCPMCWQPISLKDPT       
Sbjct: 59  --------------------CKHEFHLQCILEWCQRSSQCPMCWQPISLKDPT------- 91

Query: 115 ARNYLRRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGF 174
                         +L  +E    F  R   + +  +F       F  Q+          
Sbjct: 92  -----------SQELLEAVERERNF--RFNPSRNATIFHHPTLGDFELQH---------- 128

Query: 175 ILILFPSMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVF 234
                    LPVGA+DA+LEERIIQHLAAAAAMGRARH+ RRE QRNRSSAQ R  F VF
Sbjct: 129 ---------LPVGASDADLEERIIQHLAAAAAMGRARHVARREGQRNRSSAQGRQHFLVF 179

Query: 235 STHPNTSTADPVSSSPTQR-EGEPTPTVTVPTPSSPAAAGEES-------PEQSTQLLSA 286
           STHPN+    P SSSP+QR + EPTPT+ V   S   A GEES       P Q+ Q+ SA
Sbjct: 180 STHPNSPPMAPASSSPSQRGDDEPTPTIDVANLSPTPATGEESSQPTLVSPVQAEQV-SA 238

Query: 287 SASGSSALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKES 346
           S SG++ALA+    S+ NNRRSPNQ SP+SQDRAGPS+ QSFSESLKS+ NAVS RYKES
Sbjct: 239 SGSGTTALATDHQGSSYNNRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRYKES 298

Query: 347 ISKSTRGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNN-SSSTASVSN 405
           ISKSTRGWKER+FSR NT SDLGSEVRRE +AGI  VS MMERLETRDNN S+S ++ SN
Sbjct: 299 ISKSTRGWKERWFSRNNTMSDLGSEVRREVNAGIATVSRMMERLETRDNNRSNSNSAPSN 358

Query: 406 SPNNSVPESNNQQVSETAHNNPM-NDTNAQGSCGASSGTN 444
             + SV  SN+Q ++       +  D N + SC A S +N
Sbjct: 359 IEDGSVQGSNDQTLTAGNEGGSLVRDNNTKASCAAGSSSN 398

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481051|ref|XP_002270570.2| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Vitis vinifera]

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 241/453 (53%), Positives = 273/453 (60%), Gaps = 80/453 (17%)

Query: 1   MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVIL 60
           MEE K  +  +TS AAFVEGG+Q+ACDDACSICLE F DSDPST                
Sbjct: 6   MEEVKNSENHMTSAAAFVEGGVQEACDDACSICLEAFCDSDPST---------------- 49

Query: 61  RDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLR 120
                      LTSC+HEFHLQC+LEWCQRSSQCPMCWQ ISLKDPT   +  A     R
Sbjct: 50  -----------LTSCKHEFHLQCILEWCQRSSQCPMCWQSISLKDPTSQELLEAVE---R 95

Query: 121 RSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFP 180
             N       IRL  PP   I    TL                        G F L    
Sbjct: 96  ERN-------IRL-TPPRSAIFHHPTL------------------------GDFEL---- 119

Query: 181 SMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNT 240
              LPVG  D ELEERIIQHLAAAAAMGRA HI RRE QR+RSSA  R  F VFSTHPN 
Sbjct: 120 -QHLPVGTNDPELEERIIQHLAAAAAMGRAHHIARREGQRSRSSAHGRSHFLVFSTHPNA 178

Query: 241 STADPVSSSPTQ-REGEPTPTVTVPTPSSPAAAGEESPEQS--------TQLLSASASGS 291
           + + PV +S  Q  E EP   +TV +PS P  AG + P Q         T  +SASAS S
Sbjct: 179 TASGPVPASLVQVGENEPA-AITVASPSIPLPAGGDEPSQEIPQFPSVQTDHMSASASRS 237

Query: 292 SALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKST 351
              A +    + NNR S +Q SP  QDRAGPS+ QSFSESLKSR NAVSMRYKESISKST
Sbjct: 238 ---AVTPRRISFNNRSSASQSSPPDQDRAGPSELQSFSESLKSRLNAVSMRYKESISKST 294

Query: 352 RGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNSPNNSV 411
           RGWKER FSR N+ +DLGSEVRRE +AGI  VS MMERL+TR+NN +  ASVS+   +SV
Sbjct: 295 RGWKERLFSRNNSMADLGSEVRREVNAGIASVSRMMERLDTRENNGAGQASVSSHLADSV 354

Query: 412 PESNNQQVSETAHNNPMNDTNAQGSCGASSGTN 444
            E +NQ   ET   NP+ND+N   +C ASSG+N
Sbjct: 355 TEQSNQNERETRAENPLNDSNTPAACAASSGSN 387

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357453313|ref|XP_003596933.1| RING finger protein [Medicago truncatula] gi|355485981|gb|AES67184.1| RING finger protein [Medicago truncatula]

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 238/453 (52%), Positives = 283/453 (62%), Gaps = 86/453 (18%)

Query: 1   MEENK-QCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVI 59
           +EEN+ + +A LTS AAFVEGGIQDACDD+CSICLE F DSDPSTVTS            
Sbjct: 7   IEENETKSEAHLTSAAAFVEGGIQDACDDSCSICLEEFIDSDPSTVTS------------ 54

Query: 60  LRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYL 119
                          C+HEFHLQC+LEWCQRSSQCPMCWQ ISLKDPT            
Sbjct: 55  ---------------CKHEFHLQCILEWCQRSSQCPMCWQSISLKDPT------------ 87

Query: 120 RRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILF 179
                 G  +L  +E      IR   T +  +F       F  Q+               
Sbjct: 88  ------GQELLEAVER--ERNIRFNPTRNATIFHHPTLGDFELQH--------------- 124

Query: 180 PSMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPN 239
               LPVGA DA+LEERI+QH AAAAAMGRARHI RRE QRNRSSAQ RPQ+ VFS HPN
Sbjct: 125 ----LPVGANDADLEERILQHFAAAAAMGRARHIARREGQRNRSSAQGRPQYMVFSAHPN 180

Query: 240 TSTADPVSSSPTQR-EGEPTPTVTVPTPSSPAAAGEESPEQS------TQLLSASASGSS 292
           +    P SSSP QR +GE TP           A GEE P+ +      T  +SAS SGS+
Sbjct: 181 SPPMAPASSSPPQRGDGEQTP-----------ATGEEPPQLTLVPPVQTDQVSASGSGSA 229

Query: 293 ALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTR 352
           ALA+     + N+RRSPNQ SP+SQDRAGPS+ QSFSESLKS+ NAVS RYKESISKSTR
Sbjct: 230 ALATDNLGLSYNSRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRYKESISKSTR 289

Query: 353 GWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNN-SSSTASVSNSPNNSV 411
           GWKER+FSR +  SDLGSEV+RE +AGI  VS MMERLETRDNN SSS  + SN  +  +
Sbjct: 290 GWKERWFSRTSPMSDLGSEVKREVNAGIATVSRMMERLETRDNNRSSSDTAPSNLADGPI 349

Query: 412 PESNNQQVSETAHNNPMNDTNAQGSCGASSGTN 444
             S++Q +++T  ++P+ D N++ SC A S +N
Sbjct: 350 QGSSDQHLTDTERDSPLRDNNSKTSCTAGSSSN 382

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543652|ref|XP_003540274.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Glycine max]

 Score =  372 bits (954), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 241/446 (54%), Positives = 278/446 (62%), Gaps = 75/446 (16%)

Query: 8   DARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFS 67
           +A LTS AAFVEGGIQDACDDACSICLE F DSDPSTVTS                    
Sbjct: 22  EAHLTSAAAFVEGGIQDACDDACSICLEAFCDSDPSTVTS-------------------- 61

Query: 68  LLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGA 127
                  C+HEFHLQC+LEWCQRSSQCPMCWQPISLKDPT                    
Sbjct: 62  -------CKHEFHLQCILEWCQRSSQCPMCWQPISLKDPT------------------SQ 96

Query: 128 LVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVG 187
            +L  +E    F  R   + +  +F       F  Q+                   LPVG
Sbjct: 97  ELLEAVERERNF--RFNPSRNATIFHHPTLGDFELQH-------------------LPVG 135

Query: 188 ATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNTSTADPVS 247
           A+DA+LEERIIQHLAAAAAMGRARHI RRE QRNRSSAQ RP F VFST+PN+    P S
Sbjct: 136 ASDADLEERIIQHLAAAAAMGRARHIARREGQRNRSSAQGRPHFLVFSTNPNSPPMAPAS 195

Query: 248 SSPTQR-EGEPTPTVTVPTPSSPAAAGEES------PEQSTQLLSASASGSSALASSQHE 300
           SSP+QR + EP PT+ V   S   A GEES      P    + +SAS SGS+ALA+    
Sbjct: 196 SSPSQRGDDEPIPTIAVANLSPTPATGEESSQLTLVPPIQAEQVSASGSGSTALATDHQG 255

Query: 301 STLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTRGWKERFFS 360
           S+ NNRRSPNQ SP+SQDRAGPS+ QSFSESLKS+ NAVS RYKESISKSTRGWKER+FS
Sbjct: 256 SSYNNRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRYKESISKSTRGWKERWFS 315

Query: 361 RYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNS-PNNSVPESNNQQV 419
           R NT SDLGSEVRRE +AGI  VS MMERLET DNN S++ S  ++  + SV E N Q +
Sbjct: 316 RNNTMSDLGSEVRREVNAGIATVSRMMERLETSDNNRSNSNSAPSNIEDGSVQEYNGQTL 375

Query: 420 SETAHNNP-MNDTNAQGSCGASSGTN 444
           +     +  + D N + SC A S +N
Sbjct: 376 TPGNEGDGLLRDNNTKASCAAGSSSN 401

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357453317|ref|XP_003596935.1| RING finger protein [Medicago truncatula] gi|355485983|gb|AES67186.1| RING finger protein [Medicago truncatula]

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 238/454 (52%), Positives = 283/454 (62%), Gaps = 87/454 (19%)

Query: 1   MEENK-QCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVI 59
           +EEN+ + +A LTS AAFVEGGIQDACDD+CSICLE F DSDPSTVTS            
Sbjct: 7   IEENETKSEAHLTSAAAFVEGGIQDACDDSCSICLEEFIDSDPSTVTS------------ 54

Query: 60  LRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYL 119
                          C+HEFHLQC+LEWCQRSSQCPMCWQ ISLKDPT            
Sbjct: 55  ---------------CKHEFHLQCILEWCQRSSQCPMCWQSISLKDPT------------ 87

Query: 120 RRSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILF 179
                 G  +L  +E      IR   T +  +F       F  Q+               
Sbjct: 88  ------GQELLEAVER--ERNIRFNPTRNATIFHHPTLGDFELQH--------------- 124

Query: 180 PSMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPN 239
               LPVGA DA+LEERI+QH AAAAAMGRARHI RRE QRNRSSAQ RPQ+ VFS HPN
Sbjct: 125 ----LPVGANDADLEERILQHFAAAAAMGRARHIARREGQRNRSSAQGRPQYMVFSAHPN 180

Query: 240 TSTADPVSSSPTQR-EGEPTPTVTVPTPSSPAAAGEESPEQS------TQLLSASASGSS 292
           +    P SSSP QR +GE TP           A GEE P+ +      T  +SAS SGS+
Sbjct: 181 SPPMAPASSSPPQRGDGEQTP-----------ATGEEPPQLTLVPPVQTDQVSASGSGSA 229

Query: 293 ALASSQHESTLNN-RRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKST 351
           ALA+     + N+ RRSPNQ SP+SQDRAGPS+ QSFSESLKS+ NAVS RYKESISKST
Sbjct: 230 ALATDNLGLSYNSSRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRYKESISKST 289

Query: 352 RGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNN-SSSTASVSNSPNNS 410
           RGWKER+FSR +  SDLGSEV+RE +AGI  VS MMERLETRDNN SSS  + SN  +  
Sbjct: 290 RGWKERWFSRTSPMSDLGSEVKREVNAGIATVSRMMERLETRDNNRSSSDTAPSNLADGP 349

Query: 411 VPESNNQQVSETAHNNPMNDTNAQGSCGASSGTN 444
           +  S++Q +++T  ++P+ D N++ SC A S +N
Sbjct: 350 IQGSSDQHLTDTERDSPLRDNNSKTSCTAGSSSN 383

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637379|gb|ACU19018.1| unknown [Glycine max]

 Score =  367 bits (942), Expect = 6e-99,   Method: Compositional matrix adjust.
 Identities = 239/446 (53%), Positives = 276/446 (61%), Gaps = 75/446 (16%)

Query: 8   DARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFS 67
           +A LTS AAFVEGGIQDACDDACSICLE F DSDPSTVTS                    
Sbjct: 22  EAHLTSAAAFVEGGIQDACDDACSICLEAFCDSDPSTVTS-------------------- 61

Query: 68  LLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGA 127
                  C+HEFHLQC+LEWCQRSSQCPMCWQPISLKDPT                    
Sbjct: 62  -------CKHEFHLQCILEWCQRSSQCPMCWQPISLKDPT------------------SQ 96

Query: 128 LVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFPSMQLPVG 187
            +L  +E    F  R   + +  +F       F  Q+                   LPVG
Sbjct: 97  ELLEAVERERNF--RFNPSRNATIFHHPTLGDFELQH-------------------LPVG 135

Query: 188 ATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNTSTADPVS 247
           A+DA+LEERIIQHLAAAAAMGRARHI RRE QRNRSSAQ RP F  FST+PN+    P S
Sbjct: 136 ASDADLEERIIQHLAAAAAMGRARHIARREGQRNRSSAQGRPHFLAFSTNPNSPPMAPAS 195

Query: 248 SSPTQR-EGEPTPTVTVPTPSSPAAAGEES------PEQSTQLLSASASGSSALASSQHE 300
           SSP+QR + EP PT+ V   S   A GEES      P    + +SAS SGS+ALA+    
Sbjct: 196 SSPSQRGDDEPIPTIAVANLSPTPATGEESSQLTLVPPIQAEQVSASGSGSTALATDHQG 255

Query: 301 STLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTRGWKERFFS 360
           S+ NNRRSPNQ SP+SQDRAGPS+ QSFSESLKS+ NAVS RYKESISKSTRGWKER+FS
Sbjct: 256 SSYNNRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRYKESISKSTRGWKERWFS 315

Query: 361 RYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNS-PNNSVPESNNQQV 419
           R NT SDLGSEVRRE +AGI  VS MMERLET DNN S++ S  ++  + SV E N Q +
Sbjct: 316 RNNTMSDLGSEVRREVNAGIATVSRMMERLETSDNNRSNSNSAPSNIEDGSVQEYNGQTL 375

Query: 420 SETAHNNP-MNDTNAQGSCGASSGTN 444
           +     +  + D N + SC A   +N
Sbjct: 376 TPGNEGDGLLRDNNTKASCAAGFSSN 401

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138254|ref|XP_002322768.1| predicted protein [Populus trichocarpa] gi|222867398|gb|EEF04529.1| predicted protein [Populus trichocarpa]

 Score =  361 bits (926), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 215/439 (48%), Positives = 268/439 (61%), Gaps = 75/439 (17%)

Query: 1   MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVIL 60
           M+E K+ +  +TS AAFVEGGIQD+CDDACSICLE F +SDPSTVT+             
Sbjct: 1   MDEAKKPEVHMTSAAAFVEGGIQDSCDDACSICLEEFCESDPSTVTN------------- 47

Query: 61  RDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLR 120
                         C+HEFHLQC+LEWCQRSS+CPMC Q ISLKDPT   + F A    R
Sbjct: 48  --------------CKHEFHLQCILEWCQRSSECPMCLQSISLKDPTSQEL-FEAVERER 92

Query: 121 RSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFP 180
           +                   IR   + +  +F       F  Q+                
Sbjct: 93  K-------------------IRAAPSRNATIFHHPTLGDFELQH---------------- 117

Query: 181 SMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNT 240
              LPVG +D+ELEERIIQHLAAAAAMGR RH GRRE QRNR+S+  RP F VFSTHP  
Sbjct: 118 ---LPVGVSDSELEERIIQHLAAAAAMGRTRHFGRREGQRNRTSSHGRPHFLVFSTHPGA 174

Query: 241 STADPVSSSPTQREGEPTPT-VTVPTPSSP-AAAGEESPEQSTQ---LL---SASASGSS 292
             +  VSSS TQ  GE  P  V+V +PS+   + G+E P+Q+ Q   +L   S+SASGS+
Sbjct: 175 QPSGHVSSSLTQLGGENEPAPVSVASPSTQLTSVGDEPPQQALQSPSVLTDQSSSASGST 234

Query: 293 ALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKSTR 352
           A+ ++    + NNR + +Q S  +QDRAGPS+ QSFSESLKSR NAVSMRYKESIS+STR
Sbjct: 235 AMPANNQGVSFNNRSASSQSSLPNQDRAGPSELQSFSESLKSRLNAVSMRYKESISRSTR 294

Query: 353 GWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVSNS-PNNSV 411
           GWKER FSR ++ SD+ S+VRRE +AGI  VS MMERLETRD+   +  SVSN   + S 
Sbjct: 295 GWKERLFSRNSSMSDISSDVRREVNAGIATVSRMMERLETRDDGGDNQVSVSNHLTDRSN 354

Query: 412 PESNNQQVSETAHNNPMND 430
            E +NQ  + T   +P+N+
Sbjct: 355 VERSNQNTAATHIESPLNE 373

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089345|emb|CBI39117.3| unnamed protein product [Vitis vinifera]

 Score =  358 bits (919), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 223/413 (53%), Positives = 248/413 (60%), Gaps = 80/413 (19%)

Query: 1   MEENKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVIL 60
           MEE K  +  +TS AAFVEGG+Q+ACDDACSICLE F DSDPST                
Sbjct: 6   MEEVKNSENHMTSAAAFVEGGVQEACDDACSICLEAFCDSDPST---------------- 49

Query: 61  RDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLR 120
                      LTSC+HEFHLQC+LEWCQRSSQCPMCWQ ISLKDPT   +  A     R
Sbjct: 50  -----------LTSCKHEFHLQCILEWCQRSSQCPMCWQSISLKDPTSQELLEAVE---R 95

Query: 121 RSNKRGALVLIRLEIPPYFIIRLWETLSYRVFVFCLWASFRQQYQVSLILSGGFILILFP 180
             N       IRL  PP   I    TL                        G F L    
Sbjct: 96  ERN-------IRL-TPPRSAIFHHPTL------------------------GDFEL---- 119

Query: 181 SMQLPVGATDAELEERIIQHLAAAAAMGRARHIGRRESQRNRSSAQARPQFFVFSTHPNT 240
              LPVG  D ELEERIIQHLAAAAAMGRA HI RRE QR+RSSA  R  F VFSTHPN 
Sbjct: 120 -QHLPVGTNDPELEERIIQHLAAAAAMGRAHHIARREGQRSRSSAHGRSHFLVFSTHPNA 178

Query: 241 STADPVSSSPTQ-REGEPTPTVTVPTPSSPAAAGEESPEQS--------TQLLSASASGS 291
           + + PV +S  Q  E EP   +TV +PS P  AG + P Q         T  +SASAS S
Sbjct: 179 TASGPVPASLVQVGENEPA-AITVASPSIPLPAGGDEPSQEIPQFPSVQTDHMSASASRS 237

Query: 292 SALASSQHESTLNNRRSPNQPSPNSQDRAGPSDFQSFSESLKSRFNAVSMRYKESISKST 351
              A +    + NNR S +Q SP  QDRAGPS+ QSFSESLKSR NAVSMRYKESISKST
Sbjct: 238 ---AVTPRRISFNNRSSASQSSPPDQDRAGPSELQSFSESLKSRLNAVSMRYKESISKST 294

Query: 352 RGWKERFFSRYNTTSDLGSEVRREDDAGIERVSGMMERLETRDNNSSSTASVS 404
           RGWKER FSR N+ +DLGSEVRRE +AGI  VS MMERL+TR+NN +  ASVS
Sbjct: 295 RGWKERLFSRNNSMADLGSEVRREVNAGIASVSRMMERLDTRENNGAGQASVS 347

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	444
TAIR|locus:2129525	371	RHF1A "RING-H2 group F1A" [Ara	0.078	0.094	0.628	1.5e-19
UNIPROTKB|G4NGM3	104	MGG_04088 "Anaphase-promoting	0.056	0.240	0.535	6e-06
RGD|1561238	95	RGD1561238 "similar to ring fi	0.074	0.347	0.393	1.3e-05
TAIR|locus:2139044	71	AT4G12190 [Arabidopsis thalian	0.054	0.338	0.5	2.1e-05
TAIR|locus:505006415	190	RHB1A "RING-H2 finger B1A" [Ar	0.074	0.173	0.515	0.00012
POMBASE|SPAC343.03	94	apc11 "anaphase-promoting comp	0.074	0.351	0.388	0.00021
RGD|1306670	100	Rnf139 "ring finger protein 13	0.117	0.52	0.307	0.00052
ASPGD|ASPL0000035856	104	AN10394 [Emericella nidulans (	0.074	0.317	0.472	0.00086
FB|FBgn0038627	147	CG7694 [Drosophila melanogaste	0.081	0.244	0.361	0.0009

TAIR|locus:2129525 RHF1A "RING-H2 group F1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 1.5e-19, Sum P(2) = 1.5e-19
 Identities = 22/35 (62%), Positives = 30/35 (85%)

Query:    72 LTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP 106
             +TSC+HE+HLQC++EW QRS +CP+CWQ   L+DP
Sbjct:    61 VTSCKHEYHLQCIIEWSQRSKECPICWQLFVLRDP 95

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016020 "membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009561 "megagametogenesis" evidence=IGI

GO:0010498 "proteasomal protein catabolic process" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0051726 "regulation of cell cycle" evidence=IGI

GO:0055046 "microgametogenesis" evidence=IGI

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

UNIPROTKB|G4NGM3 MGG_04088 "Anaphase-promoting complex subunit 11" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 92 (37.4 bits), Expect = 6.0e-06, Sum P(2) = 6.0e-06
 Identities = 15/28 (53%), Positives = 19/28 (67%)

Query:    75 CRHEFHLQCVLEWCQRSS---QCPMCWQ 99
             C H FH+ C+LEW ++ S   QCPMC Q
Sbjct:    52 CGHNFHMHCILEWIKQDSAKGQCPMCRQ 79

GO:0005575 "cellular_component" evidence=ND

RGD|1561238 RGD1561238 "similar to ring finger protein 122 homolog" [Rattus norvegicus (taxid:10116)]

 Score = 87 (35.7 bits), Expect = 1.3e-05, Sum P(2) = 1.3e-05
 Identities = 13/33 (39%), Positives = 22/33 (66%)

Query:    70 LQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS 102
             L +  C+H FH +C+++W +    CPMC +PI+
Sbjct:    46 LGVLPCQHAFHRKCLVKWLEVRCVCPMCNKPIA 78

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2139044 AT4G12190 [Arabidopsis thaliana (taxid:3702)]

 Score = 86 (35.3 bits), Expect = 2.1e-05, Sum P(2) = 2.1e-05
 Identities = 12/24 (50%), Positives = 17/24 (70%)

Query:    74 SCRHEFHLQCVLEWCQRSSQCPMC 97
             +C H FH  C+LEW +R + CP+C
Sbjct:    42 TCSHVFHNGCLLEWLKRKNTCPLC 65

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

TAIR|locus:505006415 RHB1A "RING-H2 finger B1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 114 (45.2 bits), Expect = 0.00012, P = 0.00012
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query:    73 TSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD 105
             T C HEFHL C+LEW +RS +CP+C + +   D
Sbjct:   155 TKCEHEFHLSCLLEWIERSDRCPICDKEVVFDD 187

GO:0005634 "nucleus" evidence=ISM

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

GO:0048573 "photoperiodism, flowering" evidence=RCA

POMBASE|SPAC343.03 apc11 "anaphase-promoting complex subunit Apc11" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 70 (29.7 bits), Expect = 0.00021, Sum P(2) = 0.00021
 Identities = 14/36 (38%), Positives = 17/36 (47%)

Query:    75 CRHEFHLQCVLEWCQRSS---QCPMCWQPISLKDPT 107
             C+H FH  C+  W   S    QCPM  Q   + D T
Sbjct:    52 CKHIFHAHCIQNWLATSGSQGQCPMDRQTFVVADST 87

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0008054 "cyclin catabolic process" evidence=IC

GO:0008270 "zinc ion binding" evidence=ISM

GO:0016567 "protein ubiquitination" evidence=IC

GO:0030071 "regulation of mitotic metaphase/anaphase transition" evidence=IC

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=IC

RGD|1306670 Rnf139 "ring finger protein 139" [Rattus norvegicus (taxid:10116)]

 Score = 94 (38.1 bits), Expect = 0.00052, P = 0.00052
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query:    66 FSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARN 117
             F+   ++T C H FH  C+ +W      CPMC Q + ++D  +   N +  N
Sbjct:    35 FTTSARITPCNHYFHALCLRKWLYIQDTCPMCHQKVYIEDDIKDNSNVSNNN 86

GO:0003674 "molecular_function" evidence=ND

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

GO:0005575 "cellular_component" evidence=ND

GO:0005783 "endoplasmic reticulum" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0017148 "negative regulation of translation" evidence=ISO

GO:0019787 "small conjugating protein ligase activity" evidence=ISO

GO:0031396 "regulation of protein ubiquitination" evidence=ISO

GO:0060628 "regulation of ER to Golgi vesicle-mediated transport" evidence=ISO

GO:0070613 "regulation of protein processing" evidence=ISO

ASPGD|ASPL0000035856 AN10394 [Emericella nidulans (taxid:162425)]

 Score = 92 (37.4 bits), Expect = 0.00086, P = 0.00086
 Identities = 17/36 (47%), Positives = 21/36 (58%)

Query:    70 LQLTSCRHEFHLQCVLEWCQRSSQ---CPMCWQPIS 102
             L L  C H FH+ C++ W Q+ S    CPMC Q IS
Sbjct:    47 LLLGKCGHSFHMHCLMTWIQQESSKGLCPMCRQSIS 82

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

FB|FBgn0038627 CG7694 [Drosophila melanogaster (taxid:7227)]

 Score = 101 (40.6 bits), Expect = 0.00090, P = 0.00090
 Identities = 13/36 (36%), Positives = 24/36 (66%)

Query:    71 QLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP 106
             ++  C+HEFH +C+L W ++++ CP+C   +   DP
Sbjct:    84 RILPCKHEFHEECILLWLKKTNSCPLCRYELETDDP 119


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.131   0.399    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      444       343   0.00096  116 3  11 22  0.38    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  613 (65 KB)
  Total size of DFA:  248 KB (2134 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  21.93u 0.15s 22.08t   Elapsed:  00:00:01
  Total cpu time:  21.93u 0.15s 22.08t   Elapsed:  00:00:01
  Start:  Fri May 10 16:22:35 2013   End:  Fri May 10 16:22:36 2013

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZT42	RHF2A_ARATH	6, ., 3, ., 2, ., -	0.4615	0.8288	0.9813	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	444
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-08
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-08
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-07
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	9e-07
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-05
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-04
smart00184	40	smart00184, RING, Ring finger	3e-04
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	5e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	0.002

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 27/68 (39%)

Query: 30 CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
          C ICL+ F   +               VV+L              C H FH +C+ +W +
Sbjct: 3  CPICLDEFEPGE--------------EVVVL-------------PCGHVFHKECLDKWLR 35

Query: 90 RSSQCPMC 97
           S+ CP+C
Sbjct: 36 SSNTCPLC 43

Length = 46

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

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 17/74 (22%)

Query: 24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
          D  DD C+IC   F  + P   +  D                    +    C H FHL C
Sbjct: 16 DIEDDVCAICRNHFDGTCPECKSPGD-----------------DCPVVWGECGHAFHLHC 58

Query: 84 VLEWCQRSSQCPMC 97
          +  W +  + CP+C
Sbjct: 59 ISRWLKTRNTCPLC 72

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|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 = 47.4 bits (113), Expect = 1e-07
 Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 30/73 (41%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C ICLE F +                              + L  C H F   C+ +W +
Sbjct: 2   CPICLEEFREP-----------------------------VVLLPCGHVFCRSCIDKWLK 32

Query: 90  R-SSQCPMCWQPI 101
              + CP+C  PI
Sbjct: 33  SGKNTCPLCRTPI 45

Length = 45

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

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 20/84 (23%)

Query: 25  ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCV 84
             DD C IC   F  + P      D               +  L+     C+H FH+ C+
Sbjct: 19  PSDDVCGICRVSFDGTCPQCKFPGD---------------DCPLVW--GKCKHNFHMHCI 61

Query: 85  LEWCQRSS---QCPMCWQPISLKD 105
           L+W    +    CPMC Q     +
Sbjct: 62  LKWLATETSKGLCPMCRQTFVFAE 85

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

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 11/34 (32%), Positives = 13/34 (38%)

Query: 75  CRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTR 108
           C H FH  C+  W      CP+  Q   L D   
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDRQTWVLADGGA 87

Length = 88

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 29/71 (40%)

Query: 27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
          +  C ICL+   D                              + LT C H F  +C+L 
Sbjct: 2  ELECPICLDLLRDP-----------------------------VVLTPCGHVFCRECILR 32

Query: 87 WCQRSSQCPMC 97
          + ++ S+CP+C
Sbjct: 33 YLKKKSKCPIC 43

Length = 45

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

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 1/36 (2%)

Query: 63 LGNFSLLLQLTSCRHEFHLQCVLEWC-QRSSQCPMC 97
          L  +     +  C H F   C+ +W    ++ CP+C
Sbjct: 5  LEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 41.3 bits (97), Expect = 5e-04
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 22/83 (26%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
           D  C+IC+E   D +            +F +              L++C H F ++C+  
Sbjct: 174 DKECAICMEKVYDKE--------IKNMYFGI--------------LSNCNHVFCIECIDI 211

Query: 87  WCQRSSQCPMCWQPISLKDPTRF 109
           W +  + CP+C  P      +RF
Sbjct: 212 WKKEKNTCPVCRTPFISVIKSRF 234

Length = 238

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

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 75  CRHEFHLQCVLEWCQRSSQCPMCWQPI 101
           C H  HL C+  W +R   CP+C +P+
Sbjct: 318 CGHILHLHCLKNWLERQQTCPICRRPV 344

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	444
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.41
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.32
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.25
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.23
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.23
PHA02929	238	N1R/p28-like protein; Provisional	99.11
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.05
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.03
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.89
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.86
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.84
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.8
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.77
PHA02926	242	zinc finger-like protein; Provisional	98.76
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.74
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.71
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.68
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.65
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.64
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.63
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.62
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.57
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.53
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.52
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.49
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.37
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.35
PF14634	44	zf-RING_5: zinc-RING finger domain	98.34
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.25
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.23
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.23
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.04
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.94
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.84
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.84
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	97.83
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.73
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.73
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.69
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.61
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.46
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.45
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.35
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.31
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.3
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.17
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.16
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.12
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.9
KOG2660	331	consensus Locus-specific chromosome binding protei	96.71
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.7
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.67
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	96.6
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.49
KOG4445	368	consensus Uncharacterized conserved protein, conta	96.43
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.13
COG5152	259	Uncharacterized conserved protein, contains RING a	96.11
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.08
PHA03096	284	p28-like protein; Provisional	96.02
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	95.72
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.57
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.24
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.12
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.02
PF04641	260	Rtf2: Rtf2 RING-finger	94.82
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	94.72
PHA02862	156	5L protein; Provisional	94.68
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.56
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	94.39
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	94.38
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	94.38
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.13
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.13
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.12
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.07
COG5236	493	Uncharacterized conserved protein, contains RING Z	93.99
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	93.83
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.57
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	92.59
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	92.55
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	92.04
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	91.9
KOG4739	233	consensus Uncharacterized protein involved in syna	91.85
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	91.77
KOG1001	674	consensus Helicase-like transcription factor HLTF/	91.34
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	90.91
KOG1940	276	consensus Zn-finger protein [General function pred	89.67
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	88.81
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	88.73
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	86.79
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	86.29
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	84.83
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	84.09
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	83.78
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	82.61
KOG3899	381	consensus Uncharacterized conserved protein [Funct	81.9
KOG3053	293	consensus Uncharacterized conserved protein [Funct	81.66
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	81.02
KOG1609	323	consensus Protein involved in mRNA turnover and st	80.32
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	80.2

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

Probab=99.41  E-value=1.3e-13  Score=115.61  Aligned_cols=63  Identities=41%  Similarity=0.870  Sum_probs=52.0

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc---CCCCCCcccCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR---SSQCPMCWQPI  101 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~---sssCP~CRq~i  101 (444)
                      .+|+.|.||+..|...++.+..++|                 .++++++.|+|.||.+||.+|++.   ..+|||||+++
T Consensus        19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd-----------------~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w   81 (85)
T PF12861_consen   19 ANDDVCGICRMPFDGCCPDCKFPGD-----------------DCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW   81 (85)
T ss_pred             CCCCceeeEecccccCCCCccCCCC-----------------CCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence            3489999999999998888777433                 235667799999999999999976   35899999998


Q ss_pred             CCC
Q 013396          102 SLK  104 (444)
Q Consensus       102 ~~k  104 (444)
                      ..+
T Consensus        82 ~~k   84 (85)
T PF12861_consen   82 KFK   84 (85)
T ss_pred             eeC
Confidence            765

>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=99.32  E-value=8.1e-13  Score=106.55  Aligned_cols=55  Identities=33%  Similarity=0.847  Sum_probs=41.7

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcc
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCW   98 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CR   98 (444)
                      ++.|+||++.|.+.++....+.                 ..+.++++.|||.||.+||.+|++...+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~-----------------~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQ-----------------DECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCT-----------------TTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCc-----------------cccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            5569999999987665443311                 123445568999999999999999999999997

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 ....

>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=99.25  E-value=1.2e-12  Score=94.93  Aligned_cols=44  Identities=50%  Similarity=1.180  Sum_probs=36.2

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcc
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCW   98 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CR   98 (444)
                      +.|+||++.|..+..              ++.|             +|||.||..||.+|++.+..||+||
T Consensus         1 d~C~IC~~~~~~~~~--------------~~~l-------------~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEK--------------VVKL-------------PCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSC--------------EEEE-------------TTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCe--------------EEEc-------------cCCCeeCHHHHHHHHHhCCcCCccC
Confidence            479999999976443              3444             7999999999999999999999997

...

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

Probab=99.23  E-value=3.9e-12  Score=106.05  Aligned_cols=76  Identities=24%  Similarity=0.440  Sum_probs=62.7

Q ss_pred             CchhhhcCCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC
Q 013396           13 SPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS   92 (444)
Q Consensus        13 S~~a~ve~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss   92 (444)
                      .+.+++..++.   -+.|+||+..|.+.++++...-              .-.++++++++.|+|.||.+||.+||++..
T Consensus         9 ~aVa~Wswdi~---id~CaICRnhim~~C~eCq~~~--------------~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~   71 (88)
T COG5194           9 HAVALWSWDIP---IDVCAICRNHIMGTCPECQFGM--------------TPGDECPVVWGVCNHAFHDHCIYRWLDTKG   71 (88)
T ss_pred             eEEEEEecccc---cchhhhhhccccCcCcccccCC--------------CCCCcceEEEEecchHHHHHHHHHHHhhCC
Confidence            34677777776   4899999999999998886610              124567889999999999999999999999


Q ss_pred             CCCCcccCCCCCC
Q 013396           93 QCPMCWQPISLKD  105 (444)
Q Consensus        93 sCP~CRq~i~~k~  105 (444)
                      .||+||+.+...+
T Consensus        72 ~CPld~q~w~~~~   84 (88)
T COG5194          72 VCPLDRQTWVLAD   84 (88)
T ss_pred             CCCCCCceeEEec
Confidence            9999999987654

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

Probab=99.23  E-value=2.4e-12  Score=106.55  Aligned_cols=62  Identities=37%  Similarity=0.778  Sum_probs=52.0

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC---CCCCCcccCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS---SQCPMCWQPIS  102 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s---ssCP~CRq~i~  102 (444)
                      .+++|.||+-.|...++.++.++|                 .++++++.|.|.||.+||.+|+...   .+|||||+.|.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgD-----------------dCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGD-----------------DCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCC-----------------CCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            356999999999999999988544                 3466788999999999999999653   47999999986


Q ss_pred             CC
Q 013396          103 LK  104 (444)
Q Consensus       103 ~k  104 (444)
                      .+
T Consensus        82 ~~   83 (84)
T KOG1493|consen   82 FK   83 (84)
T ss_pred             ec
Confidence            54

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.11  E-value=5e-11  Score=115.91  Aligned_cols=72  Identities=24%  Similarity=0.575  Sum_probs=49.0

Q ss_pred             hhcCchhhhc---CCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHH
Q 013396           10 RLTSPAAFVE---GGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE   86 (444)
Q Consensus        10 ~l~S~~a~ve---~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~   86 (444)
                      -+.+.+.++.   .......+..|+||++.+.+......          +            ..++++|+|.||..||.+
T Consensus       154 ~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~----------~------------~~vl~~C~H~FC~~CI~~  211 (238)
T PHA02929        154 FLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNM----------Y------------FGILSNCNHVFCIECIDI  211 (238)
T ss_pred             HHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccc----------c------------ceecCCCCCcccHHHHHH
Confidence            3444455542   22234557899999999876321100          0            112338999999999999


Q ss_pred             HhccCCCCCCcccCCCC
Q 013396           87 WCQRSSQCPMCWQPISL  103 (444)
Q Consensus        87 Wlk~sssCP~CRq~i~~  103 (444)
                      |++...+||+||..+..
T Consensus       212 Wl~~~~tCPlCR~~~~~  228 (238)
T PHA02929        212 WKKEKNTCPVCRTPFIS  228 (238)
T ss_pred             HHhcCCCCCCCCCEeeE
Confidence            99999999999998753

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

Probab=99.05  E-value=8.7e-11  Score=119.51  Aligned_cols=51  Identities=37%  Similarity=0.969  Sum_probs=43.0

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISLKD  105 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~k~  105 (444)
                      +.|+||+|.|..++...              +|             +|+|.||..||..|+... ..||+||+.+....
T Consensus       230 ~~CaIClEdY~~GdklR--------------iL-------------PC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLR--------------IL-------------PCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDS  281 (348)
T ss_pred             ceEEEeecccccCCeee--------------Ee-------------cCCCchhhccchhhHhhcCccCCCCCCcCCCCC
Confidence            59999999999988643              34             899999999999999775 56999999876544

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

Probab=99.03  E-value=1.5e-10  Score=118.54  Aligned_cols=76  Identities=26%  Similarity=0.658  Sum_probs=51.4

Q ss_pred             ccchhhhhcCchhhhcCCCCCCCCCcccccccCCCCCC-CCcccccccccceeeeeeeccCCccccccccCCCCChhcHH
Q 013396            4 NKQCDARLTSPAAFVEGGIQDACDDACSICLEPFSDSD-PSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQ   82 (444)
Q Consensus         4 ~~~~~~~l~S~~a~ve~~iqd~~Dd~CsICLE~F~~~~-~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~   82 (444)
                      +|+.++.+..+....    ...+|..|.||||.+-..+ ......+|     +-|..|             +|||+||.+
T Consensus       268 ~kdl~~~~~t~t~eq----l~n~D~~C~ICmde~~h~~~~~~~~~~~-----~~pKrL-------------pCGHilHl~  325 (491)
T COG5243         268 TKDLNAMYPTATEEQ----LTNSDRTCTICMDEMFHPDHEPLPRGLD-----MTPKRL-------------PCGHILHLH  325 (491)
T ss_pred             hhHHHhhcchhhhhh----hcCCCCeEEEecccccCCCCccCccccc-----CCcccc-------------cccceeeHH
Confidence            355555554332221    2456889999999955443 22211111     225556             899999999


Q ss_pred             HHHHHhccCCCCCCcccCC
Q 013396           83 CVLEWCQRSSQCPMCWQPI  101 (444)
Q Consensus        83 CI~~Wlk~sssCP~CRq~i  101 (444)
                      |++.|++++++||+||.++
T Consensus       326 CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         326 CLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             HHHHHHHhccCCCcccCcc
Confidence            9999999999999999984

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.89  E-value=1.2e-09  Score=103.68  Aligned_cols=52  Identities=31%  Similarity=0.741  Sum_probs=41.6

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-------------
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-------------   90 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-------------   90 (444)
                      ..++..|+||++.+.+                 ||++             .|||.||..||.+|+..             
T Consensus        15 ~~~~~~CpICld~~~d-----------------PVvT-------------~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~   64 (193)
T PLN03208         15 SGGDFDCNICLDQVRD-----------------PVVT-------------LCGHLFCWPCIHKWTYASNNSRQRVDQYDH   64 (193)
T ss_pred             CCCccCCccCCCcCCC-----------------cEEc-------------CCCchhHHHHHHHHHHhccccccccccccc
Confidence            3456789999998866                 5556             89999999999999842             


Q ss_pred             ---CCCCCCcccCCCCCC
Q 013396           91 ---SSQCPMCWQPISLKD  105 (444)
Q Consensus        91 ---sssCP~CRq~i~~k~  105 (444)
                         ...||+||..+....
T Consensus        65 ~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         65 KREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             cCCCCcCCCCCCcCChhc
Confidence               237999999986544

>smart00504 Ubox Modified RING finger domain

Probab=98.86  E-value=2.7e-09  Score=81.20  Aligned_cols=53  Identities=25%  Similarity=0.419  Sum_probs=44.5

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      +..|+||++.|.+                 ||++             +|||.|++.||.+|++....||+|++.+...+.
T Consensus         1 ~~~Cpi~~~~~~~-----------------Pv~~-------------~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l   50 (63)
T smart00504        1 EFLCPISLEVMKD-----------------PVIL-------------PSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDL   50 (63)
T ss_pred             CcCCcCCCCcCCC-----------------CEEC-------------CCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhc
Confidence            3579999999887                 6666             899999999999999888899999999866554


Q ss_pred             Ccc
Q 013396          107 TRF  109 (444)
Q Consensus       107 ~~~  109 (444)
                      .++
T Consensus        51 ~~~   53 (63)
T smart00504       51 IPN   53 (63)
T ss_pred             eeC
Confidence            443

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

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

Probab=98.84  E-value=4e-10  Score=98.03  Aligned_cols=78  Identities=19%  Similarity=0.374  Sum_probs=60.9

Q ss_pred             hhcCchhhhcCCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc
Q 013396           10 RLTSPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ   89 (444)
Q Consensus        10 ~l~S~~a~ve~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk   89 (444)
                      |.=.+.|++.++|.   -+.|+||+..+.+.|..+...            . .....++.+++|.|+|.||.+||.+|++
T Consensus        32 KKWnAvAlWaWDi~---vDnCAICRnHIMd~CieCQa~------------~-~~~~~EC~VaWG~CNHaFH~hCisrWlk   95 (114)
T KOG2930|consen   32 KKWNAVALWAWDIV---VDNCAICRNHIMDLCIECQAN------------Q-SATSEECTVAWGVCNHAFHFHCISRWLK   95 (114)
T ss_pred             eeeeeeeeeeeeee---echhHHHHHHHHHHHHhhccC------------C-CCCCCceEEEeeecchHHHHHHHHHHHh
Confidence            34456788877775   578999999998876555441            0 0134567889999999999999999999


Q ss_pred             cCCCCCCcccCCCC
Q 013396           90 RSSQCPMCWQPISL  103 (444)
Q Consensus        90 ~sssCP~CRq~i~~  103 (444)
                      +...||+|.+.+..
T Consensus        96 tr~vCPLdn~eW~~  109 (114)
T KOG2930|consen   96 TRNVCPLDNKEWVF  109 (114)
T ss_pred             hcCcCCCcCcceeE
Confidence            99999999888754

>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=98.80  E-value=3.2e-09  Score=79.10  Aligned_cols=46  Identities=43%  Similarity=0.966  Sum_probs=38.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      +..|.||++...+                 ++++             +|||. ||..|+.+|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~-----------------~~~~-------------pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD-----------------VVLL-------------PCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS-----------------EEEE-------------TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc-----------------eEEe-------------CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            5789999998655                 4555             89999 999999999999999999999875

...

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

Probab=98.77  E-value=5.1e-09  Score=76.74  Aligned_cols=38  Identities=39%  Similarity=0.926  Sum_probs=30.2

Q ss_pred             ccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC----CCCCCc
Q 013396           30 CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS----SQCPMC   97 (444)
Q Consensus        30 CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s----ssCP~C   97 (444)
                      |+||++.|.+                 ||+|             +|||.||..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~-----------------Pv~l-------------~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD-----------------PVSL-------------PCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS-----------------EEE--------------SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC-----------------cccc-------------CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999988                 8999             899999999999999764    369998

>PHA02926 zinc finger-like protein; Provisional

Probab=98.76  E-value=4.9e-09  Score=101.64  Aligned_cols=63  Identities=22%  Similarity=0.524  Sum_probs=44.1

Q ss_pred             CCCCCCcccccccCCCCCC-CCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC------CCCC
Q 013396           23 QDACDDACSICLEPFSDSD-PSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS------SQCP   95 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~-~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s------ssCP   95 (444)
                      +...|..|+||||...+.. +...          ++.            .+++|+|.||..||..|.+..      ..||
T Consensus       166 ~~SkE~eCgICmE~I~eK~~~~eR----------rFG------------IL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCP  223 (242)
T PHA02926        166 RVSKEKECGICYEVVYSKRLENDR----------YFG------------LLDSCNHIFCITCINIWHRTRRETGASDNCP  223 (242)
T ss_pred             hccCCCCCccCccccccccccccc----------ccc------------ccCCCCchHHHHHHHHHHHhccccCcCCcCC
Confidence            4456789999999875431 1100          122            234899999999999999753      3699


Q ss_pred             CcccCCCCCCCC
Q 013396           96 MCWQPISLKDPT  107 (444)
Q Consensus        96 ~CRq~i~~k~~~  107 (444)
                      +||+.+....+.
T Consensus       224 iCR~~f~~I~pS  235 (242)
T PHA02926        224 ICRTRFRNITMS  235 (242)
T ss_pred             CCcceeeeeccc
Confidence            999988765543

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

Probab=98.74  E-value=7.3e-09  Score=103.16  Aligned_cols=53  Identities=34%  Similarity=0.871  Sum_probs=42.7

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      ....+..|.||||...+..                              .++|||+||..||.+|+.....||+||+.+.
T Consensus       235 i~~a~~kC~LCLe~~~~pS------------------------------aTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~  284 (293)
T KOG0317|consen  235 IPEATRKCSLCLENRSNPS------------------------------ATPCGHIFCWSCILEWCSEKAECPLCREKFQ  284 (293)
T ss_pred             CCCCCCceEEEecCCCCCC------------------------------cCcCcchHHHHHHHHHHccccCCCcccccCC
Confidence            3455678999999865521                              2289999999999999999999999999886


Q ss_pred             CCC
Q 013396          103 LKD  105 (444)
Q Consensus       103 ~k~  105 (444)
                      ...
T Consensus       285 psk  287 (293)
T KOG0317|consen  285 PSK  287 (293)
T ss_pred             Ccc
Confidence            543

>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=98.71  E-value=8.1e-09  Score=73.53  Aligned_cols=38  Identities=34%  Similarity=1.059  Sum_probs=31.5

Q ss_pred             ccccccCCCCCCCCcccccccccceeee-eeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCc
Q 013396           30 CSICLEPFSDSDPSTVTSFDFHVRFFRV-VILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMC   97 (444)
Q Consensus        30 CsICLE~F~~~~~~~~~~~~~~~~~~~p-ViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~C   97 (444)
                      |+||++.+.+                 | |++             +|||.||..||.+|++....||+|
T Consensus         1 C~iC~~~~~~-----------------~~~~~-------------~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD-----------------PVVVT-------------PCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS-----------------EEEEC-------------TTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC-----------------cCEEC-------------CCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999998776                 4 344             899999999999999888899998

>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=98.68  E-value=1.3e-08  Score=70.50  Aligned_cols=28  Identities=36%  Similarity=1.057  Sum_probs=25.1

Q ss_pred             CCCChhcHHHHHHHhcc-CCCCCCcccCC
Q 013396           74 SCRHEFHLQCVLEWCQR-SSQCPMCWQPI  101 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~-sssCP~CRq~i  101 (444)
                      +|+|.||..|+..|++. ...||+|+..+
T Consensus        17 ~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162          17 PCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            69999999999999987 67899998754

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.65  E-value=2.4e-08  Score=103.55  Aligned_cols=59  Identities=22%  Similarity=0.432  Sum_probs=46.6

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      .+..|+||++.|..                 ||++             +|||.||..||..|+.....||+|+..+....
T Consensus        25 ~~l~C~IC~d~~~~-----------------Pvit-------------pCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~   74 (397)
T TIGR00599        25 TSLRCHICKDFFDV-----------------PVLT-------------SCSHTFCSLCIRRCLSNQPKCPLCRAEDQESK   74 (397)
T ss_pred             cccCCCcCchhhhC-----------------ccCC-------------CCCCchhHHHHHHHHhCCCCCCCCCCcccccc
Confidence            46789999999876                 5555             89999999999999988888999999987654


Q ss_pred             CCccchHHH
Q 013396          106 PTRFCVNFA  114 (444)
Q Consensus       106 ~~~~~~~~a  114 (444)
                      ...+..+..
T Consensus        75 Lr~N~~L~~   83 (397)
T TIGR00599        75 LRSNWLVSE   83 (397)
T ss_pred             CccchHHHH
Confidence            444443333

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

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

Probab=98.64  E-value=1.2e-08  Score=95.89  Aligned_cols=50  Identities=32%  Similarity=0.705  Sum_probs=42.0

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      -.|+|||+.|....               ||..             +|||+||..||+.-++....||+|++.+..+.
T Consensus       132 ~~CPiCl~~~sek~---------------~vsT-------------kCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  132 YKCPICLDSVSEKV---------------PVST-------------KCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cCCCceecchhhcc---------------cccc-------------ccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            56999999988732               2333             89999999999999999999999999877664

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

Probab=98.63  E-value=1.7e-08  Score=97.87  Aligned_cols=55  Identities=31%  Similarity=0.707  Sum_probs=44.0

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC---CCCCCccc
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS---SQCPMCWQ   99 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s---ssCP~CRq   99 (444)
                      .+...-.|.||||.-.+                 ||++             .|||.||.-||.+|+..+   ..||+||.
T Consensus        43 ~~~~~FdCNICLd~akd-----------------PVvT-------------lCGHLFCWpClyqWl~~~~~~~~cPVCK~   92 (230)
T KOG0823|consen   43 RDGGFFDCNICLDLAKD-----------------PVVT-------------LCGHLFCWPCLYQWLQTRPNSKECPVCKA   92 (230)
T ss_pred             CCCCceeeeeeccccCC-----------------CEEe-------------ecccceehHHHHHHHhhcCCCeeCCcccc
Confidence            35567789999998555                 6666             799999999999999764   47999999


Q ss_pred             CCCCCCCC
Q 013396          100 PISLKDPT  107 (444)
Q Consensus       100 ~i~~k~~~  107 (444)
                      .+..+...
T Consensus        93 ~Vs~~~vv  100 (230)
T KOG0823|consen   93 EVSIDTVV  100 (230)
T ss_pred             ccccceEE
Confidence            88765543

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

Probab=98.62  E-value=1.3e-08  Score=102.50  Aligned_cols=49  Identities=39%  Similarity=0.958  Sum_probs=40.3

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc-cCCCCCCcccCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ-RSSQCPMCWQPISL  103 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk-~sssCP~CRq~i~~  103 (444)
                      -.|+|||+.|...+              +.++|             +|.|.||..||.+|+. -+..||+||..+..
T Consensus       324 veCaICms~fiK~d--------------~~~vl-------------PC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         324 VECAICMSNFIKND--------------RLRVL-------------PCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             ceEEEEhhhhcccc--------------eEEEe-------------ccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            57999999996433              34556             9999999999999997 46799999998753

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

Probab=98.57  E-value=2e-08  Score=106.80  Aligned_cols=54  Identities=33%  Similarity=0.721  Sum_probs=43.5

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..++.|+||+|.+..+...  .          |.+|             +|+|+||..|+..|+++.++||+||..+..
T Consensus       289 ~~~~~C~IC~e~l~~~~~~--~----------~~rL-------------~C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNI--T----------PKRL-------------PCGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             hcCCeeeeechhhcccccc--c----------ccee-------------ecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            4478999999999875431  1          2344             799999999999999999999999995443

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

Probab=98.53  E-value=1e-07  Score=76.54  Aligned_cols=65  Identities=23%  Similarity=0.334  Sum_probs=48.0

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLKD  105 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k~  105 (444)
                      +..|+||.+.|.+                 ||++             +|||.|.+.||.+|++. ...||+|++.+...+
T Consensus         4 ~f~CpIt~~lM~d-----------------PVi~-------------~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    4 EFLCPITGELMRD-----------------PVIL-------------PSGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGB-TTTSSB-SS-----------------EEEE-------------TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             ccCCcCcCcHhhC-----------------ceeC-------------CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            5689999999988                 8999             89999999999999988 789999999998877


Q ss_pred             CCccchHHHH-HHHHHh
Q 013396          106 PTRFCVNFAA-RNYLRR  121 (444)
Q Consensus       106 ~~~~~~~~av-r~~lR~  121 (444)
                      ..++..+... ..++..
T Consensus        54 l~pn~~Lk~~I~~~~~~   70 (73)
T PF04564_consen   54 LIPNRALKSAIEEWCAE   70 (73)
T ss_dssp             SEE-HHHHHHHHHHHHH
T ss_pred             ceECHHHHHHHHHHHHH
Confidence            7666555443 444443

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

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

Probab=98.52  E-value=6.1e-08  Score=68.81  Aligned_cols=38  Identities=50%  Similarity=1.281  Sum_probs=32.0

Q ss_pred             ccccccCCCCCCCCcccccccccceeeee-eeccCCccccccccCCCCChhcHHHHHHHhc--cCCCCCCc
Q 013396           30 CSICLEPFSDSDPSTVTSFDFHVRFFRVV-ILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ--RSSQCPMC   97 (444)
Q Consensus        30 CsICLE~F~~~~~~~~~~~~~~~~~~~pV-iL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk--~sssCP~C   97 (444)
                      |+||++.+..                 ++ ++             +|||.||..||.+|++  ....||+|
T Consensus         1 C~iC~~~~~~-----------------~~~~~-------------~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED-----------------PVILL-------------PCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS-----------------EEEET-------------TTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC-----------------CCEEe-------------cCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999999877                 34 33             8999999999999998  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=98.49  E-value=1.3e-07  Score=63.23  Aligned_cols=24  Identities=33%  Similarity=1.140  Sum_probs=21.7

Q ss_pred             CCCChhcHHHHHHHhc-cCCCCCCc
Q 013396           74 SCRHEFHLQCVLEWCQ-RSSQCPMC   97 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk-~sssCP~C   97 (444)
                      +|+|.||..|+..|++ ....||+|
T Consensus        15 ~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184       15 PCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             cCCChHHHHHHHHHHHhCcCCCCCC
Confidence            8999999999999998 55679998

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)

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

Probab=98.37  E-value=1.5e-07  Score=99.65  Aligned_cols=50  Identities=46%  Similarity=0.858  Sum_probs=40.4

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-----CCCCCcccCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-----SQCPMCWQPI  101 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-----ssCP~CRq~i  101 (444)
                      +..|+|||+....                 |++             +.|||+||..||..+|...     ..||+||..+
T Consensus       186 ~~~CPICL~~~~~-----------------p~~-------------t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I  235 (513)
T KOG2164|consen  186 DMQCPICLEPPSV-----------------PVR-------------TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTI  235 (513)
T ss_pred             CCcCCcccCCCCc-----------------ccc-------------cccCceeeHHHHHHHHhhhcccCCccCCchhhhc
Confidence            7899999998543                 233             3799999999999988654     4799999999


Q ss_pred             CCCCC
Q 013396          102 SLKDP  106 (444)
Q Consensus       102 ~~k~~  106 (444)
                      .+++.
T Consensus       236 ~~kdl  240 (513)
T KOG2164|consen  236 TLKDL  240 (513)
T ss_pred             cccce
Confidence            88664

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

Probab=98.35  E-value=2.1e-07  Score=95.04  Aligned_cols=59  Identities=25%  Similarity=0.488  Sum_probs=49.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      -..|.||.|.|..                 |||+             +|+|.||.-||..+|..+..||.|+..+...+.
T Consensus        23 lLRC~IC~eyf~i-----------------p~it-------------pCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   23 LLRCGICFEYFNI-----------------PMIT-------------PCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHhHHHHHhcC-----------------ceec-------------cccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence            3579999999987                 5666             999999999999999999999999999988776


Q ss_pred             CccchHHHH
Q 013396          107 TRFCVNFAA  115 (444)
Q Consensus       107 ~~~~~~~av  115 (444)
                      ..+..+..+
T Consensus        73 r~n~il~Ei   81 (442)
T KOG0287|consen   73 RNNRILDEI   81 (442)
T ss_pred             hhhhHHHHH
Confidence            666555544

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.34  E-value=3.6e-07  Score=66.87  Aligned_cols=44  Identities=34%  Similarity=0.841  Sum_probs=35.2

Q ss_pred             cccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCccc
Q 013396           29 ACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        29 ~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      .|.||++.|....              .|++|             +|||+||..||..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~--------------~~~l~-------------~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEER--------------RPRLT-------------SCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCC--------------CeEEc-------------ccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4999999993321              14555             89999999999999966778999985

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

Probab=98.25  E-value=4.4e-07  Score=96.09  Aligned_cols=33  Identities=42%  Similarity=1.038  Sum_probs=29.3

Q ss_pred             cccCCCCChhcHHHHHHHhcc-CCCCCCcccCCC
Q 013396           70 LQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPIS  102 (444)
Q Consensus        70 ~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~  102 (444)
                      +++++|+|+||..|++.|+.+ ...||+||+++.
T Consensus       601 Ym~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  601 YMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             ccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            577899999999999999995 559999999875

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

Probab=98.23  E-value=6.2e-07  Score=88.76  Aligned_cols=51  Identities=31%  Similarity=0.714  Sum_probs=41.2

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHH-HhccCCC-CCCcccCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE-WCQRSSQ-CPMCWQPIS  102 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~-Wlk~sss-CP~CRq~i~  102 (444)
                      ..|..|.||++....                 |+.+             +|||+||..||.. |-++... ||+||+...
T Consensus       213 ~~d~kC~lC~e~~~~-----------------ps~t-------------~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~  262 (271)
T COG5574         213 LADYKCFLCLEEPEV-----------------PSCT-------------PCGHLFCLSCLLISWTKKKYEFCPLCRAKVY  262 (271)
T ss_pred             ccccceeeeecccCC-----------------cccc-------------cccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence            457889999998554                 3333             8999999999999 8877665 999999887


Q ss_pred             CCC
Q 013396          103 LKD  105 (444)
Q Consensus       103 ~k~  105 (444)
                      ++.
T Consensus       263 pk~  265 (271)
T COG5574         263 PKK  265 (271)
T ss_pred             chh
Confidence            665

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

Probab=98.23  E-value=4.6e-07  Score=81.39  Aligned_cols=45  Identities=33%  Similarity=0.792  Sum_probs=38.1

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCccc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      .++..|+||++.|...                 ++|             +|+|.||..||..|+.....||.||.
T Consensus        11 ~~~~~C~iC~~~~~~p-----------------~~l-------------~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP-----------------VLL-------------PCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             cccccChhhHHHhhcC-----------------ccc-------------cccchHhHHHHHHhcCCCcCCcccCC
Confidence            3577899999999883                 344             89999999999999885568999995

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

Probab=98.04  E-value=2.9e-06  Score=63.09  Aligned_cols=39  Identities=36%  Similarity=0.872  Sum_probs=22.6

Q ss_pred             ccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC----CCCC
Q 013396           30 CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS----SQCP   95 (444)
Q Consensus        30 CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s----ssCP   95 (444)
                      |+||+| |.+.+-             -|++|             +|||.||.+||.+|+++.    ..||
T Consensus         1 CpIc~e-~~~~~n-------------~P~~L-------------~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEEN-------------PPMVL-------------PCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS--------------EEE--------------SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCC-------------CCEEE-------------eCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 765432             17777             899999999999999754    2576

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

Probab=97.94  E-value=5.6e-06  Score=83.51  Aligned_cols=52  Identities=21%  Similarity=0.352  Sum_probs=43.2

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      -+.|-||-+.|..                 |+++             +|||.||.-||...|..+.-||+||.+......
T Consensus        25 ~lrC~IC~~~i~i-----------------p~~T-------------tCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrl   74 (391)
T COG5432          25 MLRCRICDCRISI-----------------PCET-------------TCGHTFCSLCIRRHLGTQPFCPVCREDPCESRL   74 (391)
T ss_pred             HHHhhhhhheeec-----------------ceec-------------ccccchhHHHHHHHhcCCCCCccccccHHhhhc
Confidence            3579999998887                 4444             899999999999999999999999998765544


Q ss_pred             Cc
Q 013396          107 TR  108 (444)
Q Consensus       107 ~~  108 (444)
                      ..
T Consensus        75 r~   76 (391)
T COG5432          75 RG   76 (391)
T ss_pred             cc
Confidence            33

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

Probab=97.84  E-value=2.5e-06  Score=68.77  Aligned_cols=30  Identities=50%  Similarity=1.121  Sum_probs=18.0

Q ss_pred             CCCChhcHHHHHHHhcc---C--------CCCCCcccCCCC
Q 013396           74 SCRHEFHLQCVLEWCQR---S--------SQCPMCWQPISL  103 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~---s--------ssCP~CRq~i~~  103 (444)
                      .|++.||..||.+|+..   .        ..||.|+.++..
T Consensus        27 ~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen   27 SCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             T----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             ccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            79999999999999953   1        259999998754

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.84  E-value=1.5e-05  Score=80.70  Aligned_cols=33  Identities=27%  Similarity=0.547  Sum_probs=27.5

Q ss_pred             CCCChhcHHHHHHHh-ccCCCCCCcccCCCCCCC
Q 013396           74 SCRHEFHLQCVLEWC-QRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wl-k~sssCP~CRq~i~~k~~  106 (444)
                      .|||.||..||...| .....||.|+.++.....
T Consensus        25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f   58 (309)
T TIGR00570        25 VCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF   58 (309)
T ss_pred             CCCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence            799999999999955 545689999998876653

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).

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

Probab=97.83  E-value=4.1e-06  Score=83.68  Aligned_cols=61  Identities=30%  Similarity=0.679  Sum_probs=42.5

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHh--ccCCCCCCcccCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWC--QRSSQCPMCWQPIS  102 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wl--k~sssCP~CRq~i~  102 (444)
                      .+|..|+||-..|..+......       ++---.|             .|+|.||..||..|+  .+.++||.|+..+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegv-------ienty~L-------------sCnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGV-------IENTYKL-------------SCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCcchhHhhcchheeecchhhh-------hhhheee-------------ecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            4578899999988764311100       0111122             699999999999998  44678999999887


Q ss_pred             CCC
Q 013396          103 LKD  105 (444)
Q Consensus       103 ~k~  105 (444)
                      .+.
T Consensus       282 l~r  284 (328)
T KOG1734|consen  282 LKR  284 (328)
T ss_pred             Hhh
Confidence            654

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

Probab=97.73  E-value=1.2e-05  Score=65.08  Aligned_cols=54  Identities=30%  Similarity=0.613  Sum_probs=26.3

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPT  107 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~~  107 (444)
                      ..|+||.+.|..                 ||.|            +.|.|+||..||..-+.  ..||+|..+...++..
T Consensus         8 LrCs~C~~~l~~-----------------pv~l------------~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    8 LRCSICFDILKE-----------------PVCL------------GGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TS-SSS-S--SS------------------B---------------SSS--B-TTTGGGGTT--TB-SSS--B-S-SS--
T ss_pred             cCCcHHHHHhcC-----------------Ccee------------ccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHH
Confidence            479999999887                 5554            38999999999987554  3599999988777654


Q ss_pred             ccchH
Q 013396          108 RFCVN  112 (444)
Q Consensus       108 ~~~~~  112 (444)
                      .+.++
T Consensus        57 ~NrqL   61 (65)
T PF14835_consen   57 INRQL   61 (65)
T ss_dssp             --HHH
T ss_pred             hhhhh
Confidence            44443

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

Probab=97.73  E-value=2.2e-05  Score=80.47  Aligned_cols=64  Identities=33%  Similarity=0.822  Sum_probs=45.5

Q ss_pred             CCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHh--cc-----CCC
Q 013396           21 GIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWC--QR-----SSQ   93 (444)
Q Consensus        21 ~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wl--k~-----sss   93 (444)
                      ..+...|..|.||||...+.-+          +.-|..|            +++|.|.||..||..|-  .+     ...
T Consensus       155 a~~~s~~k~CGICme~i~ek~~----------~~~rfgi------------lpnC~H~~Cl~Cir~wr~~~q~~~~~sks  212 (344)
T KOG1039|consen  155 ALQKSSEKECGICMETINEKAA----------SERRFGI------------LPNCNHSFCLNCIRKWRQATQFESKTSKS  212 (344)
T ss_pred             CcCccccccceehhhhccccch----------hhhhccc------------CCCcchhhhhcHhHhhhhhhccccccccC
Confidence            4456778999999999776321          0112222            34799999999999998  33     458


Q ss_pred             CCCcccCCCCCCC
Q 013396           94 CPMCWQPISLKDP  106 (444)
Q Consensus        94 CP~CRq~i~~k~~  106 (444)
                      ||.||.......+
T Consensus       213 CP~CRv~s~~v~p  225 (344)
T KOG1039|consen  213 CPFCRVPSSFVNP  225 (344)
T ss_pred             CCcccCccccccc
Confidence            9999998765543

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

Probab=97.69  E-value=1.9e-05  Score=82.12  Aligned_cols=29  Identities=31%  Similarity=0.966  Sum_probs=24.3

Q ss_pred             ccCCCCChhcHHHHHHHhccC---CCCCCccc
Q 013396           71 QLTSCRHEFHLQCVLEWCQRS---SQCPMCWQ   99 (444)
Q Consensus        71 ~l~~CgH~FH~~CI~~Wlk~s---ssCP~CRq   99 (444)
                      .++.|||+||..|+..|+...   ..||+|+-
T Consensus        22 ~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i   53 (465)
T KOG0827|consen   22 PIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI   53 (465)
T ss_pred             cccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence            444699999999999999873   47999983

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

Probab=97.61  E-value=1.6e-05  Score=89.40  Aligned_cols=54  Identities=30%  Similarity=0.835  Sum_probs=40.7

Q ss_pred             CCCCCCcccccccCCCCCC---CCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--CCCCCCc
Q 013396           23 QDACDDACSICLEPFSDSD---PSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--SSQCPMC   97 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~---~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--sssCP~C   97 (444)
                      +-.+-+.|+||+..+..-+   |...+                          +.|.|.||..|+.+|+..  +..||+|
T Consensus      1465 ~fsG~eECaICYsvL~~vdr~lPskrC--------------------------~TCknKFH~~CLyKWf~Ss~~s~CPlC 1518 (1525)
T COG5219        1465 KFSGHEECAICYSVLDMVDRSLPSKRC--------------------------ATCKNKFHTRCLYKWFASSARSNCPLC 1518 (1525)
T ss_pred             hcCCcchhhHHHHHHHHHhccCCcccc--------------------------chhhhhhhHHHHHHHHHhcCCCCCCcc
Confidence            4466789999998877221   33222                          269999999999999976  4689999


Q ss_pred             ccCCC
Q 013396           98 WQPIS  102 (444)
Q Consensus        98 Rq~i~  102 (444)
                      |..+.
T Consensus      1519 Rseit 1523 (1525)
T COG5219        1519 RSEIT 1523 (1525)
T ss_pred             ccccc
Confidence            97764

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

Probab=97.46  E-value=9.3e-05  Score=56.11  Aligned_cols=25  Identities=32%  Similarity=0.927  Sum_probs=21.0

Q ss_pred             CCC-----ChhcHHHHHHHhccC--CCCCCcc
Q 013396           74 SCR-----HEFHLQCVLEWCQRS--SQCPMCW   98 (444)
Q Consensus        74 ~Cg-----H~FH~~CI~~Wlk~s--ssCP~CR   98 (444)
                      +|.     |.+|..||.+|+..+  ..||+|+
T Consensus        18 PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744       18 PCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             ccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            675     899999999999554  4899995

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

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

Probab=97.45  E-value=6e-05  Score=81.01  Aligned_cols=117  Identities=21%  Similarity=0.402  Sum_probs=71.0

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-----CCCCCCc
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-----SSQCPMC   97 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-----sssCP~C   97 (444)
                      .+.++..|.+|.++-.+                 ++..             .|+|.||+.||.++...     .-+||.|
T Consensus       532 enk~~~~C~lc~d~aed-----------------~i~s-------------~ChH~FCrlCi~eyv~~f~~~~nvtCP~C  581 (791)
T KOG1002|consen  532 ENKGEVECGLCHDPAED-----------------YIES-------------SCHHKFCRLCIKEYVESFMENNNVTCPVC  581 (791)
T ss_pred             cccCceeecccCChhhh-----------------hHhh-------------hhhHHHHHHHHHHHHHhhhcccCCCCccc
Confidence            44567789999987544                 2222             89999999999998754     3589999


Q ss_pred             ccCCCCCCCCccchHHHHHHHHHhcccCCCeeeeeecCChh----HHHHHhhh--------cccchhhhhhhhhhhhhhh
Q 013396           98 WQPISLKDPTRFCVNFAARNYLRRSNKRGALVLIRLEIPPY----FIIRLWET--------LSYRVFVFCLWASFRQQYQ  165 (444)
Q Consensus        98 Rq~i~~k~~~~~~~~~avr~~lR~~~~r~A~IliRleipp~----fi~rl~e~--------~~~~~f~~~lw~sfr~~yq  165 (444)
                      -..+......+.  ++..    .....+++.|+-|+++..+    .|..|.|+        -+.+.++|+.+.||.++..
T Consensus       582 ~i~LsiDlse~a--lek~----~l~~Fk~sSIlnRinm~~~qsSTKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~  655 (791)
T KOG1002|consen  582 HIGLSIDLSEPA--LEKT----DLKGFKASSILNRINMDDWQSSTKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIE  655 (791)
T ss_pred             cccccccccchh--hhhc----chhhhhhHHHhhhcchhhhcchhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHH
Confidence            877765432222  1111    0111223445555555432    23334333        3478899999999999876


Q ss_pred             hhcccCcceee
Q 013396          166 VSLILSGGFIL  176 (444)
Q Consensus       166 ~s~~~~g~f~~  176 (444)
                      --+-- .+|.-
T Consensus       656 ~rL~k-aGfsc  665 (791)
T KOG1002|consen  656 WRLGK-AGFSC  665 (791)
T ss_pred             HHhhc-cCceE
Confidence            53333 34443

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

Probab=97.35  E-value=9e-05  Score=78.21  Aligned_cols=50  Identities=30%  Similarity=0.780  Sum_probs=36.8

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      .+-.+|+||||.+...-.-  .           +.             ..|.|.||-.|+.+|+..  +||+||--..
T Consensus       173 tELPTCpVCLERMD~s~~g--i-----------~t-------------~~c~Hsfh~~cl~~w~~~--scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTG--I-----------LT-------------ILCNHSFHCSCLMKWWDS--SCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccc--e-----------ee-------------eecccccchHHHhhcccC--cChhhhhhcC
Confidence            3456899999998764211  1           11             169999999999999865  5999987543

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

Probab=97.34  E-value=0.00011  Score=74.46  Aligned_cols=48  Identities=27%  Similarity=0.568  Sum_probs=38.1

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~k  104 (444)
                      +..|.||+....                 +||+|             .|+|.||..||+.-+++. ..|++||++|...
T Consensus         7 ~~eC~IC~nt~n-----------------~Pv~l-------------~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGN-----------------CPVNL-------------YCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCC-----------------cCccc-------------cccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            568999998633                 26777             899999999999866554 5699999998654

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

Probab=97.31  E-value=3.9e-05  Score=78.90  Aligned_cols=50  Identities=24%  Similarity=0.652  Sum_probs=39.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLKD  105 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k~  105 (444)
                      +..|+|||+.+.....                             ...|.|.||.+||.+-+.. ...||.||+.+.-+.
T Consensus        43 ~v~c~icl~llk~tmt-----------------------------tkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr   93 (381)
T KOG0311|consen   43 QVICPICLSLLKKTMT-----------------------------TKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR   93 (381)
T ss_pred             hhccHHHHHHHHhhcc-----------------------------cHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence            5689999999886321                             1169999999999988755 668999999887654

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

Probab=97.30  E-value=4.6e-05  Score=84.61  Aligned_cols=85  Identities=20%  Similarity=0.239  Sum_probs=49.8

Q ss_pred             CCCCCCCCcccccccCCCCCC-CCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCccc
Q 013396           21 GIQDACDDACSICLEPFSDSD-PSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        21 ~iqd~~Dd~CsICLE~F~~~~-~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      ++.....+.|.||.-.|.... ....++.+-++.-++|.-|.. ...-++..--+|+|+||.+||..|.....+||+||.
T Consensus        90 DeK~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~  168 (1134)
T KOG0825|consen   90 DEKTAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRG  168 (1134)
T ss_pred             CcccccccccchhheecCCcccccCcCchhhhhhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhhcccCchhhh
Confidence            444555677888877777622 111111111122222222210 011123344479999999999999999999999999


Q ss_pred             CCCCCCC
Q 013396          100 PISLKDP  106 (444)
Q Consensus       100 ~i~~k~~  106 (444)
                      .|.....
T Consensus       169 EF~~v~V  175 (1134)
T KOG0825|consen  169 EFGEVKV  175 (1134)
T ss_pred             hhheeee
Confidence            9875543

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

Probab=97.17  E-value=0.00022  Score=74.59  Aligned_cols=60  Identities=23%  Similarity=0.609  Sum_probs=49.1

Q ss_pred             chhhhcCCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCC
Q 013396           14 PAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQ   93 (444)
Q Consensus        14 ~~a~ve~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sss   93 (444)
                      +.++..+..+...+..|.||+..|..                 ||.+             +|||.||..||.+-+.....
T Consensus        71 ~~~~~s~~~~~~sef~c~vc~~~l~~-----------------pv~t-------------pcghs~c~~Cl~r~ld~~~~  120 (398)
T KOG4159|consen   71 PKALLSGPEEIRSEFECCVCSRALYP-----------------PVVT-------------PCGHSFCLECLDRSLDQETE  120 (398)
T ss_pred             hhhhhccCccccchhhhhhhHhhcCC-----------------Cccc-------------cccccccHHHHHHHhccCCC
Confidence            34555566666788899999888765                 6666             99999999999998888889


Q ss_pred             CCCcccCCCC
Q 013396           94 CPMCWQPISL  103 (444)
Q Consensus        94 CP~CRq~i~~  103 (444)
                      ||.||..+..
T Consensus       121 cp~Cr~~l~e  130 (398)
T KOG4159|consen  121 CPLCRDELVE  130 (398)
T ss_pred             Cccccccccc
Confidence            9999998865

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

Probab=97.16  E-value=0.00013  Score=80.54  Aligned_cols=49  Identities=31%  Similarity=0.649  Sum_probs=39.8

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLKD  105 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k~  105 (444)
                      -..|+.|...+.+                 .||+             .|+|.||..||..-+.. ...||.|-..|..-+
T Consensus       643 ~LkCs~Cn~R~Kd-----------------~vI~-------------kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD-----------------AVIT-------------KCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             ceeCCCccCchhh-----------------HHHH-------------hcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            4579999977666                 3444             89999999999998865 568999999987655

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

Probab=97.12  E-value=0.00014  Score=57.69  Aligned_cols=29  Identities=31%  Similarity=0.751  Sum_probs=24.0

Q ss_pred             CCCCh-hcHHHHHHHhc-cCCCCCCcccCCC
Q 013396           74 SCRHE-FHLQCVLEWCQ-RSSQCPMCWQPIS  102 (444)
Q Consensus        74 ~CgH~-FH~~CI~~Wlk-~sssCP~CRq~i~  102 (444)
                      .|||+ .|..|-.+-++ .+.+||+||+++.
T Consensus        24 tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen   24 TCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             HcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            59997 79999887555 6789999999864

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

Probab=96.90  E-value=0.00066  Score=71.24  Aligned_cols=50  Identities=36%  Similarity=0.961  Sum_probs=38.7

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--CCCCCCcccC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--SSQCPMCWQP  100 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--sssCP~CRq~  100 (444)
                      +-.+|+||++.+...-.            +|-|+|             .|||.|..+||.+|+-+  ...||.|...
T Consensus         3 ~g~tcpiclds~~~~g~------------hr~vsl-------------~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGN------------HRIVSL-------------QCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             ccccCceeeeeeeecCc------------eEEeee-------------cccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            45689999999875321            356677             79999999999999953  2479999754

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

Probab=96.71  E-value=0.00063  Score=69.57  Aligned_cols=51  Identities=29%  Similarity=0.664  Sum_probs=41.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      -.+|.+|-..|.+..  ++.                           .|-|.||..||.+++.....||+|...+....+
T Consensus        15 ~itC~LC~GYliDAT--TI~---------------------------eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~p   65 (331)
T KOG2660|consen   15 HITCRLCGGYLIDAT--TIT---------------------------ECLHTFCKSCIVKYLEESKYCPTCDIVIHKTHP   65 (331)
T ss_pred             ceehhhccceeecch--hHH---------------------------HHHHHHHHHHHHHHHHHhccCCccceeccCccc
Confidence            358999999888732  222                           799999999999999999999999988765543

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

Probab=96.70  E-value=0.0011  Score=51.98  Aligned_cols=41  Identities=39%  Similarity=0.849  Sum_probs=28.4

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--CCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--SSQCPM   96 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--sssCP~   96 (444)
                      ...|+|.+..|.+                 ||.-+            .|||.|-+..|.+|+++  ...||+
T Consensus        11 ~~~CPiT~~~~~~-----------------PV~s~------------~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFED-----------------PVKSK------------KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SS-----------------EEEES------------SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhC-----------------CcCcC------------CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            5689999999887                 66653            89999999999999944  347998

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

Probab=96.67  E-value=0.00078  Score=69.92  Aligned_cols=52  Identities=29%  Similarity=0.692  Sum_probs=42.6

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      .++..|+||+..+.+.-..                             +.|||.||..||..|+..+..||.|++.+...
T Consensus        19 ~~~l~C~~C~~vl~~p~~~-----------------------------~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT-----------------------------TTCGHRFCAGCLLESLSNHQKCPVCRQELTQA   69 (391)
T ss_pred             cccccCccccccccCCCCC-----------------------------CCCCCcccccccchhhccCcCCcccccccchh
Confidence            4578899999998873211                             27999999999999999989999999887655


Q ss_pred             C
Q 013396          105 D  105 (444)
Q Consensus       105 ~  105 (444)
                      .
T Consensus        70 ~   70 (391)
T KOG0297|consen   70 E   70 (391)
T ss_pred             h
Confidence            4

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

Probab=96.60  E-value=0.0016  Score=67.25  Aligned_cols=46  Identities=37%  Similarity=0.837  Sum_probs=38.0

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      -..|.|||..-.+                 .|+|             +|.|. .|..|-+...-....||+||+++.
T Consensus       290 gkeCVIClse~rd-----------------t~vL-------------PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  290 GKECVICLSESRD-----------------TVVL-------------PCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             CCeeEEEecCCcc-----------------eEEe-------------cchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            4579999998666                 5677             99997 799999887666778999999874

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

Probab=96.49  E-value=0.0014  Score=76.81  Aligned_cols=30  Identities=37%  Similarity=0.814  Sum_probs=24.1

Q ss_pred             CCCChhcHHHHHHHhccC----------CCCCCcccCCCC
Q 013396           74 SCRHEFHLQCVLEWCQRS----------SQCPMCWQPISL  103 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~s----------ssCP~CRq~i~~  103 (444)
                      .|+|+||++|...-+++.          -+||+|++++..
T Consensus      3506 ~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3506 DCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             CCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            699999999998766543          279999998753

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

Probab=96.43  E-value=0.00079  Score=68.53  Aligned_cols=52  Identities=33%  Similarity=0.809  Sum_probs=40.4

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc----------------
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR----------------   90 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~----------------   90 (444)
                      ...|.|||.-|.+++..+++                           .|-|.||..|+.++|..                
T Consensus       115 ~gqCvICLygfa~~~~ft~T---------------------------~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~  167 (368)
T KOG4445|consen  115 NGQCVICLYGFASSPAFTVT---------------------------ACDHYMHFACLARYLTECLTGLRQEIQDAQKER  167 (368)
T ss_pred             CCceEEEEEeecCCCceeee---------------------------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35799999999987765555                           89999999999877632                


Q ss_pred             -------CCCCCCcccCCCCCC
Q 013396           91 -------SSQCPMCWQPISLKD  105 (444)
Q Consensus        91 -------sssCP~CRq~i~~k~  105 (444)
                             ...||+||..+....
T Consensus       168 qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  168 QHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             HHhhhhHhhhhhHhhhhccccc
Confidence                   125999999886543

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

Probab=96.13  E-value=0.0076  Score=59.68  Aligned_cols=69  Identities=30%  Similarity=0.518  Sum_probs=50.2

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--------CCCCCCc
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--------SSQCPMC   97 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--------sssCP~C   97 (444)
                      -+..|..|--.+..++..               .|             -|-|.||..|+.+|-..        ..+||.|
T Consensus        49 Y~pNC~LC~t~La~gdt~---------------RL-------------vCyhlfHW~ClneraA~lPanTAPaGyqCP~C  100 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTT---------------RL-------------VCYHLFHWKCLNERAANLPANTAPAGYQCPCC  100 (299)
T ss_pred             CCCCCceeCCccccCcce---------------ee-------------hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCC
Confidence            356799998888876532               33             59999999999999754        2389999


Q ss_pred             ccCCCCCCCCccchHHHHHHHHHhc
Q 013396           98 WQPISLKDPTRFCVNFAARNYLRRS  122 (444)
Q Consensus        98 Rq~i~~k~~~~~~~~~avr~~lR~~  122 (444)
                      -++|....-...++.++++..+...
T Consensus       101 s~eiFPp~NlvsPva~aLre~L~qv  125 (299)
T KOG3970|consen  101 SQEIFPPINLVSPVAEALREQLKQV  125 (299)
T ss_pred             CCccCCCccccchhHHHHHHHHHhh
Confidence            9998766555556666666555543

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

Probab=96.11  E-value=0.0028  Score=61.63  Aligned_cols=45  Identities=24%  Similarity=0.641  Sum_probs=38.3

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPI  101 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i  101 (444)
                      --.|.||-+.|..                 ||+.             .|||.||..|...-++....|-+|-...
T Consensus       196 PF~C~iCKkdy~s-----------------pvvt-------------~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYES-----------------PVVT-------------ECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccc-----------------hhhh-------------hcchhHHHHHHHHHhccCCcceecchhh
Confidence            3479999999887                 5555             7999999999999999999999997653

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

Probab=96.08  E-value=0.002  Score=65.35  Aligned_cols=45  Identities=31%  Similarity=0.574  Sum_probs=39.4

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      ..|-||.+.|..                 ||+.             .|+|.||..|-..-+++...|++|-+.+.
T Consensus       242 f~c~icr~~f~~-----------------pVvt-------------~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYR-----------------PVVT-------------KCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             cccccccccccc-----------------chhh-------------cCCceeehhhhccccccCCcceecccccc
Confidence            459999999887                 6666             89999999999999999999999987654

>PHA03096 p28-like protein; Provisional

Probab=96.02  E-value=0.0032  Score=63.39  Aligned_cols=50  Identities=28%  Similarity=0.494  Sum_probs=33.8

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC---CCCCCccc
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS---SQCPMCWQ   99 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s---ssCP~CRq   99 (444)
                      -.|.||||.........          .+..+|            +.|.|.||..||..|....   ..||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~----------~~fgil------------~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIK----------KYYGIL------------SEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhcccc----------cccccc------------ccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            57999999877532111          112334            4899999999999998653   25666654

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

Probab=95.72  E-value=0.0054  Score=64.70  Aligned_cols=32  Identities=25%  Similarity=0.720  Sum_probs=27.0

Q ss_pred             CCCChhcHHHHHHHhcc--CCCCCCcccCCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQR--SSQCPMCWQPISLKD  105 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~--sssCP~CRq~i~~k~  105 (444)
                      +|||..|..|+..|...  .+.||.||..|.-..
T Consensus       386 PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  386 PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             cccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            89999999999999844  468999999885443

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

Probab=95.57  E-value=0.0047  Score=64.94  Aligned_cols=50  Identities=30%  Similarity=0.675  Sum_probs=36.6

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC--CCCCCcccCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS--SQCPMCWQPI  101 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s--ssCP~CRq~i  101 (444)
                      -+..|..|-|.+.....             +--.|             +|.|+||..|+.+++.++  .+||.||...
T Consensus       364 ~~L~Cg~CGe~~Glk~e-------------~LqAL-------------pCsHIfH~rCl~e~L~~n~~rsCP~Crklr  415 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNE-------------RLQAL-------------PCSHIFHLRCLQEILENNGTRSCPNCRKLR  415 (518)
T ss_pred             HhhhhhhhhhhhcCCcc-------------ccccc-------------chhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            35679999998765331             11122             799999999999999664  5899998543

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

Probab=95.24  E-value=0.013  Score=56.38  Aligned_cols=32  Identities=41%  Similarity=1.014  Sum_probs=26.8

Q ss_pred             CCCChhcHHHHHHHhcc---C--------CCCCCcccCCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQR---S--------SQCPMCWQPISLKD  105 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~---s--------ssCP~CRq~i~~k~  105 (444)
                      +||.-||.-|+..||..   +        ..||.|-.++..|.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            79999999999999954   1        26999999887664

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

Probab=95.12  E-value=0.02  Score=44.02  Aligned_cols=28  Identities=21%  Similarity=0.638  Sum_probs=16.4

Q ss_pred             CCCChhcHHHHHHHhc-cCCCCCCcccCC
Q 013396           74 SCRHEFHLQCVLEWCQ-RSSQCPMCWQPI  101 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk-~sssCP~CRq~i  101 (444)
                      +||+..|+.|...-++ ....||-||+++
T Consensus        19 ~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen   19 ECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            6999999999988886 467899999876

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.02  E-value=0.019  Score=59.76  Aligned_cols=56  Identities=21%  Similarity=0.549  Sum_probs=38.7

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPIS  102 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~  102 (444)
                      +++|+.|+.|+|++...+.-...                    |      +||...|.-|-..--+. +..||-||+.+.
T Consensus        11 edeed~cplcie~mditdknf~p--------------------c------~cgy~ic~fc~~~irq~lngrcpacrr~y~   64 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFP--------------------C------PCGYQICQFCYNNIRQNLNGRCPACRRKYD   64 (480)
T ss_pred             ccccccCcccccccccccCCccc--------------------C------CcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence            45577799999998875532211                    1      79988777775543332 557999999987


Q ss_pred             CCC
Q 013396          103 LKD  105 (444)
Q Consensus       103 ~k~  105 (444)
                      ..+
T Consensus        65 den   67 (480)
T COG5175          65 DEN   67 (480)
T ss_pred             ccc
Confidence            655

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.82  E-value=0.036  Score=54.48  Aligned_cols=54  Identities=26%  Similarity=0.546  Sum_probs=39.9

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      .....|+|+...|...              .++|+|+            +|||+|...||.+-- ....||+|-.+|...
T Consensus       111 ~~~~~CPvt~~~~~~~--------------~~fv~l~------------~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGK--------------HKFVYLR------------PCGCVFSEKALKELK-KSKKCPVCGKPFTEE  163 (260)
T ss_pred             CceeECCCCCcccCCc--------------eeEEEEc------------CCCCEeeHHHHHhhc-ccccccccCCccccC
Confidence            3455788888887542              2355554            899999999999983 456799999998744


Q ss_pred             C
Q 013396          105 D  105 (444)
Q Consensus       105 ~  105 (444)
                      +
T Consensus       164 D  164 (260)
T PF04641_consen  164 D  164 (260)
T ss_pred             C
Confidence            3

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

Probab=94.72  E-value=0.025  Score=57.17  Aligned_cols=32  Identities=22%  Similarity=0.570  Sum_probs=25.0

Q ss_pred             ccCCCCChhcHHHHHHHhc--cCCCCCCcccCCC
Q 013396           71 QLTSCRHEFHLQCVLEWCQ--RSSQCPMCWQPIS  102 (444)
Q Consensus        71 ~l~~CgH~FH~~CI~~Wlk--~sssCP~CRq~i~  102 (444)
                      ++++|+|+||.-||..=+.  .+-.||.|-....
T Consensus       254 ~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  254 VIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             eeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            3448999999999998654  3568999977654

>PHA02862 5L protein; Provisional

Probab=94.68  E-value=0.025  Score=52.70  Aligned_cols=29  Identities=24%  Similarity=0.705  Sum_probs=23.8

Q ss_pred             ChhcHHHHHHHhccC--CCCCCcccCCCCCC
Q 013396           77 HEFHLQCVLEWCQRS--SQCPMCWQPISLKD  105 (444)
Q Consensus        77 H~FH~~CI~~Wlk~s--ssCP~CRq~i~~k~  105 (444)
                      ..-|..|+.+|++.+  ..|++|+.++..+.
T Consensus        26 K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~   56 (156)
T PHA02862         26 KVVHIKCMQLWINYSKKKECNLCKTKYNIKK   56 (156)
T ss_pred             hhHHHHHHHHHHhcCCCcCccCCCCeEEEEE
Confidence            578999999999664  47999999886543

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

Probab=94.56  E-value=0.045  Score=56.25  Aligned_cols=53  Identities=21%  Similarity=0.412  Sum_probs=37.8

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHh-ccCCCCCCccc-CCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWC-QRSSQCPMCWQ-PISLKD  105 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wl-k~sssCP~CRq-~i~~k~  105 (444)
                      +.|+.|...+...+.                 +            +.|+|.||.+||..-| .....||.|-+ .+.+..
T Consensus       275 LkCplc~~Llrnp~k-----------------T------------~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~  325 (427)
T COG5222         275 LKCPLCHCLLRNPMK-----------------T------------PCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDG  325 (427)
T ss_pred             ccCcchhhhhhCccc-----------------C------------ccccchHHHHHHhhhhhhccccCCCcccccchhhc
Confidence            789999888776331                 1            2699999999999766 45568999954 454444


Q ss_pred             CCcc
Q 013396          106 PTRF  109 (444)
Q Consensus       106 ~~~~  109 (444)
                      .++.
T Consensus       326 l~pD  329 (427)
T COG5222         326 LTPD  329 (427)
T ss_pred             cCcc
Confidence            4444

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=94.39  E-value=0.013  Score=53.46  Aligned_cols=35  Identities=26%  Similarity=0.609  Sum_probs=26.8

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCC------ChhcHHHHHHHh
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR------HEFHLQCVLEWC   88 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~Cg------H~FH~~CI~~Wl   88 (444)
                      ...|.||++.+.+.++              +|.+             .||      |+||..|+.+|-
T Consensus        26 ~~EC~IC~~~I~~~~G--------------vV~v-------------t~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDG--------------VVYV-------------TDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCC--------------EEEE-------------ecCCeehHHHHHHHHHHHHHH
Confidence            4579999999987333              3444             454      999999999994

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.

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

Probab=94.38  E-value=0.03  Score=58.59  Aligned_cols=53  Identities=19%  Similarity=0.458  Sum_probs=42.1

Q ss_pred             CCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCccc
Q 013396           20 GGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        20 ~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      .+..+.+|+.|+||+..=.                              -.+..+|+|.-|..||.+-+.+.+.|=.|+.
T Consensus       415 ~~lp~sEd~lCpICyA~pi------------------------------~Avf~PC~H~SC~~CI~qHlmN~k~CFfCkt  464 (489)
T KOG4692|consen  415 KDLPDSEDNLCPICYAGPI------------------------------NAVFAPCSHRSCYGCITQHLMNCKRCFFCKT  464 (489)
T ss_pred             CCCCCcccccCcceecccc------------------------------hhhccCCCCchHHHHHHHHHhcCCeeeEecc
Confidence            3456788999999985411                              1234499999999999999999999999988


Q ss_pred             CCC
Q 013396          100 PIS  102 (444)
Q Consensus       100 ~i~  102 (444)
                      .+.
T Consensus       465 Tv~  467 (489)
T KOG4692|consen  465 TVI  467 (489)
T ss_pred             eee
Confidence            765

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

Probab=94.38  E-value=0.022  Score=59.17  Aligned_cols=45  Identities=33%  Similarity=0.687  Sum_probs=32.7

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      +..+.|.||++...+                 -+.+             +|||.-|  |+..-... .+||+||+.+.
T Consensus       303 ~~p~lcVVcl~e~~~-----------------~~fv-------------pcGh~cc--ct~cs~~l-~~CPvCR~rI~  347 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS-----------------AVFV-------------PCGHVCC--CTLCSKHL-PQCPVCRQRIR  347 (355)
T ss_pred             CCCCceEEecCCccc-----------------eeee-------------cCCcEEE--chHHHhhC-CCCchhHHHHH
Confidence            446789999998776                 2334             8999977  77654433 35999999764

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.13  E-value=0.049  Score=51.26  Aligned_cols=31  Identities=32%  Similarity=0.898  Sum_probs=24.2

Q ss_pred             CCCC---hhcHHHHHHHhccC--CCCCCcccCCCCC
Q 013396           74 SCRH---EFHLQCVLEWCQRS--SQCPMCWQPISLK  104 (444)
Q Consensus        74 ~CgH---~FH~~CI~~Wlk~s--ssCP~CRq~i~~k  104 (444)
                      .|..   .-|..|+.+|+..+  ..|++|.+++..+
T Consensus        26 ~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825         26 NCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             ccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4555   56999999999664  4799999987654

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

Probab=94.13  E-value=0.042  Score=64.58  Aligned_cols=55  Identities=25%  Similarity=0.401  Sum_probs=35.5

Q ss_pred             CCCChhcHHHHHHHhccCCCCCCcccCCCCCCCCccchHHHHHHHHHhcccCCCee
Q 013396           74 SCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPTRFCVNFAARNYLRRSNKRGALV  129 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~~~~~~~~avr~~lR~~~~r~A~I  129 (444)
                      .|||.||..|+..|+..+..||+|+.....-...-..+... ..+++-.+...+.|
T Consensus      1171 ~cgh~~c~~c~~~~l~~~s~~~~~ksi~~dfg~kI~~v~~~-il~iK~k~~qekvI 1225 (1394)
T KOG0298|consen 1171 GCGHEPCCRCDELWLYASSRCPICKSIKGDFGTKIDSVVIA-ILYIKFKNEQEKVI 1225 (1394)
T ss_pred             eechhHhhhHHHHHHHHhccCcchhhhhhhhccCchhHHHH-HHHHhccCcCceEE
Confidence            69999999999999999999999985433222111111111 25555555555544

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.12  E-value=0.044  Score=54.99  Aligned_cols=54  Identities=20%  Similarity=0.247  Sum_probs=38.5

Q ss_pred             ceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           53 RFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        53 ~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      ||.|||.-..+.|.--.+++.+|||.|+++|..+.+.....||+|-.++...+.
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdi  274 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDI  274 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccce
Confidence            444444433333322234555999999999999999999999999988876653

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

Probab=94.07  E-value=0.05  Score=53.47  Aligned_cols=53  Identities=26%  Similarity=0.631  Sum_probs=40.0

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISLK  104 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~k  104 (444)
                      ..|-||-++|...++...           |-+|             .|||.||..|+.+-+... ..||.||......
T Consensus         4 ~~c~~c~~~~s~~~~~~~-----------p~~l-------------~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~   57 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHI-----------PRVL-------------KCGHTICQNCASKLLGNSRILCPFCRETTEIP   57 (296)
T ss_pred             CceeecCccccccCcccC-----------Cccc-------------ccCceehHhHHHHHhcCceeeccCCCCcccCC
Confidence            479999999998643321           2333             699999999998888665 4799999996433

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

Probab=93.99  E-value=0.052  Score=56.74  Aligned_cols=69  Identities=20%  Similarity=0.408  Sum_probs=46.9

Q ss_pred             cchhhhhcCchhhhcCC--CCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHH
Q 013396            5 KQCDARLTSPAAFVEGG--IQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQ   82 (444)
Q Consensus         5 ~~~~~~l~S~~a~ve~~--iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~   82 (444)
                      ||.+..|..-+.++...  .+|.++..|-||-+.+.-.+                 ++             +|+|..|.-
T Consensus        37 kqkKNnlsaEPnlttsSaddtDEen~~C~ICA~~~TYs~-----------------~~-------------PC~H~~CH~   86 (493)
T COG5236          37 KQKKNNLSAEPNLTTSSADDTDEENMNCQICAGSTTYSA-----------------RY-------------PCGHQICHA   86 (493)
T ss_pred             hccccccccCCccccccccccccccceeEEecCCceEEE-----------------ec-------------cCCchHHHH
Confidence            34445555555555443  34566677999988765421                 22             899999999


Q ss_pred             HHHHH--hccCCCCCCcccCCCC
Q 013396           83 CVLEW--CQRSSQCPMCWQPISL  103 (444)
Q Consensus        83 CI~~W--lk~sssCP~CRq~i~~  103 (444)
                      |-.+.  |-....||+||..+..
T Consensus        87 Ca~RlRALY~~K~C~~CrTE~e~  109 (493)
T COG5236          87 CAVRLRALYMQKGCPLCRTETEA  109 (493)
T ss_pred             HHHHHHHHHhccCCCccccccce
Confidence            98763  4556789999998753

>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=93.83  E-value=0.026  Score=46.59  Aligned_cols=33  Identities=30%  Similarity=0.775  Sum_probs=24.7

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHH
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVL   85 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~   85 (444)
                      ..+..|+||-..|..+.               +++.             ||||.||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~~~---------------f~~~-------------p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNSV---------------FVVF-------------PCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCCce---------------EEEe-------------CCCeEEeccccc
Confidence            44678999999987621               2233             899999999974

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

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

Probab=93.57  E-value=0.025  Score=64.04  Aligned_cols=23  Identities=30%  Similarity=1.012  Sum_probs=20.2

Q ss_pred             CCCChhcHHHHHHHhccCCCCCCccc
Q 013396           74 SCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      .|||.||.+|+.   .+...||.|+.
T Consensus       858 ~CgHsyHqhC~e---~~~~~CP~C~~  880 (933)
T KOG2114|consen  858 LCGHSYHQHCLE---DKEDKCPKCLP  880 (933)
T ss_pred             ecccHHHHHhhc---cCcccCCccch
Confidence            699999999998   55678999977

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

Probab=92.59  E-value=0.064  Score=56.83  Aligned_cols=45  Identities=24%  Similarity=0.513  Sum_probs=33.7

Q ss_pred             cccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--------CCCCCCcccC
Q 013396           29 ACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--------SSQCPMCWQP  100 (444)
Q Consensus        29 ~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--------sssCP~CRq~  100 (444)
                      .|.||++......              +.+.|             +|+|.||+.|+..++..        ...||-|...
T Consensus       186 ~C~ICf~e~~G~~--------------c~~~l-------------pC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  186 DCCICFEEQMGQH--------------CFKFL-------------PCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             cceeeehhhcCcc--------------eeeec-------------ccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            6999999977632              23444             89999999999999843        1268877654

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

Probab=92.55  E-value=0.021  Score=58.32  Aligned_cols=41  Identities=34%  Similarity=0.761  Sum_probs=30.3

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPI  101 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i  101 (444)
                      +..|.|||+.-.+             |    |.|             +|||. -|.+|-...    ..||+||+.+
T Consensus       300 ~~LC~ICmDaP~D-------------C----vfL-------------eCGHmVtCt~CGkrm----~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAPRD-------------C----VFL-------------ECGHMVTCTKCGKRM----NECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCCcc-------------e----EEe-------------ecCcEEeehhhcccc----ccCchHHHHH
Confidence            6789999997444             2    344             89997 588886544    3899999865

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

Probab=92.04  E-value=0.12  Score=53.83  Aligned_cols=32  Identities=28%  Similarity=0.790  Sum_probs=24.1

Q ss_pred             CCCChhcHHHHHHHhccC-------------CCCCCcccCCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQRS-------------SQCPMCWQPISLKD  105 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~s-------------ssCP~CRq~i~~k~  105 (444)
                      -|.=+.|..|+-+|+...             -.||+||+.|..-+
T Consensus       310 ~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  310 YCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             cccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence            355677999999998331             27999999987544

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

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

Probab=91.90  E-value=0.078  Score=60.27  Aligned_cols=48  Identities=35%  Similarity=0.815  Sum_probs=35.8

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-------CCCCCcc
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-------SQCPMCW   98 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-------ssCP~CR   98 (444)
                      .-..|.||++.+....+.--.                          ..|=|+||+.||.+|....       -.||.|.
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC--------------------------~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cq  243 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSC--------------------------KSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQ  243 (950)
T ss_pred             CceEEEEeeeeccccCCceec--------------------------chhhhhhhHHHHHHHHHHhhhccCccccCCccc
Confidence            456899999999876543211                          1588999999999998542       2699997


Q ss_pred             c
Q 013396           99 Q   99 (444)
Q Consensus        99 q   99 (444)
                      .
T Consensus       244 s  244 (950)
T KOG1952|consen  244 S  244 (950)
T ss_pred             c
Confidence            3

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

Probab=91.85  E-value=0.041  Score=54.35  Aligned_cols=32  Identities=34%  Similarity=0.777  Sum_probs=24.0

Q ss_pred             cCCCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           72 LTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        72 l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      |+.|+|+||..|...-..  ..||+|++.+....
T Consensus        20 LTaC~HvfC~~C~k~~~~--~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen   20 LTACRHVFCEPCLKASSP--DVCPLCKKSIRIIQ   51 (233)
T ss_pred             eeechhhhhhhhcccCCc--cccccccceeeeee
Confidence            348999999999754322  28999999876544

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

Probab=91.77  E-value=0.15  Score=52.82  Aligned_cols=53  Identities=19%  Similarity=0.488  Sum_probs=39.4

Q ss_pred             cCCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcc
Q 013396           19 EGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCW   98 (444)
Q Consensus        19 e~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CR   98 (444)
                      |+.+.......|+||+.....++               ++.              --|-.||..||..++.+...||+=-
T Consensus       292 e~e~l~~~~~~CpvClk~r~Npt---------------vl~--------------vSGyVfCY~Ci~~Yv~~~~~CPVT~  342 (357)
T KOG0826|consen  292 ESELLPPDREVCPVCLKKRQNPT---------------VLE--------------VSGYVFCYPCIFSYVVNYGHCPVTG  342 (357)
T ss_pred             ccccCCCccccChhHHhccCCCc---------------eEE--------------ecceEEeHHHHHHHHHhcCCCCccC
Confidence            33445566788999998866532               111              3589999999999999999999865


Q ss_pred             cC
Q 013396           99 QP  100 (444)
Q Consensus        99 q~  100 (444)
                      .+
T Consensus       343 ~p  344 (357)
T KOG0826|consen  343 YP  344 (357)
T ss_pred             Cc
Confidence            44

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

Probab=91.34  E-value=0.11  Score=58.08  Aligned_cols=32  Identities=31%  Similarity=0.812  Sum_probs=25.8

Q ss_pred             CCCChhcHHHHHHHhccC--CCCCCcccCCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQRS--SQCPMCWQPISLKD  105 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~s--ssCP~CRq~i~~k~  105 (444)
                      .|+|.||..|+.+-+...  ..||+||..+..+.
T Consensus       470 ~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  470 RCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            799999999999987553  36999998765443

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

Probab=90.91  E-value=0.12  Score=38.86  Aligned_cols=20  Identities=25%  Similarity=0.908  Sum_probs=15.4

Q ss_pred             hhcHHHHHHHhcc--CCCCCCc
Q 013396           78 EFHLQCVLEWCQR--SSQCPMC   97 (444)
Q Consensus        78 ~FH~~CI~~Wlk~--sssCP~C   97 (444)
                      ..|..||.+|+..  ...|++|
T Consensus        26 ~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen   26 YVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             SEECCHHHHHHHHHT-SB-TTT
T ss_pred             hhHHHHHHHHHHhcCCCcCCCC
Confidence            7899999999964  4579987

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

Probab=89.67  E-value=0.22  Score=50.36  Aligned_cols=48  Identities=29%  Similarity=0.553  Sum_probs=37.5

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCccc
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      .+..|+||.+.+....+.             |..+             +|||.-|..|+.+.....-.||+|..
T Consensus       157 ~~~ncPic~e~l~~s~~~-------------~~~~-------------~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFED-------------AGVL-------------KCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhcccccc-------------CCcc-------------CcccchHHHHHHHHhccCCCCCcccc
Confidence            345599999987765422             2333             89999999999999877799999977

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

Probab=88.81  E-value=0.35  Score=55.21  Aligned_cols=54  Identities=30%  Similarity=0.732  Sum_probs=38.8

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCC-----ChhcHHHHHHHhccC--CCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR-----HEFHLQCVLEWCQRS--SQCPM   96 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~Cg-----H~FH~~CI~~Wlk~s--ssCP~   96 (444)
                      .+++..|-||...=..++|..      |                      ||+     -..|.+|+.+|+.-+  ..|-+
T Consensus         9 N~d~~~CRICr~e~~~d~pLf------h----------------------PCKC~GSIkYiH~eCL~eW~~~s~~~kCdi   60 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLF------H----------------------PCKCSGSIKYIHRECLMEWMECSGTKKCDI   60 (1175)
T ss_pred             CccchhceeecCCCCCCCcCc------c----------------------cccccchhHHHHHHHHHHHHhcCCCcceee
Confidence            345688999998755544432      1                      455     358999999999754  46999


Q ss_pred             cccCCCCCC
Q 013396           97 CWQPISLKD  105 (444)
Q Consensus        97 CRq~i~~k~  105 (444)
                      |..++..|+
T Consensus        61 Chy~~~Fk~   69 (1175)
T COG5183          61 CHYEYKFKD   69 (1175)
T ss_pred             ecceeeeee
Confidence            998876554

>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=88.73  E-value=0.26  Score=36.63  Aligned_cols=24  Identities=29%  Similarity=0.883  Sum_probs=15.9

Q ss_pred             CCCChhcHHHHHHHhccCC--CCCCc
Q 013396           74 SCRHEFHLQCVLEWCQRSS--QCPMC   97 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~ss--sCP~C   97 (444)
                      .|+=.+|..|+..++....  .||.|
T Consensus        18 ~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen   18 DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            5888999999999997754  69988

; PDB: 3NW0_A 2CT0_A.

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

Probab=86.79  E-value=0.34  Score=54.96  Aligned_cols=40  Identities=28%  Similarity=0.614  Sum_probs=31.5

Q ss_pred             cceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCC
Q 013396           52 VRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPM   96 (444)
Q Consensus        52 ~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~   96 (444)
                      .|.+|=+.+++...+|     +.|+|.-|..|..+|+.....||.
T Consensus      1030 ~C~~C~l~V~gss~~C-----g~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSNFC-----GTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEeeccchhh-----ccccccccHHHHHHHHhcCCcCCC
Confidence            3566666666555554     469999999999999999989985

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

Probab=86.29  E-value=0.29  Score=56.01  Aligned_cols=37  Identities=27%  Similarity=0.664  Sum_probs=27.1

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHh
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWC   88 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wl   88 (444)
                      -.-++.|.||.-.|... +              +++.             +|||.||..||.+-.
T Consensus       814 ~ep~d~C~~C~~~ll~~-p--------------F~vf-------------~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIK-P--------------FYVF-------------PCGHCFHRDCLIRHV  850 (911)
T ss_pred             ecCccchHHhcchhhcC-c--------------ceee-------------eccchHHHHHHHHHH
Confidence            34567999999887752 1              1222             899999999998754

>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=84.83  E-value=0.33  Score=37.80  Aligned_cols=30  Identities=33%  Similarity=0.844  Sum_probs=22.4

Q ss_pred             CCC-ChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           74 SCR-HEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        74 ~Cg-H~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      .|. |..|+.|+...+..+..||+|+.++..
T Consensus        17 ~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   17 KCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             E-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             eecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            575 999999999999999999999988754

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.

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

Probab=84.09  E-value=0.069  Score=56.39  Aligned_cols=32  Identities=19%  Similarity=0.526  Sum_probs=28.2

Q ss_pred             CCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      .|||.+|..||.+|+.....||.|+..+....
T Consensus       217 ~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  217 VCGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             hhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            59999999999999998889999999876443

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

Probab=83.78  E-value=0.41  Score=53.68  Aligned_cols=49  Identities=29%  Similarity=0.607  Sum_probs=37.3

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHh--c-cCCCCCCcccCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWC--Q-RSSQCPMCWQPISL  103 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wl--k-~sssCP~CRq~i~~  103 (444)
                      +..|+||+..+.+                 |+.+             .|.|.||.-|+..-+  + ....||+|+..+..
T Consensus        21 ~lEc~ic~~~~~~-----------------p~~~-------------kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   21 ILECPICLEHVKE-----------------PSLL-------------KCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             hccCCceeEEeec-----------------cchh-------------hhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            6689999998776                 4445             899999999998633  3 36689999976654


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      ..
T Consensus        71 ~s   72 (684)
T KOG4362|consen   71 RS   72 (684)
T ss_pred             hh
Confidence            43

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

Probab=82.61  E-value=0.6  Score=52.26  Aligned_cols=43  Identities=30%  Similarity=0.547  Sum_probs=33.2

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCccc
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQ   99 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq   99 (444)
                      ..|.||+..|...             -++||.|             .|||..|.+|+..-+..  +|| |+.
T Consensus        12 l~c~ic~n~f~~~-------------~~~Pvsl-------------~cghtic~~c~~~lyn~--scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQ-------------RLEPVSL-------------QCGHTICGHCVQLLYNA--SCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHH-------------hcCcccc-------------cccchHHHHHHHhHhhc--cCC-CCc
Confidence            5799998887653             2458888             89999999999887755  577 543

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.90  E-value=0.67  Score=47.79  Aligned_cols=32  Identities=28%  Similarity=0.681  Sum_probs=25.1

Q ss_pred             CCCChhcHHHHHHHhcc-------------CCCCCCcccCCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQR-------------SSQCPMCWQPISLKD  105 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~-------------sssCP~CRq~i~~k~  105 (444)
                      -|.-..|..|+-+|+-.             +-+||+||+.+...+
T Consensus       324 ~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  324 ICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             ccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            47788999999999843             238999999886544

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.66  E-value=1.2  Score=45.10  Aligned_cols=39  Identities=18%  Similarity=0.359  Sum_probs=28.2

Q ss_pred             ChhcHHHHHHHhccC--------CCCCCcccCCCCCCCCccchHHHH
Q 013396           77 HEFHLQCVLEWCQRS--------SQCPMCWQPISLKDPTRFCVNFAA  115 (444)
Q Consensus        77 H~FH~~CI~~Wlk~s--------ssCP~CRq~i~~k~~~~~~~~~av  115 (444)
                      |.-|..||..|+...        -.||.|++.+...-+.......++
T Consensus        49 KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~L   95 (293)
T KOG3053|consen   49 KWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVL   95 (293)
T ss_pred             HHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHH
Confidence            899999999999442        169999998876655544444443

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

Probab=81.02  E-value=0.72  Score=48.29  Aligned_cols=17  Identities=29%  Similarity=0.663  Sum_probs=15.4

Q ss_pred             CCCChhcHHHHHHHhcc
Q 013396           74 SCRHEFHLQCVLEWCQR   90 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~   90 (444)
                      .|+|.||.+|+.+.++.
T Consensus       167 ~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  167 KCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             cccchhhhHHhHHHhhh
Confidence            69999999999998864

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

Probab=80.32  E-value=1.2  Score=43.18  Aligned_cols=28  Identities=18%  Similarity=0.434  Sum_probs=22.5

Q ss_pred             ChhcHHHHHHHhc--cCCCCCCcccCCCCC
Q 013396           77 HEFHLQCVLEWCQ--RSSQCPMCWQPISLK  104 (444)
Q Consensus        77 H~FH~~CI~~Wlk--~sssCP~CRq~i~~k  104 (444)
                      +..|..|+..|+.  ....|.+|+..+...
T Consensus       107 ~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen  107 AYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             HHHHHHHHHhhhccccCeeeecccccceec
Confidence            6679999999997  456899998866543

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

Probab=80.20  E-value=0.89  Score=47.22  Aligned_cols=29  Identities=28%  Similarity=0.851  Sum_probs=21.1

Q ss_pred             ccCCCCChhcHHHHHHHhccCCCCCCcccCC
Q 013396           71 QLTSCRHEFHLQCVLEWCQRSSQCPMCWQPI  101 (444)
Q Consensus        71 ~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i  101 (444)
                      .+-+|+|.||++|...  ...+.||.|-..+
T Consensus       105 RmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen  105 RMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             cccccchhhhhhhhhc--CccccCcCcccHH
Confidence            4557999999999643  3355899995543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	444
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-12
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-11
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-11
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	7e-11
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-10
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-10
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-09
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-09
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	8e-09
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	1e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-08
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	5e-08
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-07
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-06
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-06
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	5e-06
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	9e-06
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-04
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	3e-04
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	6e-04
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	6e-04

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

 Score = 61.7 bits (150), Expect = 1e-12
 Identities = 15/79 (18%), Positives = 23/79 (29%), Gaps = 29/79 (36%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
               + C ICLE  S+                                   C H F   C
Sbjct: 2   ATVAERCPICLEDPSNY-----------------------------SMALPCLHAFCYVC 32

Query: 84  VLEWCQRSSQCPMCWQPIS 102
           +  W +++  CP+C  P+ 
Sbjct: 33  ITRWIRQNPTCPLCKVPVE 51

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

 Score = 61.5 bits (149), Expect = 3e-12
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 15/81 (18%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
           D   D C+IC     D+                     +      ++    C H FH  C
Sbjct: 12  DVECDTCAICRVQVMDACL---------------RCQAENKQEDCVVVWGECNHSFHNCC 56

Query: 84  VLEWCQRSSQCPMCWQPISLK 104
           +  W +++++CP+C Q   ++
Sbjct: 57  MSLWVKQNNRCPLCQQDWVVQ 77

>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 = 60.2 bits (145), Expect = 2e-11
 Identities = 13/81 (16%), Positives = 22/81 (27%), Gaps = 12/81 (14%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
           D   D C+IC                  +            +    +    C H FH  C
Sbjct: 45  DIVVDNCAICRNHI------------MDLCIECQANQASATSEECTVAWGVCNHAFHFHC 92

Query: 84  VLEWCQRSSQCPMCWQPISLK 104
           +  W +    CP+  +    +
Sbjct: 93  ISRWLKTRQVCPLDNREWEFQ 113

>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 = 58.7 bits (142), Expect = 2e-11
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 23/85 (27%)

Query: 21  GIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFH 80
           G++ +   +C IC++ +S+   +                             T C H F 
Sbjct: 4   GLRPSGTVSCPICMDGYSEIVQNGRLIV-----------------------STECGHVFC 40

Query: 81  LQCVLEWCQRSSQCPMCWQPISLKD 105
            QC+ +  + ++ CP C + I+ K 
Sbjct: 41  SQCLRDSLKNANTCPTCRKKINHKR 65

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

 Score = 57.9 bits (140), Expect = 3e-11
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 23/76 (30%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC++ +S+   +                             T C H F  QC+ +  +
Sbjct: 6   CPICMDGYSEIVQNGRLIV-----------------------STECGHVFCSQCLRDSLK 42

Query: 90  RSSQCPMCWQPISLKD 105
            ++ CP C + I+ K 
Sbjct: 43  NANTCPTCRKKINHKR 58

>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 = 58.3 bits (140), Expect = 7e-11
 Identities = 13/81 (16%), Positives = 22/81 (27%), Gaps = 12/81 (14%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
           D   D C+IC                  +            +    +    C H FH  C
Sbjct: 34  DIVVDNCAICRNHI------------MDLCIECQANQASATSEECTVAWGVCNHAFHFHC 81

Query: 84  VLEWCQRSSQCPMCWQPISLK 104
           +  W +    CP+  +    +
Sbjct: 82  ISRWLKTRQVCPLDNREWEFQ 102

>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 = 56.2 bits (136), Expect = 1e-10
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 27/89 (30%)

Query: 19  EGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE 78
           E G ++  ++ C+ICL    + +                  +R L           C H 
Sbjct: 6   EEGTEEDTEEKCTICLSILEEGE-----------------DVRRL----------PCMHL 38

Query: 79  FHLQCVLEWCQRSSQCPMCWQPISLKDPT 107
           FH  CV +W   + +CP+C   I  + P+
Sbjct: 39  FHQVCVDQWLITNKKCPICRVDIEAQLPS 67

>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 = 54.2 bits (131), Expect = 4e-10
 Identities = 17/78 (21%), Positives = 22/78 (28%), Gaps = 26/78 (33%)

Query: 25  ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCV 84
           +    C ICLE    S                  +L              C H  H  C 
Sbjct: 3   SGSSGCPICLEDIHTSRVV-------------AHVLP-------------CGHLLHRTCY 36

Query: 85  LEWCQRSSQCPMCWQPIS 102
            E  +   +CP+C  P S
Sbjct: 37  EEMLKEGYRCPLCSGPSS 54

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

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 23/75 (30%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC++ +S+   +                         L+  T C H F  QC+ +  +
Sbjct: 18  CPICMDGYSEIVQN-----------------------GRLIVSTECGHVFCSQCLRDSLK 54

Query: 90  RSSQCPMCWQPISLK 104
            ++ CP C + I+ K
Sbjct: 55  NANTCPTCRKKINHK 69

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

 Score = 52.5 bits (126), Expect = 3e-09
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 27/79 (34%)

Query: 23  QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQ 82
           +    + C++CLE F   D                  L              C+H FH +
Sbjct: 11  ELNLHELCAVCLEDFKPRD-----------------ELGIC----------PCKHAFHRK 43

Query: 83  CVLEWCQRSSQCPMCWQPI 101
           C+++W +    CP+C  P+
Sbjct: 44  CLIKWLEVRKVCPLCNMPV 62

>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 = 52.5 bits (125), Expect = 8e-09
 Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 17/76 (22%)

Query: 27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
          ++ C IC+E  + +   +  +    +    V             +LT C H FHL C+L 
Sbjct: 25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVG------------RLTKCSHAFHLLCLLA 72

Query: 87 WCQRSS-----QCPMC 97
               +     QCP C
Sbjct: 73 MYCNGNKDGSLQCPSC 88

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 27/76 (35%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
              C +C+  F                     +LR L           C HEFH +CV +
Sbjct: 23  QTLCVVCMCDFESRQ-----------------LLRVL----------PCNHEFHAKCVDK 55

Query: 87  WCQRSSQCPMCWQPIS 102
           W + +  CP+C     
Sbjct: 56  WLKANRTCPICRADSG 71

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

 Score = 49.5 bits (118), Expect = 3e-08
 Identities = 17/78 (21%), Positives = 24/78 (30%), Gaps = 30/78 (38%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
           +     C IC + F +  P                              T CRH F   C
Sbjct: 12  EEIPFRCFICRQAFQN--PVV----------------------------TKCRHYFCESC 41

Query: 84  VLEWCQRSSQCPMCWQPI 101
            LE  + + +C +C QP 
Sbjct: 42  ALEHFRATPRCYICDQPT 59

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

 Score = 48.9 bits (117), Expect = 5e-08
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 31/79 (39%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
           ++ C IC++  +D                  +IL              C H F  +C+ +
Sbjct: 15  EEECCICMDGRAD------------------LIL-------------PCAHSFCQKCIDK 43

Query: 87  WCQRSSQCPMCWQPISLKD 105
           W  R   CP+C   ++  +
Sbjct: 44  WSDRHRNCPICRLQMTGAN 62

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

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 18/77 (23%), Positives = 25/77 (32%), Gaps = 28/77 (36%)

Query: 21 GIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFH 80
           + D  +  C++CL    D +                   R          L  C H FH
Sbjct: 1  AMDDGVE--CAVCLAELEDGE-----------------EAR---------FLPRCGHGFH 32

Query: 81 LQCVLEWCQRSSQCPMC 97
           +CV  W    S CP+C
Sbjct: 33 AECVDMWLGSHSTCPLC 49

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 18/81 (22%), Positives = 24/81 (29%), Gaps = 27/81 (33%)

Query: 17 FVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR 76
            E       +  C IC   +   D                 +  +L           C 
Sbjct: 30 VTEDHGAVGQEMCCPICCSEYVKGD-----------------VATEL----------PCH 62

Query: 77 HEFHLQCVLEWCQRSSQCPMC 97
          H FH  CV  W Q+S  CP+C
Sbjct: 63 HYFHKPCVSIWLQKSGTCPVC 83

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

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 14/76 (18%), Positives = 20/76 (26%), Gaps = 30/76 (39%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
              C+ICL+      P +                              C+H F   CV  
Sbjct: 15  VPECAICLQTCVH--PVS----------------------------LPCKHVFCYLCVKG 44

Query: 87  WCQRSSQCPMCWQPIS 102
                 +C +C Q I 
Sbjct: 45  ASWLGKRCALCRQEIP 60

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

 Score = 46.7 bits (110), Expect = 1e-06
 Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 23/81 (28%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC++ +S+   +                             T C H F  QC+ +  +
Sbjct: 10  CPICMDGYSEIVQNGRLIV-----------------------STECGHVFCSQCLRDSLK 46

Query: 90  RSSQCPMCWQPISLKDPTRFC 110
            ++ CP C + I+ K      
Sbjct: 47  NANTCPTCRKKINHKRYHPIY 67

>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 = 45.1 bits (107), Expect = 1e-06
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 27/84 (32%)

Query: 23  QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQ 82
                  C +C E ++  +                  +R L           C H FH  
Sbjct: 11  HVGSGLECPVCKEDYALGE-----------------SVRQL----------PCNHLFHDS 43

Query: 83  CVLEWCQRSSQCPMCWQPISLKDP 106
           C++ W ++   CP+C + ++ ++ 
Sbjct: 44  CIVPWLEQHDSCPVCRKSLTGQNT 67

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

 Score = 43.2 bits (102), Expect = 5e-06
 Identities = 16/77 (20%), Positives = 23/77 (29%), Gaps = 29/77 (37%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           CSIC     D   +T                           +T C H F   C++    
Sbjct: 18  CSICKGYLID--ATT---------------------------ITECLHTFCKSCIVRHFY 48

Query: 90  RSSQCPMCWQPISLKDP 106
            S++CP C   +    P
Sbjct: 49  YSNRCPKCNIVVHQTQP 65

>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 = 43.3 bits (102), Expect = 9e-06
 Identities = 14/77 (18%), Positives = 20/77 (25%), Gaps = 30/77 (38%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC+E   D                                   C       C+  W  
Sbjct: 25  CFICMEKLRD--ARLCPH---------------------------CSKLCCFSCIRRWLT 55

Query: 90  RS-SQCPMCWQPISLKD 105
              +QCP C  P+ L++
Sbjct: 56  EQRAQCPHCRAPLQLRE 72

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

 Score = 43.9 bits (103), Expect = 2e-05
 Identities = 22/108 (20%), Positives = 37/108 (34%), Gaps = 32/108 (29%)

Query: 1   MEENKQCDARLTSPAAFVEGGIQDAC--DDACSICLEPFSDSDPSTVTSFDFHVRFFRVV 58
           +E+ K+   ++ +    V   + D    +  C IC E F +    T              
Sbjct: 36  LEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIE--AVT-------------- 79

Query: 59  ILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP 106
                          +C H F   C+ EW +R  +CP+C + I  K  
Sbjct: 80  --------------LNCAHSFCSYCINEWMKRKIECPICRKDIKSKTY 113

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 14/79 (17%), Positives = 22/79 (27%), Gaps = 29/79 (36%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C +C   F D      T                         +  C H F   C++ + +
Sbjct: 18  CVLCGGYFID----ATT-------------------------IIECLHSFCKTCIVRYLE 48

Query: 90  RSSQCPMCWQPISLKDPTR 108
            S  CP+C   +    P  
Sbjct: 49  TSKYCPICDVQVHKTRPLL 67

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 17/96 (17%), Positives = 26/96 (27%), Gaps = 29/96 (30%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC+E F++                                L  C H    QC+ +   
Sbjct: 18  CPICMESFTEEQLRPK--------------------------LLHCGHTICRQCLEKLLA 51

Query: 90  RSS---QCPMCWQPISLKDPTRFCVNFAARNYLRRS 122
            S    +CP C +   +   T+   N         S
Sbjct: 52  SSINGVRCPFCSKITRITSLTQLTDNLTVLKSGPSS 87

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

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 14/88 (15%), Positives = 23/88 (26%), Gaps = 32/88 (36%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC E F+                                 +  C H +   C+ ++  
Sbjct: 25  CGICFEYFNI--AMI---------------------------IPQCSHNYCSLCIRKFLS 55

Query: 90  RSSQCPMCWQPISLKDPTRFCVNFAARN 117
             +QCP C   ++  D      N     
Sbjct: 56  YKTQCPTCCVTVTEPD---LKNNRILDE 80

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

 Score = 41.0 bits (95), Expect = 6e-04
 Identities = 14/89 (15%), Positives = 21/89 (23%), Gaps = 33/89 (37%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
           +  C+IC     D                            +      C  + H  C+ E
Sbjct: 308 ELRCNICFAYRLDGGEVP----------------------LVSCDNAKCVLKCHAVCLEE 345

Query: 87  WCQRSS-----------QCPMCWQPISLK 104
           W +              QCP C   +S  
Sbjct: 346 WFKTLMDGKTFLEVSFGQCPFCKAKLSTS 374

>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 = 40.9 bits (95), Expect = 6e-04
 Identities = 16/81 (19%), Positives = 19/81 (23%), Gaps = 31/81 (38%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
              C IC E   D                 V I               C H     C+  
Sbjct: 332 FQLCKICAENDKD-----------------VKI-------------EPCGHLMCTSCLTS 361

Query: 87  WCQ-RSSQCPMCWQPISLKDP 106
           W +     CP C   I   +P
Sbjct: 362 WQESEGQGCPFCRCEIKGTEP 382

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	444
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.42
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.36
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.35
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.34
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.34
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.34
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.33
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.33
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.3
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.3
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.29
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.28
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.28
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.28
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.25
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.25
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.25
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.23
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.21
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.21
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.21
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.18
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.18
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.18
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.16
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.16
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.16
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.15
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.15
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.14
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.13
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.13
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.12
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.12
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.09
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.07
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.06
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.06
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.06
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.03
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.0
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.0
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.99
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.96
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.96
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.94
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.94
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.93
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.91
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.89
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.88
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.86
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.79
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.78
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.73
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.71
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.69
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.69
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.62
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.55
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.48
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.41
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.41
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.4
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.39
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.32
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.27
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.25
3nw0_A	238	Non-structural maintenance of chromosomes element	97.62
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.4
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	92.75
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	92.71
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	91.3
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	91.06
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	86.66
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	83.65
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	83.11
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	80.19

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

Probab=99.42  E-value=5.3e-14  Score=112.32  Aligned_cols=65  Identities=23%  Similarity=0.523  Sum_probs=48.3

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      .+++.|+||++.|.+.++.+.....               ....++++++|+|.||..||.+|++.+.+||+||+.+...
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~---------------~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENK---------------QEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTC---------------TTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCCcccChhhhccCcccccccC---------------CCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            4578899999999887655433100               1112334447999999999999999999999999988643

>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=99.36  E-value=5.6e-13  Score=110.68  Aligned_cols=73  Identities=29%  Similarity=0.476  Sum_probs=47.8

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHh-----ccCCCCCCccc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWC-----QRSSQCPMCWQ   99 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wl-----k~sssCP~CRq   99 (444)
                      ..++.|+||++.|..................            .+..+.+|+|.||..||..|+     +....||+||.
T Consensus        23 ~~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~   90 (114)
T 1v87_A           23 APEEDCIICMEKLAVASGYSDMTDSKALGPM------------VVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT   90 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSS------------CCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCC
T ss_pred             CCCCcCccCChhhcCcccccccccccccCcc------------cceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCC
Confidence            3467999999999875422111000000000            112234899999999999999     45678999999


Q ss_pred             CCCCCCCCcc
Q 013396          100 PISLKDPTRF  109 (444)
Q Consensus       100 ~i~~k~~~~~  109 (444)
                      .+..+..+++
T Consensus        91 ~~~~~~g~qp  100 (114)
T 1v87_A           91 IYGEKTGTQP  100 (114)
T ss_dssp             BSSSCSSSCT
T ss_pred             ccCCCCCCCC
Confidence            9987765544

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

Probab=99.35  E-value=1.3e-12  Score=101.82  Aligned_cols=67  Identities=19%  Similarity=0.243  Sum_probs=53.0

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPIS  102 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~  102 (444)
                      -..+..|+||++.|.+                 ||++             +|||.||..||.+|++. ...||+||+.+.
T Consensus         5 ~~~~~~C~IC~~~~~~-----------------Pv~~-------------~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~   54 (78)
T 1t1h_A            5 FPEYFRCPISLELMKD-----------------PVIV-------------STGQTYERSSIQKWLDAGHKTCPKSQETLL   54 (78)
T ss_dssp             CSSSSSCTTTSCCCSS-----------------EEEE-------------TTTEEEEHHHHHHHHTTTCCBCTTTCCBCS
T ss_pred             CcccCCCCCccccccC-----------------CEEc-------------CCCCeecHHHHHHHHHHCcCCCCCCcCCCC
Confidence            3457899999999877                 7788             89999999999999987 678999999998


Q ss_pred             CCCCCccchHHHH-HHHHH
Q 013396          103 LKDPTRFCVNFAA-RNYLR  120 (444)
Q Consensus       103 ~k~~~~~~~~~av-r~~lR  120 (444)
                      ..+..++..+..+ ..+.+
T Consensus        55 ~~~l~~n~~l~~~i~~~~~   73 (78)
T 1t1h_A           55 HAGLTPNYVLKSLIALWCE   73 (78)
T ss_dssp             SCCCEECTTTHHHHHHHHH
T ss_pred             hhhCccCHHHHHHHHHHHH
Confidence            7766555544444 34433

>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=99.34  E-value=7.8e-13  Score=100.82  Aligned_cols=55  Identities=31%  Similarity=0.764  Sum_probs=45.0

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ...+..|+||++.|..+..              +++|             +|||.||..||.+|++....||+||+.+..
T Consensus        11 ~~~~~~C~IC~~~~~~~~~--------------~~~~-------------~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGED--------------VRRL-------------PCMHLFHQVCVDQWLITNKKCPICRVDIEA   63 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSC--------------EEEC-------------TTSCEEEHHHHHHHHHHCSBCTTTCSBSCS
T ss_pred             CCCCCCCeeCCccccCCCc--------------EEEe-------------CCCCHHHHHHHHHHHHcCCCCcCcCccccC
Confidence            4456789999999876432              3444             899999999999999998899999999876


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      ..
T Consensus        64 ~~   65 (69)
T 2kiz_A           64 QL   65 (69)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

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

Probab=99.34  E-value=5.4e-13  Score=97.35  Aligned_cols=51  Identities=31%  Similarity=0.799  Sum_probs=41.7

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      ++..|+||++.|..++..              +++            +.|||.||..||.+|++.+..||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~--------------~~~------------~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEA--------------RFL------------PRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCC--------------EEC------------SSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCce--------------EEC------------CCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            467899999999875432              223            249999999999999999999999999874

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

Probab=99.34  E-value=3.2e-13  Score=109.53  Aligned_cols=70  Identities=24%  Similarity=0.530  Sum_probs=52.0

Q ss_pred             hhhhhcCchhhhcCCCC--CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHH
Q 013396            7 CDARLTSPAAFVEGGIQ--DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCV   84 (444)
Q Consensus         7 ~~~~l~S~~a~ve~~iq--d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI   84 (444)
                      .++.+.+.+.++.....  ...+..|+||++.|..+..              +++|             +|||.||..||
T Consensus        18 s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~--------------~~~l-------------~C~H~Fh~~Ci   70 (91)
T 2l0b_A           18 SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDV--------------ATEL-------------PCHHYFHKPCV   70 (91)
T ss_dssp             CHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCE--------------EEEE-------------TTTEEEEHHHH
T ss_pred             CHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCc--------------EEec-------------CCCChHHHHHH
Confidence            44555555555543322  3456789999999987432              3445             79999999999


Q ss_pred             HHHhccCCCCCCcccCCCC
Q 013396           85 LEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        85 ~~Wlk~sssCP~CRq~i~~  103 (444)
                      .+|++.+..||+||+.+..
T Consensus        71 ~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           71 SIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             HHHHTTTCBCTTTCCBSSC
T ss_pred             HHHHHcCCcCcCcCccCCC
Confidence            9999999999999998753

>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=99.33  E-value=5.6e-13  Score=113.00  Aligned_cols=67  Identities=19%  Similarity=0.427  Sum_probs=47.3

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      +++.|+||++.|.+.++.+.......           .| ..+++++.+|+|.||..||.+|++.+.+||+||+.|..+
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~-----------~~-~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~~  102 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASA-----------TS-EECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ  102 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---------------CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCCCccCChhHhCcCchhhcccccc-----------CC-ccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcceee
Confidence            47899999999998776443200000           00 011223338999999999999999999999999997643

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

Probab=99.33  E-value=6.7e-13  Score=103.41  Aligned_cols=56  Identities=25%  Similarity=0.755  Sum_probs=45.6

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      ..+..|+||++.|.....              +++|             +|+|.||..||.+|++....||+||+.+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~--------------~~~~-------------~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           13 GSGLECPVCKEDYALGES--------------VRQL-------------PCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSC--------------EEEC-------------TTSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CCCCCCeeCCccccCCCC--------------EEEe-------------CCCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            446789999999986432              2333             7999999999999999989999999999876


Q ss_pred             CCC
Q 013396          105 DPT  107 (444)
Q Consensus       105 ~~~  107 (444)
                      +..
T Consensus        66 ~~~   68 (78)
T 2ect_A           66 NTA   68 (78)
T ss_dssp             CSC
T ss_pred             ccC
Confidence            543

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

Probab=99.30  E-value=1.4e-12  Score=100.69  Aligned_cols=54  Identities=31%  Similarity=0.864  Sum_probs=44.1

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      ..+..|+||++.|.....              .++|             +|+|.||..||.+|++....||+||+.+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~--------------~~~~-------------~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDE--------------LGIC-------------PCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSC--------------EEEE-------------TTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCCcCCCcccCCCCc--------------EEEc-------------CCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            446789999999987432              2334             7999999999999999888999999998654


Q ss_pred             C
Q 013396          105 D  105 (444)
Q Consensus       105 ~  105 (444)
                      .
T Consensus        66 ~   66 (74)
T 2ep4_A           66 A   66 (74)
T ss_dssp             C
T ss_pred             c
Confidence            3

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

Probab=99.30  E-value=6.1e-13  Score=103.37  Aligned_cols=54  Identities=28%  Similarity=0.768  Sum_probs=44.4

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..++..|+||++.|..+..              +++|             +|+|.||..||.+|++.+..||+||+.+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~--------------~~~l-------------~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQL--------------LRVL-------------PCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCE--------------EEEE-------------TTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCe--------------EEEE-------------CCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            3457789999999887432              3444             799999999999999999999999998865


Q ss_pred             C
Q 013396          104 K  104 (444)
Q Consensus       104 k  104 (444)
                      .
T Consensus        73 ~   73 (75)
T 1x4j_A           73 S   73 (75)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=1.4e-12  Score=98.24  Aligned_cols=57  Identities=25%  Similarity=0.575  Sum_probs=44.1

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..++..|+||++.|.+......          .++++             +|||.||..||.+|++....||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~----------~~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGR----------LIVST-------------ECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTC----------CEEEC-------------SSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccC----------CeEeC-------------CCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3457789999999876321111          13445             899999999999999998899999998754

>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=99.28  E-value=1.9e-13  Score=118.44  Aligned_cols=77  Identities=19%  Similarity=0.380  Sum_probs=6.5

Q ss_pred             CchhhhcCCCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC
Q 013396           13 SPAAFVEGGIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS   92 (444)
Q Consensus        13 S~~a~ve~~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss   92 (444)
                      .+.+++.+++.   ++.|+||++.|.+.++.+......            .....+.+++++|+|.||.+||.+|++.+.
T Consensus        37 ~ava~w~wd~~---~d~CaICl~~~~~~c~~C~~~~~~------------~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~  101 (117)
T 4a0k_B           37 NAVALWAWDIV---VDNCAICRNHIMDLCIECQANQAS------------ATSEECTVAWGVCNHAFHFHCISRWLKTRQ  101 (117)
T ss_dssp             EEEEEEEECCC---C-----------------------------------------------------------------
T ss_pred             EEEEEEeecCC---CCcCeECChhhcCcChhhhccccc------------ccccccccccCCcCceEcHHHHHHHHHcCC
Confidence            34555665553   689999999999876544331000            001123344558999999999999999999


Q ss_pred             CCCCcccCCCCC
Q 013396           93 QCPMCWQPISLK  104 (444)
Q Consensus        93 sCP~CRq~i~~k  104 (444)
                      +||+||+.|..+
T Consensus       102 ~CP~Cr~~~~~~  113 (117)
T 4a0k_B          102 VCPLDNREWEFQ  113 (117)
T ss_dssp             ------------
T ss_pred             cCCCCCCeeeee
Confidence            999999997643

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

Probab=99.28  E-value=1.1e-12  Score=99.76  Aligned_cols=61  Identities=25%  Similarity=0.538  Sum_probs=46.5

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      ...++..|+||++.|.+.....          ..++++             +|||.||..||.+|++....||+||+.+.
T Consensus         6 ~~~~~~~C~IC~~~~~~~~~~~----------~~~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   62 (71)
T 3ng2_A            6 RPSGTVSCPICMDGYSEIVQNG----------RLIVST-------------ECGHVFCSQCLRDSLKNANTCPTCRKKIN   62 (71)
T ss_dssp             CCTTCCBCTTTCCBHHHHHTTT----------CCEEEC-------------TTSCEEEHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCCCCCCcccChhhhcccccc----------CCeEeC-------------CCCChHhHHHHHHHHHcCCCCCCCCCccC
Confidence            4456789999999987631000          012444             89999999999999999999999999987


Q ss_pred             CCCC
Q 013396          103 LKDP  106 (444)
Q Consensus       103 ~k~~  106 (444)
                      ..+.
T Consensus        63 ~~~~   66 (71)
T 3ng2_A           63 HKRY   66 (71)
T ss_dssp             CCSC
T ss_pred             hhhe
Confidence            6653

>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=99.28  E-value=2.4e-12  Score=93.67  Aligned_cols=51  Identities=33%  Similarity=0.696  Sum_probs=41.8

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      .+..|+||++.|.+....             ++++             +|+|.||..||.+|++....||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~-------------~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVV-------------AHVL-------------PCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSC-------------EEEC-------------TTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcC-------------eEec-------------CCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            467899999998754311             3444             89999999999999998899999999864

>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=99.25  E-value=3.5e-12  Score=105.03  Aligned_cols=63  Identities=24%  Similarity=0.554  Sum_probs=50.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeee-eccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVI-LRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pVi-L~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~k  104 (444)
                      +..|+||++.|.+                 ||+ +             +|||.||..||.+|++.. ..||+||..+...
T Consensus        22 ~~~C~IC~~~~~~-----------------p~~~~-------------~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           22 VFRCFICMEKLRD-----------------ARLCP-------------HCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HTBCTTTCSBCSS-----------------EEECT-------------TTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCccCCccccC-----------------ccccC-------------CCCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            5689999999876                 566 5             899999999999999887 6999999999877


Q ss_pred             CCCccchHHHHHHHH
Q 013396          105 DPTRFCVNFAARNYL  119 (444)
Q Consensus       105 ~~~~~~~~~avr~~l  119 (444)
                      +.........+...+
T Consensus        72 ~l~~~~~~~~i~~~~   86 (100)
T 3lrq_A           72 ELVNCRWAEEVTQQL   86 (100)
T ss_dssp             GCEECTTHHHHHHHH
T ss_pred             HhHhhHHHHHHHHHH
Confidence            666666555553333

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

Probab=99.25  E-value=3.8e-12  Score=98.36  Aligned_cols=54  Identities=28%  Similarity=0.543  Sum_probs=44.6

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      .+..|+||++.|.+                 ||++            ++|||.||..||.+|++....||+||+.+...+
T Consensus        14 ~~~~C~IC~~~~~~-----------------p~~~------------~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           14 PYILCSICKGYLID-----------------ATTI------------TECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             GGGSCTTTSSCCSS-----------------CEEC------------SSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             CCCCCCCCChHHHC-----------------cCEE------------CCCCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            36789999999876                 3333            289999999999999998889999999998766


Q ss_pred             CCc
Q 013396          106 PTR  108 (444)
Q Consensus       106 ~~~  108 (444)
                      +..
T Consensus        65 ~~~   67 (72)
T 2djb_A           65 PLS   67 (72)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            543

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

Probab=99.25  E-value=4e-12  Score=97.99  Aligned_cols=50  Identities=30%  Similarity=0.589  Sum_probs=43.5

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..++..|+||++.|.+                 ||++             +|||.||..||.+|++....||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~~~-----------------~~~~-------------~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           12 SLTVPECAICLQTCVH-----------------PVSL-------------PCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSSCCBCSSSSSBCSS-----------------EEEE-------------TTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCCccCCcccCC-----------------CEEc-------------cCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            4456789999999866                 6667             899999999999999988999999998864

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

Probab=99.23  E-value=8.2e-12  Score=98.29  Aligned_cols=49  Identities=33%  Similarity=0.711  Sum_probs=43.0

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      ...+..|+||++.|.+                 ||++             +|||.||..||.+|++....||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQN-----------------PVVT-------------KCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCS-----------------EEEC-------------TTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcC-----------------eeEc-------------cCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3456789999999876                 6666             89999999999999998889999999986

>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=5.1e-12  Score=109.35  Aligned_cols=48  Identities=40%  Similarity=0.895  Sum_probs=42.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      +..|+||++.|.+                 ||+|             +|||.||..||..|+.....||+||+++...
T Consensus        53 ~~~C~iC~~~~~~-----------------~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIE-----------------AVTL-------------NCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSS-----------------EEEE-------------TTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCC-----------------ceEC-------------CCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            5679999999876                 7778             8999999999999999999999999998644

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

Probab=99.21  E-value=4e-12  Score=94.45  Aligned_cols=57  Identities=26%  Similarity=0.579  Sum_probs=44.0

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      ++..|+||++.|.+.....          ..++++             +|||.||..||.+|++.+..||+||+.+...+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~----------~~~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNG----------RLIVST-------------ECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTT----------CCEEEE-------------TTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccC----------CCEEeC-------------CCCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            3678999999987631000          013455             89999999999999999889999999987654

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

Probab=99.21  E-value=1.2e-11  Score=94.78  Aligned_cols=51  Identities=25%  Similarity=0.669  Sum_probs=42.9

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc---cCCCCCCcccCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ---RSSQCPMCWQPI  101 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk---~sssCP~CRq~i  101 (444)
                      ..+..|+||++.|.+                 ||+|             +|||.||..||.+|++   ....||+||+.+
T Consensus        18 ~~~~~C~IC~~~~~~-----------------~~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   67 (73)
T 2ysl_A           18 QEEVICPICLDILQK-----------------PVTI-------------DCGHNFCLKCITQIGETSCGFFKCPLCKTSV   67 (73)
T ss_dssp             CCCCBCTTTCSBCSS-----------------EEEC-------------TTCCEEEHHHHHHHCSSSCSCCCCSSSCCCC
T ss_pred             ccCCEeccCCcccCC-----------------eEEc-------------CCCChhhHHHHHHHHHcCCCCCCCCCCCCcC
Confidence            446789999999876                 6666             8999999999999997   345899999998


Q ss_pred             CCCC
Q 013396          102 SLKD  105 (444)
Q Consensus       102 ~~k~  105 (444)
                      ...+
T Consensus        68 ~~~~   71 (73)
T 2ysl_A           68 RKNA   71 (73)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            7654

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

Probab=99.18  E-value=2.6e-11  Score=97.14  Aligned_cols=61  Identities=21%  Similarity=0.369  Sum_probs=46.6

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCC-CCChhcHHHHHHHhccC--CCCCCcccCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTS-CRHEFHLQCVLEWCQRS--SQCPMCWQPI  101 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~-CgH~FH~~CI~~Wlk~s--ssCP~CRq~i  101 (444)
                      .++..|+||++.|.+                 ||+|             + |||.||..||..|+...  ..||+||+.+
T Consensus        11 ~~~~~C~IC~~~~~~-----------------p~~~-------------~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           11 PDELLCLICKDIMTD-----------------AVVI-------------PCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             CTTTEETTTTEECSS-----------------CEEC-------------TTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             CcCCCCCCCChhhcC-----------------ceEC-------------CCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            346789999999886                 6667             7 99999999999999654  5899999997


Q ss_pred             C-CCCCCccchHHHH
Q 013396          102 S-LKDPTRFCVNFAA  115 (444)
Q Consensus       102 ~-~k~~~~~~~~~av  115 (444)
                      . ......+..+..+
T Consensus        61 ~~~~~~~~n~~l~~~   75 (92)
T 3ztg_A           61 VSPDALIANKFLRQA   75 (92)
T ss_dssp             CCTTSCEECHHHHHH
T ss_pred             CCccccCcCHHHHHH
Confidence            4 4444444444444

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

Probab=99.18  E-value=1.1e-11  Score=96.57  Aligned_cols=50  Identities=26%  Similarity=0.563  Sum_probs=41.9

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCC-CCChhcHHHHHHHhccC--CCCCCcccCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTS-CRHEFHLQCVLEWCQRS--SQCPMCWQPIS  102 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~-CgH~FH~~CI~~Wlk~s--ssCP~CRq~i~  102 (444)
                      ++..|+||++.|.+                 ||+|             + |||.||..||..|++..  ..||+||+.+.
T Consensus        14 ~~~~C~IC~~~~~~-----------------p~~~-------------~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   63 (74)
T 2yur_A           14 DELLCLICKDIMTD-----------------AVVI-------------PCCGNSYCDECIRTALLESDEHTCPTCHQNDV   63 (74)
T ss_dssp             GGGSCSSSCCCCTT-----------------CEEC-------------SSSCCEECTTHHHHHHHHSSSSCCSSSCCSSC
T ss_pred             CCCCCcCCChHHhC-----------------CeEc-------------CCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCC
Confidence            46789999999876                 5666             7 99999999999999765  58999999865


Q ss_pred             CCC
Q 013396          103 LKD  105 (444)
Q Consensus       103 ~k~  105 (444)
                      ..+
T Consensus        64 ~~~   66 (74)
T 2yur_A           64 SPD   66 (74)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            544

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

Probab=99.18  E-value=1.5e-11  Score=100.17  Aligned_cols=60  Identities=23%  Similarity=0.510  Sum_probs=48.4

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      +..|+||++.|.+                 ||++            .+|||.||..||..|+.....||+||..+...+.
T Consensus        22 ~~~C~IC~~~~~~-----------------p~~~------------~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l   72 (99)
T 2y43_A           22 LLRCGICFEYFNI-----------------AMII------------PQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDL   72 (99)
T ss_dssp             HTBCTTTCSBCSS-----------------EEEC------------TTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGC
T ss_pred             CCCcccCChhhCC-----------------cCEE------------CCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhC
Confidence            5689999999876                 4444            2799999999999999988899999999987665


Q ss_pred             CccchHHHH
Q 013396          107 TRFCVNFAA  115 (444)
Q Consensus       107 ~~~~~~~av  115 (444)
                      ..+..+..+
T Consensus        73 ~~n~~l~~~   81 (99)
T 2y43_A           73 KNNRILDEL   81 (99)
T ss_dssp             EECHHHHHH
T ss_pred             CcCHHHHHH
Confidence            555555544

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

Probab=99.16  E-value=2.9e-11  Score=95.25  Aligned_cols=55  Identities=27%  Similarity=0.608  Sum_probs=44.4

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC---CCCCCcccCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS---SQCPMCWQPI  101 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s---ssCP~CRq~i  101 (444)
                      .++..|+||++.|.+...             .|++|             +|||.||..||.+|++..   ..||+||+.+
T Consensus        13 ~~~~~C~IC~~~~~~~~~-------------~~~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   66 (88)
T 2ct2_A           13 REVLECPICMESFTEEQL-------------RPKLL-------------HCGHTICRQCLEKLLASSINGVRCPFCSKIT   66 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSS-------------CEEEC-------------SSSCEEEHHHHHHHHHHCSSCBCCTTTCCCB
T ss_pred             cCCCCCccCCccccccCC-------------CeEEC-------------CCCChhhHHHHHHHHHcCCCCcCCCCCCCcc
Confidence            346789999999987431             15666             899999999999999875   6899999988


Q ss_pred             CCCC
Q 013396          102 SLKD  105 (444)
Q Consensus       102 ~~k~  105 (444)
                      ...+
T Consensus        67 ~~~~   70 (88)
T 2ct2_A           67 RITS   70 (88)
T ss_dssp             CCSS
T ss_pred             cchh
Confidence            7654

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

Probab=99.16  E-value=2.2e-11  Score=94.70  Aligned_cols=52  Identities=27%  Similarity=0.649  Sum_probs=43.4

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc------CCCCCCcc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR------SSQCPMCW   98 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~------sssCP~CR   98 (444)
                      .++..|+||++.|.+                 ||++             +|||.||..||..|+..      ...||+||
T Consensus        17 ~~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr   66 (85)
T 2ecw_A           17 KEEVTCPICLELLKE-----------------PVSA-------------DCNHSFCRACITLNYESNRNTDGKGNCPVCR   66 (85)
T ss_dssp             CTTTSCTTTCSCCSS-----------------CEEC-------------TTSCCBCHHHHHHHHHHSBCTTSCBCCTTTC
T ss_pred             ccCCCCcCCChhhCc-----------------ceeC-------------CCCCHHHHHHHHHHHHhccCCCCCCCCCCCC
Confidence            346789999999876                 4555             89999999999999977      56899999


Q ss_pred             cCCCCCCC
Q 013396           99 QPISLKDP  106 (444)
Q Consensus        99 q~i~~k~~  106 (444)
                      +.+...+.
T Consensus        67 ~~~~~~~~   74 (85)
T 2ecw_A           67 VPYPFGNL   74 (85)
T ss_dssp             CCCCTTCC
T ss_pred             CcCCHHhC
Confidence            99876543

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

Probab=99.16  E-value=1.5e-11  Score=93.26  Aligned_cols=51  Identities=20%  Similarity=0.408  Sum_probs=41.7

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc-cCCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ-RSSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk-~sssCP~CRq~i~~  103 (444)
                      .++..|+||++.|.+                 ||++             +|||.||..||.+|++ ....||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCS-----------------PKQT-------------ECGHRFCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             CCCEECTTTCCEESS-----------------CCCC-------------SSSCCCCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             CcCCCCCCCChHhcC-----------------eeEC-------------CCCCHHHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            346789999999876                 3444             8999999999999995 56689999999875


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      .+
T Consensus        63 ~~   64 (66)
T 2ecy_A           63 DK   64 (66)
T ss_dssp             TT
T ss_pred             hh
Confidence            53

>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=99.15  E-value=4.9e-11  Score=99.62  Aligned_cols=66  Identities=12%  Similarity=0.015  Sum_probs=54.6

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      ..+..|+||++.|.+                 ||++             +|||.||+.||.+|+.....||+|++++...
T Consensus        27 p~~~~CpI~~~~m~d-----------------PV~~-------------~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   76 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD-----------------PVRL-------------PSGTIMDRSIILRHLLNSPTDPFNRQTLTES   76 (100)
T ss_dssp             STTTBCTTTCSBCSS-----------------EEEE-------------TTTEEEEHHHHHHHTTSCSBCSSSCCBCCTT
T ss_pred             cHhhCCcCccCcccC-----------------CeEC-------------CCCCEEchHHHHHHHHcCCCCCCCCCCCChh
Confidence            457889999999998                 8999             8999999999999999888999999999887


Q ss_pred             CCCccchHHHH-HHHHH
Q 013396          105 DPTRFCVNFAA-RNYLR  120 (444)
Q Consensus       105 ~~~~~~~~~av-r~~lR  120 (444)
                      +..++..+... ..+..
T Consensus        77 ~L~pn~~Lk~~I~~~~~   93 (100)
T 2kre_A           77 MLEPVPELKEQIQAWMR   93 (100)
T ss_dssp             SSEECHHHHHHHHHHHH
T ss_pred             hceECHHHHHHHHHHHH
Confidence            76666555444 34443

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

Probab=99.15  E-value=1.4e-11  Score=93.34  Aligned_cols=49  Identities=33%  Similarity=0.862  Sum_probs=41.0

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      .+..|+||++.|.+.                ++++             +|||.||..||.+|++....||+||+.+..
T Consensus         4 ~~~~C~IC~~~~~~~----------------~~~~-------------~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNY----------------SMAL-------------PCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC----------------EEET-------------TTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCC----------------cEec-------------CCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            467899999998651                2334             899999999999999988999999998753

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.15  E-value=6e-11  Score=98.76  Aligned_cols=67  Identities=10%  Similarity=0.067  Sum_probs=55.2

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCC-ChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR-HEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~Cg-H~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..+..|+||++.|.+                 ||++             +|| |.||+.||.+||.....||+||+++..
T Consensus        20 p~~~~CpI~~~~m~d-----------------PV~~-------------~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD-----------------PVVL-------------PSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS-----------------EEEC-------------TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHhcCCcCccccccC-----------------CeEC-------------CCCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            457889999999998                 8888             899 999999999999888899999999988


Q ss_pred             CCCCccchHHHH-HHHHHh
Q 013396          104 KDPTRFCVNFAA-RNYLRR  121 (444)
Q Consensus       104 k~~~~~~~~~av-r~~lR~  121 (444)
                      .+..++..+..+ ..+++.
T Consensus        70 ~~L~pn~~Lk~~I~~~~~~   88 (98)
T 1wgm_A           70 DQIRPNTELKEKIQRWLAE   88 (98)
T ss_dssp             TTSEECHHHHHHHHHHHHH
T ss_pred             hhceEcHHHHHHHHHHHHH
Confidence            777666555544 444443

>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=99.14  E-value=3.9e-11  Score=101.55  Aligned_cols=57  Identities=16%  Similarity=0.242  Sum_probs=45.4

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC-CCCCcccCCCC-C
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS-QCPMCWQPISL-K  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss-sCP~CRq~i~~-k  104 (444)
                      +..|+||++.|.+                 ||++             +|||.||..||..|+.... .||+||+.+.. .
T Consensus        52 ~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~  101 (124)
T 3fl2_A           52 TFQCICCQELVFR-----------------PITT-------------VCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSY  101 (124)
T ss_dssp             HTBCTTTSSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTC
T ss_pred             CCCCCcCChHHcC-----------------cEEe-------------eCCCcccHHHHHHHHhHCcCCCCCCCccCCCCC
Confidence            5689999999886                 7777             8999999999999998544 89999999976 3


Q ss_pred             CCCccchHH
Q 013396          105 DPTRFCVNF  113 (444)
Q Consensus       105 ~~~~~~~~~  113 (444)
                      ....+..+.
T Consensus       102 ~~~~n~~l~  110 (124)
T 3fl2_A          102 AMQVNQPLQ  110 (124)
T ss_dssp             CCCCCHHHH
T ss_pred             CCCCCHHHH
Confidence            434443333

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

Probab=99.13  E-value=3.8e-11  Score=96.99  Aligned_cols=61  Identities=11%  Similarity=-0.063  Sum_probs=51.7

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      ..+..|+||++.|.+                 ||++             +|||.||+.||.+|+.....||+|++.+...
T Consensus        12 p~~~~CpI~~~~m~d-----------------PV~~-------------~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD-----------------PVRL-------------PSGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CTTTBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             chheECcccCchhcC-----------------CeEC-------------CCCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            347789999999998                 8888             8999999999999999888999999999877


Q ss_pred             CCCccchHHHH
Q 013396          105 DPTRFCVNFAA  115 (444)
Q Consensus       105 ~~~~~~~~~av  115 (444)
                      +..++..+..+
T Consensus        62 ~l~pn~~L~~~   72 (85)
T 2kr4_A           62 MLEPVPELKEQ   72 (85)
T ss_dssp             GCEECHHHHHH
T ss_pred             hcchHHHHHHH
Confidence            66666554443

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

Probab=99.13  E-value=3e-11  Score=93.89  Aligned_cols=52  Identities=27%  Similarity=0.631  Sum_probs=43.2

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc------CCCCCCcc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR------SSQCPMCW   98 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~------sssCP~CR   98 (444)
                      ..+..|+||++.|.+                 |++|             +|||.||..||..|+..      ...||+||
T Consensus        17 ~~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr   66 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ-----------------PLSL-------------DCGHSFCQACLTANHKKSMLDKGESSCPVCR   66 (85)
T ss_dssp             CCCCCCTTTCSCCSS-----------------CBCC-------------SSSCCBCTTHHHHHHHHHHHTTSCCCCTTTC
T ss_pred             cCCCCCCCCCcccCC-----------------ceeC-------------CCCCHHHHHHHHHHHHHhhcCCCCCcCCCCC
Confidence            346789999999876                 4444             89999999999999977      67899999


Q ss_pred             cCCCCCCC
Q 013396           99 QPISLKDP  106 (444)
Q Consensus        99 q~i~~k~~  106 (444)
                      +.+...+.
T Consensus        67 ~~~~~~~~   74 (85)
T 2ecv_A           67 ISYQPENI   74 (85)
T ss_dssp             CSSCSSSC
T ss_pred             CccCHHhc
Confidence            99876543

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

Probab=99.12  E-value=1e-11  Score=96.29  Aligned_cols=51  Identities=27%  Similarity=0.630  Sum_probs=42.3

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-------CCCCCCc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-------SSQCPMC   97 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-------sssCP~C   97 (444)
                      .++..|+||++.|.+                 ||+|             +|||.||..||.+|++.       ...||+|
T Consensus        10 ~~~~~C~IC~~~~~~-----------------p~~l-------------~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~C   59 (79)
T 2egp_A           10 QEEVTCPICLELLTE-----------------PLSL-------------DCGHSLCRACITVSNKEAVTSMGGKSSCPVC   59 (79)
T ss_dssp             CCCCEETTTTEECSS-----------------CCCC-------------SSSCCCCHHHHSCCCCCCSSSCCCCCCCSSS
T ss_pred             ccCCCCcCCCcccCC-----------------eeEC-------------CCCCHHHHHHHHHHHHhcccCCCCCCcCCCC
Confidence            346789999999876                 4445             89999999999999976       5689999


Q ss_pred             ccCCCCCC
Q 013396           98 WQPISLKD  105 (444)
Q Consensus        98 Rq~i~~k~  105 (444)
                      |+.+...+
T Consensus        60 r~~~~~~~   67 (79)
T 2egp_A           60 GISYSFEH   67 (79)
T ss_dssp             CCCCCSSG
T ss_pred             CCcCCHhh
Confidence            99987643

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

Probab=99.12  E-value=1.5e-11  Score=93.99  Aligned_cols=51  Identities=29%  Similarity=0.839  Sum_probs=42.7

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..++..|+||++.|.+                  +++             +|||.||..||.+|++....||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~~~------------------~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   60 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD------------------LIL-------------PCAHSFCQKCIDKWSDRHRNCPICRLQMTG   60 (70)
T ss_dssp             CCCCCCCSSSCCSCCS------------------EEE-------------TTTEEECHHHHHHSSCCCSSCHHHHHCTTC
T ss_pred             CCCCCCCeeCCcCccC------------------ccc-------------CCCCcccHHHHHHHHHCcCcCCCcCCcccC
Confidence            3456789999998765                  233             899999999999999998999999999875


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      .+
T Consensus        61 ~~   62 (70)
T 2ecn_A           61 AN   62 (70)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=7.3e-11  Score=97.66  Aligned_cols=49  Identities=24%  Similarity=0.612  Sum_probs=42.7

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      +..|+||++.|.+                 ||++.            +|||.||..||..|++....||+||..+...
T Consensus        15 ~~~C~IC~~~~~~-----------------p~~~~------------~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFID-----------------ATTII------------ECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCSS-----------------EEEET------------TTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCCccCChHHhC-----------------cCEeC------------CCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            6689999999876                 55542            7999999999999999989999999998765

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

Probab=99.09  E-value=5.7e-11  Score=96.09  Aligned_cols=58  Identities=26%  Similarity=0.592  Sum_probs=44.9

Q ss_pred             CCCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCC-----ChhcHHHHHHHhccC--CC
Q 013396           21 GIQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR-----HEFHLQCVLEWCQRS--SQ   93 (444)
Q Consensus        21 ~iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~Cg-----H~FH~~CI~~Wlk~s--ss   93 (444)
                      ...+.+++.|.||++.|.+++               ++++             +|+     |.||..||.+|+..+  ..
T Consensus         9 s~~~~~~~~C~IC~~~~~~~~---------------~l~~-------------pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~   60 (80)
T 2d8s_A            9 SITPSSQDICRICHCEGDDES---------------PLIT-------------PCHCTGSLHFVHQACLQQWIKSSDTRC   60 (80)
T ss_dssp             CCCCTTSCCCSSSCCCCCSSS---------------CEEC-------------SSSCCSSSCCEETTHHHHHHHHHCCSB
T ss_pred             CCCCCCCCCCeEcCccccCCC---------------eeEe-------------ccccCCcCCeeCHHHHHHHHhhCCCCC
Confidence            334556789999999987643               2233             786     999999999999775  48


Q ss_pred             CCCcccCCCCCCC
Q 013396           94 CPMCWQPISLKDP  106 (444)
Q Consensus        94 CP~CRq~i~~k~~  106 (444)
                      ||+||..+.....
T Consensus        61 CplCr~~~~~~~~   73 (80)
T 2d8s_A           61 CELCKYEFIMETK   73 (80)
T ss_dssp             CSSSCCBCCCCCC
T ss_pred             CCCCCCeeecCcc
Confidence            9999999876654

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

Probab=99.07  E-value=4.1e-11  Score=99.82  Aligned_cols=59  Identities=25%  Similarity=0.528  Sum_probs=45.3

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      .++..|+||++.|.+....          ...+|++             +|||.||..||.+|++....||+||+.+...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~----------~~~~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQN----------GRLIVST-------------ECGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHT----------TCCEEEE-------------TTCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCcccc----------ccCeEec-------------CCCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            4577899999998762000          0013555             8999999999999999999999999998765


Q ss_pred             CC
Q 013396          105 DP  106 (444)
Q Consensus       105 ~~  106 (444)
                      ..
T Consensus        62 ~l   63 (133)
T 4ap4_A           62 RY   63 (133)
T ss_dssp             CE
T ss_pred             cc
Confidence            53

>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=99.06  E-value=1.3e-10  Score=103.02  Aligned_cols=58  Identities=17%  Similarity=0.297  Sum_probs=46.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC-CCCCcccCCCCC-
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS-QCPMCWQPISLK-  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss-sCP~CRq~i~~k-  104 (444)
                      +..|+||++.|.+                 ||+|             +|||.||..||..|+.... .||+||..+... 
T Consensus        78 ~~~C~IC~~~~~~-----------------pv~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~  127 (150)
T 1z6u_A           78 SFMCVCCQELVYQ-----------------PVTT-------------ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNY  127 (150)
T ss_dssp             HTBCTTTSSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTC
T ss_pred             CCEeecCChhhcC-----------------CEEc-------------CCCCchhHHHHHHHHHhCCCcCCCCCccCCCCC
Confidence            5789999999876                 6777             8999999999999998754 899999999876 


Q ss_pred             CCCccchHHH
Q 013396          105 DPTRFCVNFA  114 (444)
Q Consensus       105 ~~~~~~~~~a  114 (444)
                      ....+..+..
T Consensus       128 ~l~~n~~l~~  137 (150)
T 1z6u_A          128 IMIPNEILQT  137 (150)
T ss_dssp             CCCBCHHHHH
T ss_pred             CCCCCHHHHH
Confidence            4444433333

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

Probab=99.06  E-value=9.1e-11  Score=88.05  Aligned_cols=43  Identities=30%  Similarity=0.807  Sum_probs=36.7

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc---cCCCCCCc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ---RSSQCPMC   97 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk---~sssCP~C   97 (444)
                      .++..|+||++.|.+                 ||+|             +|||.||..||.+|++   ....||+|
T Consensus        18 ~~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK-----------------PVTI-------------DCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS-----------------CEEC-------------TTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC-----------------eEEe-------------CCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            447789999999876                 5666             8999999999999997   34589998

>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=99.06  E-value=6.6e-11  Score=97.25  Aligned_cols=52  Identities=31%  Similarity=0.632  Sum_probs=42.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC---CCCCcccCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS---QCPMCWQPISL  103 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss---sCP~CRq~i~~  103 (444)
                      +..|+||++.|.+                 ||++             +|||.||..||..|+....   .||+||..+..
T Consensus        21 ~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           21 ILECPICLELIKE-----------------PVST-------------KCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HTSCSSSCCCCSS-----------------CCBC-------------TTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CCCCcccChhhcC-----------------eEEC-------------CCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            4589999999876                 4445             8999999999999998653   89999999887


Q ss_pred             CCCCc
Q 013396          104 KDPTR  108 (444)
Q Consensus       104 k~~~~  108 (444)
                      .+...
T Consensus        71 ~~~~~   75 (112)
T 1jm7_A           71 RSLQE   75 (112)
T ss_dssp             TTCBC
T ss_pred             hhcCc
Confidence            65443

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.03  E-value=1.7e-10  Score=106.90  Aligned_cols=63  Identities=13%  Similarity=0.037  Sum_probs=51.4

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCC
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPI  101 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i  101 (444)
                      ....+..|+||++.|.+                 ||++             +|||.||..||.+|+... ..||+||.++
T Consensus       204 ~~~~~~~c~i~~~~~~d-----------------Pv~~-------------~~gh~f~~~~i~~~~~~~~~~cP~~~~~~  253 (281)
T 2c2l_A          204 DIPDYLCGKISFELMRE-----------------PCIT-------------PSGITYDRKDIEEHLQRVGHFNPVTRSPL  253 (281)
T ss_dssp             CCCSTTBCTTTCSBCSS-----------------EEEC-------------SSCCEEETTHHHHHHHHTCSSCTTTCCCC
T ss_pred             CCCcccCCcCcCCHhcC-----------------CeEC-------------CCCCEECHHHHHHHHHHCCCCCcCCCCCC
Confidence            34567889999999988                 8888             899999999999999764 4599999999


Q ss_pred             CCCCCCccchHHHH
Q 013396          102 SLKDPTRFCVNFAA  115 (444)
Q Consensus       102 ~~k~~~~~~~~~av  115 (444)
                      ...+..++..+..+
T Consensus       254 ~~~~l~~n~~l~~~  267 (281)
T 2c2l_A          254 TQEQLIPNLAMKEV  267 (281)
T ss_dssp             CGGGCEECHHHHHH
T ss_pred             chhcCcccHHHHHH
Confidence            87766666555444

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

Probab=99.00  E-value=2e-10  Score=84.13  Aligned_cols=43  Identities=37%  Similarity=1.032  Sum_probs=35.4

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc---cCCCCCCc
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ---RSSQCPMC   97 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk---~sssCP~C   97 (444)
                      .++..|+||++.|.+                 ||+|             +|||.||..||.+|+.   ....||+|
T Consensus        13 ~~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKE-----------------PVII-------------ECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSS-----------------CCCC-------------SSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCc-----------------cEeC-------------CCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            346789999999876                 3444             8999999999999964   45689998

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

Probab=99.00  E-value=2.9e-10  Score=93.08  Aligned_cols=61  Identities=20%  Similarity=0.318  Sum_probs=48.6

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCC-CCChhcHHHHHHHhccC------CCCCC-
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTS-CRHEFHLQCVLEWCQRS------SQCPM-   96 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~-CgH~FH~~CI~~Wlk~s------ssCP~-   96 (444)
                      ..+..|+||++.|.+                 ||++             + |||.||+.||.+||...      ..||+ 
T Consensus         5 ~~~~~CPI~~~~~~d-----------------PV~~-------------~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~t   54 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK-----------------PVKN-------------KVCGHTYEEDAIVRMIESRQKRKKKAYCPQI   54 (94)
T ss_dssp             SSCCBCTTTCSBCSS-----------------EEEE-------------SSSCCEEEHHHHHHHHHHHHTTTCCBCCCST
T ss_pred             CcEeECcCcCchhcC-----------------CEEc-------------CCCCCeecHHHHHHHHHHccCcCCCCCCCcC
Confidence            346789999999988                 8888             5 99999999999999753      48999 


Q ss_pred             -cccC-CCCCCCCccchHHHH
Q 013396           97 -CWQP-ISLKDPTRFCVNFAA  115 (444)
Q Consensus        97 -CRq~-i~~k~~~~~~~~~av  115 (444)
                       |+.. +...+..++..+..+
T Consensus        55 gc~~~~l~~~~L~pn~~L~~~   75 (94)
T 2yu4_A           55 GCSHTDIRKSDLIQDEALRRA   75 (94)
T ss_dssp             TCCCCCBCGGGEEECHHHHHH
T ss_pred             cCcccccCHhhCcCCHHHHHH
Confidence             9877 666666565555544

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

Probab=98.99  E-value=1.9e-10  Score=86.98  Aligned_cols=55  Identities=22%  Similarity=0.544  Sum_probs=41.7

Q ss_pred             CCCccccccc-CCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCC
Q 013396           26 CDDACSICLE-PFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISL  103 (444)
Q Consensus        26 ~Dd~CsICLE-~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~  103 (444)
                      ++..|+||++ .|.+...             .+|++             +|||.||..||.+|+.. ...||+||+.+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~-------------~~~~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   55 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSL-------------KLMVN-------------VCGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSC-------------CEEEC-------------TTCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCcCCcCCCCccCCCcc-------------CeecC-------------CCCCHhHHHHHHHHHHcCCCcCCCCCCcccc
Confidence            3678999999 7766321             12334             89999999999999755 4689999999876


Q ss_pred             CCC
Q 013396          104 KDP  106 (444)
Q Consensus       104 k~~  106 (444)
                      .+.
T Consensus        56 ~~~   58 (65)
T 1g25_A           56 SNF   58 (65)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            553

>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=98.96  E-value=2.3e-10  Score=96.42  Aligned_cols=50  Identities=22%  Similarity=0.561  Sum_probs=42.7

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC-CCCCcccCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS-QCPMCWQPISLK  104 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss-sCP~CRq~i~~k  104 (444)
                      .+..|+||++.|.+                 ||++             +|||.||..||.+|++... .||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           17 SKYECPICLMALRE-----------------AVQT-------------PCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             GGGBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCcCChhhcC-----------------eEEC-------------CcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            35789999999876                 6666             8999999999999998765 899999998764


Q ss_pred             C
Q 013396          105 D  105 (444)
Q Consensus       105 ~  105 (444)
                      .
T Consensus        67 ~   67 (118)
T 3hct_A           67 Q   67 (118)
T ss_dssp             G
T ss_pred             h
Confidence            4

>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=98.96  E-value=3e-10  Score=100.43  Aligned_cols=49  Identities=24%  Similarity=0.722  Sum_probs=40.8

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k  104 (444)
                      +..|+||++.|.+                 ||++.            +|||.||..||.+|+.. ...||+||..+...
T Consensus        54 ~~~C~IC~~~~~~-----------------p~~~~------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           54 ELMCPICLDMLKN-----------------TMTTK------------ECLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHBCTTTSSBCSS-----------------EEEET------------TTCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCcccChHhhC-----------------cCEeC------------CCCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            4589999999886                 44442            89999999999999987 67899999998643

>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=98.94  E-value=3.2e-10  Score=95.41  Aligned_cols=58  Identities=26%  Similarity=0.473  Sum_probs=45.8

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      +..|+||++.|.+                 ||++            .+|||.||..||..|+.  ..||+||..+...+.
T Consensus        22 ~~~C~IC~~~~~~-----------------pv~~------------~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~   70 (117)
T 1jm7_B           22 LLRCSRCTNILRE-----------------PVCL------------GGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (117)
T ss_dssp             TTSCSSSCSCCSS-----------------CBCC------------CSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             CCCCCCCChHhhC-----------------ccEe------------CCCCCHHHHHHHHHHhc--CCCcCCCCcCccccc
Confidence            6789999999876                 3333            27999999999999998  789999999976665


Q ss_pred             CccchHHHH
Q 013396          107 TRFCVNFAA  115 (444)
Q Consensus       107 ~~~~~~~av  115 (444)
                      ..+..+..+
T Consensus        71 ~~n~~l~~l   79 (117)
T 1jm7_B           71 KINRQLDSM   79 (117)
T ss_dssp             CCCHHHHHH
T ss_pred             cccHHHHHH
Confidence            555544444

>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=98.94  E-value=1.1e-10  Score=97.48  Aligned_cols=48  Identities=29%  Similarity=0.688  Sum_probs=41.3

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISL  103 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~  103 (444)
                      ++..|+||++.|.+                 ||+|             +|||.||..||..|+.. ...||+||+.+..
T Consensus        14 ~~~~C~iC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVE-----------------PVTL-------------PCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSS-----------------CEEC-------------TTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCc-----------------eeEc-------------CCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            36789999999876                 6667             89999999999999976 5689999998853

>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=98.93  E-value=4.6e-10  Score=93.75  Aligned_cols=50  Identities=34%  Similarity=0.622  Sum_probs=43.2

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLKD  105 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k~  105 (444)
                      +..|+||++.|.+                 ||++             +|||.||..||.+|+.. ...||+||..+...+
T Consensus        23 ~~~C~IC~~~~~~-----------------p~~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           23 SISCQICEHILAD-----------------PVET-------------SCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HTBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcHhcC-----------------cEEc-------------CCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            5689999999876                 6666             89999999999999987 678999999987655


Q ss_pred             C
Q 013396          106 P  106 (444)
Q Consensus       106 ~  106 (444)
                      .
T Consensus        73 ~   73 (116)
T 1rmd_A           73 L   73 (116)
T ss_dssp             C
T ss_pred             c
Confidence            3

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

Probab=98.91  E-value=8.5e-10  Score=88.78  Aligned_cols=52  Identities=25%  Similarity=0.592  Sum_probs=41.5

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC--CCCCCcccCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS--SQCPMCWQPISL  103 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s--ssCP~CRq~i~~  103 (444)
                      ..+.|+||++.|..+.   ..                          ..|+|.||.+||.+||+++  .+||+||+.|..
T Consensus        14 ~i~~C~IC~~~i~~g~---~C--------------------------~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQ---SC--------------------------ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             SSCBCSSSCCBCSSSE---EC--------------------------SSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             CCCcCcchhhHcccCC---cc--------------------------CCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            3468999999987421   11                          1699999999999999887  789999999976


Q ss_pred             CCC
Q 013396          104 KDP  106 (444)
Q Consensus       104 k~~  106 (444)
                      ..+
T Consensus        65 ~~~   67 (74)
T 2ct0_A           65 EIP   67 (74)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

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

Probab=98.89  E-value=3.7e-10  Score=94.06  Aligned_cols=59  Identities=25%  Similarity=0.569  Sum_probs=44.2

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ..++..|+||++.|.+.....          ..+|++             +|||.||..||.+|++....||+||..+..
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~----------~~~~~~-------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  125 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNG----------RLIVST-------------ECGHVFCSQCLRDSLKNANTCPTCRKKINH  125 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTT----------CCEEEE-------------TTSBEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCCCccccccccC----------cceEeC-------------CCCChhhHHHHHHHHHcCCCCCCCCCcCCh
Confidence            345677999998877521100          113455             899999999999999999999999999875


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      .+
T Consensus       126 ~~  127 (133)
T 4ap4_A          126 KR  127 (133)
T ss_dssp             GG
T ss_pred             hc
Confidence            54

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

Probab=98.88  E-value=1.9e-09  Score=86.53  Aligned_cols=55  Identities=20%  Similarity=0.456  Sum_probs=40.9

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~  103 (444)
                      .++..|+||++.|...+.....             +             +|||.||..||.+|++. ...||+||+.+..
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p-------------~-------------~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~   62 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFP-------------C-------------TCGYQICRFCWHRIRTDENGLCPACRKPYPE   62 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCS-------------S-------------TTSCCCCHHHHHHHTTSSCSBCTTTCCBCSS
T ss_pred             ccCCcCCccCccCccccccccc-------------c-------------CCCCCcCHHHHHHHHhcCCCCCCCCCCccCC
Confidence            4567899999988653321100             1             49999999999998854 5689999999876


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      ..
T Consensus        63 ~~   64 (78)
T 1e4u_A           63 DP   64 (78)
T ss_dssp             CS
T ss_pred             Cc
Confidence            54

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

Probab=98.86  E-value=4.5e-10  Score=83.76  Aligned_cols=49  Identities=24%  Similarity=0.457  Sum_probs=39.9

Q ss_pred             CCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           24 DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      +.++..|+||++.|.+                 |++|             +|||.||..||..|   ...||+||+.+..
T Consensus         3 e~~~~~C~IC~~~~~~-----------------p~~l-------------~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T 1bor_A            3 EFQFLRCQQCQAEAKC-----------------PKLL-------------PCLHTLCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             SCCCSSCSSSCSSCBC-----------------CSCS-------------TTSCCSBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             cccCCCceEeCCccCC-----------------eEEc-------------CCCCcccHHHHccC---CCCCCcCCcEeec
Confidence            4457789999999876                 4455             89999999999884   5579999999876


Q ss_pred             CC
Q 013396          104 KD  105 (444)
Q Consensus       104 k~  105 (444)
                      ..
T Consensus        50 ~~   51 (56)
T 1bor_A           50 GA   51 (56)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

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

Probab=98.79  E-value=3.8e-09  Score=97.46  Aligned_cols=61  Identities=13%  Similarity=0.043  Sum_probs=50.9

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~  103 (444)
                      ..+..|+||++.|.+                 ||++             +|||.||..||..|+... .+||+|+.++..
T Consensus       104 p~~f~CPI~~elm~D-----------------PV~~-------------~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          104 PDYLCGKISFELMRE-----------------PCIT-------------PSGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CGGGBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cHhhcccCccccCCC-----------------CeEC-------------CCCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            457889999999988                 8888             899999999999999764 469999999987


Q ss_pred             CCCCccchHHHH
Q 013396          104 KDPTRFCVNFAA  115 (444)
Q Consensus       104 k~~~~~~~~~av  115 (444)
                      .+..++..+..+
T Consensus       154 ~~L~pN~~Lk~~  165 (179)
T 2f42_A          154 DQLIPNLAMKEV  165 (179)
T ss_dssp             GGCEECHHHHHH
T ss_pred             hhCcchHHHHHH
Confidence            776666555444

>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=98.78  E-value=1.4e-09  Score=95.59  Aligned_cols=50  Identities=16%  Similarity=0.383  Sum_probs=42.2

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC-CCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS-QCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss-sCP~CRq~i~~  103 (444)
                      ..+..|+||++.|.+                 ||.+             +|||.||..||.+|++... .||+||.++..
T Consensus        29 ~~~~~C~IC~~~~~~-----------------pv~~-------------~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           29 EAKYLCSACRNVLRR-----------------PFQA-------------QCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             CGGGBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             CcCcCCCCCChhhcC-----------------cEEC-------------CCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            346789999999887                 6666             8999999999999998654 89999998754


Q ss_pred             C
Q 013396          104 K  104 (444)
Q Consensus       104 k  104 (444)
                      .
T Consensus        79 ~   79 (141)
T 3knv_A           79 E   79 (141)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=98.73  E-value=5.6e-09  Score=106.40  Aligned_cols=48  Identities=31%  Similarity=0.650  Sum_probs=41.4

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhc-cCCCCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ-RSSQCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk-~sssCP~CRq~i~~k  104 (444)
                      +..|+||++.+.+                 ||++             +|||.||..||..|+. ....||+||+.+...
T Consensus       332 ~~~C~ICle~~~~-----------------pv~l-------------pCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKD-----------------VKIE-------------PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCC-----------------EEEE-------------TTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCC-----------------eEEe-------------CCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            3689999999865                 6777             8999999999999998 678999999988643

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

Probab=98.71  E-value=5.3e-09  Score=92.62  Aligned_cols=51  Identities=22%  Similarity=0.531  Sum_probs=43.0

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISLK  104 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~k  104 (444)
                      ++..|+||++.|.+                 ||.+             +|||.||..||.+|+... ..||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~-----------------pv~~-------------~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALRE-----------------AVQT-------------PCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcC-----------------cEEC-------------CCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            46789999999877                 6666             899999999999999764 4899999998765


Q ss_pred             CC
Q 013396          105 DP  106 (444)
Q Consensus       105 ~~  106 (444)
                      +.
T Consensus        67 ~~   68 (170)
T 3hcs_A           67 QL   68 (170)
T ss_dssp             GC
T ss_pred             hh
Confidence            43

>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=98.69  E-value=6.2e-09  Score=79.91  Aligned_cols=50  Identities=26%  Similarity=0.531  Sum_probs=40.2

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      .++..|.||++.+.+                 +|++           ..+|||. ||..|+..|++....||+||+++.
T Consensus         6 ~~~~~C~IC~~~~~~-----------------~~~~-----------~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            6 NAIEPCVICQGRPKN-----------------GCIV-----------HGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGGSCCTTTSSSCSC-----------------EEEE-----------ETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCcCCCCcCCCCCCC-----------------EEEE-----------CCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            456789999998765                 2221           1279999 899999999998889999999874

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

Probab=98.69  E-value=5e-09  Score=82.11  Aligned_cols=43  Identities=30%  Similarity=0.790  Sum_probs=37.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      +..|.||++.+.+                 ||++             +|||. ||..|+..|    ..||+||+.+..
T Consensus        24 ~~~C~iC~~~~~~-----------------~~~~-------------pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA-----------------IVFV-------------PCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC-----------------EEEE-------------TTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC-----------------EEEc-------------CCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            5689999998776                 6777             89999 999999999    789999998753

>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=98.62  E-value=1.4e-08  Score=77.73  Aligned_cols=48  Identities=23%  Similarity=0.461  Sum_probs=38.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      +..|.||++.+.+                 ++++           ..+|||. ||..|+..|++....||+||+++.
T Consensus         7 ~~~C~IC~~~~~~-----------------~~~~-----------~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPRD-----------------GNII-----------HGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBSC-----------------EEEE-----------ETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCCCcccCCcCCC-----------------eEEE-----------ecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            5689999998665                 2211           2289998 999999999988889999999874

>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=98.55  E-value=3.1e-08  Score=96.71  Aligned_cols=61  Identities=26%  Similarity=0.489  Sum_probs=49.3

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC--CCCCC--cccCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS--SQCPM--CWQPI  101 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s--ssCP~--CRq~i  101 (444)
                      .+..|+||++.|.+                 ||+..            .|||.||+.||..|+...  ..||+  |++.+
T Consensus       180 ~el~CPIcl~~f~D-----------------PVts~------------~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l  230 (267)
T 3htk_C          180 IELTCPITCKPYEA-----------------PLISR------------KCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV  230 (267)
T ss_dssp             CCSBCTTTSSBCSS-----------------EEEES------------SSCCEEEHHHHHHHSTTCSCEECSGGGCSCEE
T ss_pred             eeeECcCccCcccC-----------------CeeeC------------CCCCcccHHHHHHHHHhCCCCCCCcccccCcC
Confidence            46789999999988                 77642            799999999999999764  47999  99998


Q ss_pred             CCCCCCccchHHHH
Q 013396          102 SLKDPTRFCVNFAA  115 (444)
Q Consensus       102 ~~k~~~~~~~~~av  115 (444)
                      ...+..++..+..+
T Consensus       231 ~~~dL~pN~~L~~l  244 (267)
T 3htk_C          231 SMRDFVRDPIMELR  244 (267)
T ss_dssp             CGGGEEECHHHHHH
T ss_pred             chhhCCcCHHHHHH
Confidence            87777666555443

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

Probab=98.48  E-value=5.8e-08  Score=75.93  Aligned_cols=43  Identities=30%  Similarity=0.790  Sum_probs=35.2

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      +..|.||++.+.+                 ||++             +|||. ||..|+..+    ..||+||+.+..
T Consensus        25 ~~~C~IC~~~~~~-----------------~~~~-------------pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIA-----------------IVFV-------------PCGHLVTCKQCAEAV----DKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCC-----------------BCCS-------------SSCCCCBCHHHHHHC----SBCTTTCCBCCC
T ss_pred             CCCCCcCCCCCCC-----------------EEEe-------------cCCCHHHHHHHhhCC----CCCccCCceecC
Confidence            4579999998766                 4555             89999 999999643    689999998864

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

Probab=98.41  E-value=1.6e-07  Score=73.20  Aligned_cols=47  Identities=32%  Similarity=0.655  Sum_probs=37.8

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCC
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPI  101 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i  101 (444)
                      .+.++..|.||++.+.+                 +|+|             +|||. ||..|+..    ...||+||+.+
T Consensus        11 ~~~~~~~C~IC~~~~~~-----------------~v~~-------------pCgH~~~C~~C~~~----~~~CP~CR~~i   56 (68)
T 2ea5_A           11 SEENSKDCVVCQNGTVN-----------------WVLL-------------PCRHTCLCDGCVKY----FQQCPMCRQFV   56 (68)
T ss_dssp             SCCCSSCCSSSSSSCCC-----------------CEET-------------TTTBCCSCTTHHHH----CSSCTTTCCCC
T ss_pred             cCCCCCCCCCcCcCCCC-----------------EEEE-------------CCCChhhhHHHHhc----CCCCCCCCcch
Confidence            34557789999998665                 4556             89999 99999984    46899999988


Q ss_pred             CC
Q 013396          102 SL  103 (444)
Q Consensus       102 ~~  103 (444)
                      ..
T Consensus        57 ~~   58 (68)
T 2ea5_A           57 QE   58 (68)
T ss_dssp             CC
T ss_pred             hc
Confidence            64

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

Probab=98.41  E-value=5.6e-08  Score=98.46  Aligned_cols=55  Identities=29%  Similarity=0.623  Sum_probs=40.2

Q ss_pred             CCCCCcccccccCCCCCC--CCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC----------
Q 013396           24 DACDDACSICLEPFSDSD--PSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS----------   91 (444)
Q Consensus        24 d~~Dd~CsICLE~F~~~~--~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s----------   91 (444)
                      +.....|+||++.+.++.  +...+                        ..+.|+|.||..||.+|++..          
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C------------------------~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi  360 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSC------------------------DNAKCVLKCHAVCLEEWFKTLMDGKTFLEVS  360 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCC------------------------SCTTCCCCBCSGGGHHHHHHHHSSSCTTTCC
T ss_pred             ccCCccCcccceeecCCCCCccccc------------------------cCCccCCccchHHHHHHHHhCCCcccccccc
Confidence            345678999999998732  11111                        123799999999999999652          


Q ss_pred             -CCCCCcccCCC
Q 013396           92 -SQCPMCWQPIS  102 (444)
Q Consensus        92 -ssCP~CRq~i~  102 (444)
                       ..||.||+++.
T Consensus       361 ~G~CPyCr~pIs  372 (381)
T 3k1l_B          361 FGQCPFCKAKLS  372 (381)
T ss_dssp             EEECTTTCCEEE
T ss_pred             CCCCCCCCCcCC
Confidence             36999999875

>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=98.40  E-value=1.1e-07  Score=73.14  Aligned_cols=51  Identities=16%  Similarity=0.265  Sum_probs=43.7

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDPT  107 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~~  107 (444)
                      ..|+||++.|.+                 ||++.            +|||.|.+.||.+|++.+..||++++++...+..
T Consensus         4 ~~CpIs~~~m~d-----------------PV~~~------------~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Li   54 (61)
T 2bay_A            4 MLCAISGKVPRR-----------------PVLSP------------KSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   54 (61)
T ss_dssp             CCCTTTCSCCSS-----------------EEEET------------TTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             EEecCCCCCCCC-----------------CEEeC------------CCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcE
Confidence            479999999987                 66662            6999999999999998888899999998766643

>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=98.39  E-value=8.2e-08  Score=76.73  Aligned_cols=43  Identities=21%  Similarity=0.539  Sum_probs=36.5

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      +..|.||++.+.+                 +|++             +|||. ||..|+..|.    .||+||+.+..
T Consensus        18 ~~~C~IC~~~~~~-----------------~v~~-------------pCgH~~~C~~C~~~~~----~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEIN-----------------STFC-------------PCGHTVCCESCAAQLQ----SCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCC-----------------EEEE-------------TTCBCCBCHHHHTTCS----BCTTTCCBCCE
T ss_pred             CCEeEEeCcccCc-----------------EEEE-------------CCCCHHHHHHHHHhcC----cCCCCCchhhC
Confidence            4589999998766                 6777             89999 9999999873    89999998753

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.32  E-value=2.7e-07  Score=70.89  Aligned_cols=26  Identities=19%  Similarity=0.584  Sum_probs=22.8

Q ss_pred             hhcHHHHHHHhcc--CCCCCCcccCCCC
Q 013396           78 EFHLQCVLEWCQR--SSQCPMCWQPISL  103 (444)
Q Consensus        78 ~FH~~CI~~Wlk~--sssCP~CRq~i~~  103 (444)
                      .||..||.+|+..  +..||+|+..|..
T Consensus        32 ~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A           32 NVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             hhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            9999999999964  5689999998864

>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=98.27  E-value=1.9e-07  Score=93.42  Aligned_cols=44  Identities=25%  Similarity=0.667  Sum_probs=38.3

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCCh-hcHHHHHHHhccCCCCCCcccCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHE-FHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~-FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      ++..|+||++.+.+                 ||+|             +|||. ||..|+..|    ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~-----------------~v~l-------------pCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS-----------------VVFI-------------PCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC-----------------EEEE-------------TTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc-----------------eEEc-------------CCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            36789999999876                 7778             89999 999999998    689999998753

>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=98.25  E-value=1.3e-07  Score=76.63  Aligned_cols=48  Identities=19%  Similarity=0.614  Sum_probs=35.8

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--------CCCCCC-
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--------SSQCPM-   96 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--------sssCP~-   96 (444)
                      ++..|+||++.|....                 .          +.+.+|||.||..||..|+..        ...||. 
T Consensus         4 ~~~~C~IC~~~~~~~~-----------------~----------~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~   56 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQ-----------------M----------TTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDA   56 (94)
T ss_dssp             SBCCCSSSCCCCBGGG-----------------E----------EEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCT
T ss_pred             CCcCCcccCccccccc-----------------c----------eEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccc
Confidence            3568999999987522                 1          112279999999999999853        137999 


Q ss_pred             -cccC
Q 013396           97 -CWQP  100 (444)
Q Consensus        97 -CRq~  100 (444)
                       |+..
T Consensus        57 ~C~~~   61 (94)
T 1wim_A           57 ACPKQ   61 (94)
T ss_dssp             TCSSC
T ss_pred             cCCCC
Confidence             9987

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

Probab=97.62  E-value=3.9e-05  Score=73.14  Aligned_cols=52  Identities=25%  Similarity=0.588  Sum_probs=40.5

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCC--CCCCcccCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSS--QCPMCWQPISLK  104 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~ss--sCP~CRq~i~~k  104 (444)
                      -..|.||.+.+..+   ..+                          +.|+|.||.+|+.+|++...  .||.|+..|...
T Consensus       180 i~~C~iC~~iv~~g---~~C--------------------------~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          180 VKICNICHSLLIQG---QSC--------------------------ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             CCBCTTTCSBCSSC---EEC--------------------------SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCcCcchhhHHhCC---ccc--------------------------CccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            45799999987753   111                          14999999999999997754  899999999766


Q ss_pred             CCC
Q 013396          105 DPT  107 (444)
Q Consensus       105 ~~~  107 (444)
                      .+.
T Consensus       231 ~~~  233 (238)
T 3nw0_A          231 IPK  233 (238)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.40  E-value=0.00011  Score=62.70  Aligned_cols=32  Identities=25%  Similarity=0.704  Sum_probs=27.2

Q ss_pred             CCCCChhcHHHHHHHhcc-CCCCCCcccCCCCC
Q 013396           73 TSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLK  104 (444)
Q Consensus        73 ~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k  104 (444)
                      -+|+|.||..|+..|.++ ...||+|+.++...
T Consensus        18 IPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A           18 IPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             ETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ccccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            389999999999999855 67899999987543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=92.75  E-value=0.042  Score=44.35  Aligned_cols=15  Identities=13%  Similarity=0.434  Sum_probs=13.3

Q ss_pred             CCCChhcHHHHHHHh
Q 013396           74 SCRHEFHLQCVLEWC   88 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wl   88 (444)
                      .|+|.||..|+..|.
T Consensus        23 ~C~~~~C~~Cl~~~h   37 (101)
T 2jun_A           23 TCEVSYCDECLKATH   37 (101)
T ss_dssp             TTTEEECHHHHHHHS
T ss_pred             cCChHHhHHHCHHHh
Confidence            799999999999843

>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=91.30  E-value=0.19  Score=56.77  Aligned_cols=67  Identities=15%  Similarity=0.079  Sum_probs=54.4

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCC-ChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR-HEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~Cg-H~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      +++-.|+|-++.+.+                 ||++             +.| +.|-+.+|.+|+..+.+||+=|+++..
T Consensus       889 P~~F~cPIs~~lM~D-----------------PVil-------------psG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          889 PDEFLDPLMYTIMKD-----------------PVIL-------------PASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             CGGGBCTTTCSBCSS-----------------EEEC-------------TTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             cHHhCCcchhhHHhC-----------------CeEc-------------CCCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            457789999999988                 8999             787 689999999999988899999999988


Q ss_pred             CCCCccchHHHH-HHHHHh
Q 013396          104 KDPTRFCVNFAA-RNYLRR  121 (444)
Q Consensus       104 k~~~~~~~~~av-r~~lR~  121 (444)
                      .+..++..+... ...+..
T Consensus       939 ~~liPN~~Lk~~I~~w~~~  957 (968)
T 3m62_A          939 EDVTPNEELRQKILCFKKQ  957 (968)
T ss_dssp             GGCEECHHHHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHH
Confidence            777776555444 444443

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=91.06  E-value=0.2  Score=39.17  Aligned_cols=28  Identities=21%  Similarity=0.566  Sum_probs=22.4

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCcccCC
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQPI  101 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq~i  101 (444)
                      .|...||..|+...+..    .-.||.|....
T Consensus        29 ~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           29 HCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             SSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            69999999999887754    23799997643

>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=86.66  E-value=0.93  Score=37.92  Aligned_cols=14  Identities=29%  Similarity=0.655  Sum_probs=12.8

Q ss_pred             CCCChhcHHHHHHH
Q 013396           74 SCRHEFHLQCVLEW   87 (444)
Q Consensus        74 ~CgH~FH~~CI~~W   87 (444)
                      -|+-.||..|+.+.
T Consensus        34 vC~RvfH~~CL~r~   47 (89)
T 1wil_A           34 VCTRVFHDGCLRRM   47 (89)
T ss_dssp             SSSSCCCHHHHHHH
T ss_pred             cccccccHhhcccc
Confidence            49999999999996

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=83.65  E-value=0.24  Score=44.54  Aligned_cols=28  Identities=25%  Similarity=0.567  Sum_probs=21.7

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCcccCC
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQPI  101 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq~i  101 (444)
                      .|.-.||..|+...+..    .-.||.|+..-
T Consensus        21 ~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A           21 KCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            69999999999776543    24799998754

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=83.11  E-value=0.27  Score=45.22  Aligned_cols=28  Identities=25%  Similarity=0.508  Sum_probs=21.7

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCcccCC
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQPI  101 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq~i  101 (444)
                      .|...||..|+...+..    .-.||.|+..-
T Consensus        24 ~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A           24 KCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            69999999999776643    23799998653

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=80.19  E-value=0.86  Score=34.64  Aligned_cols=26  Identities=23%  Similarity=0.714  Sum_probs=20.2

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCccc
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQ   99 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq   99 (444)
                      .|...||..|+..-+..    .-.||.|..
T Consensus        28 ~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           28 TCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             SSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCChhhhhhccCCCCCCCCCCceECccccc
Confidence            69999999999875533    237999965

---

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	444
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-14
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-07
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	7e-07
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-05
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-05
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	3e-05
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	7e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-04
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-04

>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 = 66.7 bits (162), Expect = 2e-14
 Identities = 15/81 (18%), Positives = 22/81 (27%), Gaps = 12/81 (14%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
           D   D C+IC     D       +          V                C H FH  C
Sbjct: 18  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW------------GVCNHAFHFHC 65

Query: 84  VLEWCQRSSQCPMCWQPISLK 104
           +  W +    CP+  +    +
Sbjct: 66  ISRWLKTRQVCPLDNREWEFQ 86

>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 = 56.4 bits (136), Expect = 2e-11
 Identities = 16/75 (21%), Positives = 22/75 (29%), Gaps = 26/75 (34%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
              C++CL    D +                              L  C H FH +CV  
Sbjct: 5   GVECAVCLAELEDGEE--------------------------ARFLPRCGHGFHAECVDM 38

Query: 87  WCQRSSQCPMCWQPI 101
           W    S CP+C   +
Sbjct: 39  WLGSHSTCPLCRLTV 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 = 51.1 bits (122), Expect = 3e-09
 Identities = 15/76 (19%), Positives = 23/76 (30%), Gaps = 29/76 (38%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
            + C ICLE  S+                                   C H F   C+  
Sbjct: 5   AERCPICLEDPSNYS-----------------------------MALPCLHAFCYVCITR 35

Query: 87  WCQRSSQCPMCWQPIS 102
           W +++  CP+C  P+ 
Sbjct: 36  WIRQNPTCPLCKVPVE 51

>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 = 45.4 bits (107), Expect = 4e-07
 Identities = 16/84 (19%), Positives = 20/84 (23%), Gaps = 31/84 (36%)

Query: 24  DACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQC 83
            +    C IC E   D                 V I               C H     C
Sbjct: 20  GSTFQLCKICAENDKD-----------------VKIE-------------PCGHLMCTSC 49

Query: 84  VLEWCQ-RSSQCPMCWQPISLKDP 106
           +  W +     CP C   I   +P
Sbjct: 50  LTSWQESEGQGCPFCRCEIKGTEP 73

>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 = 46.2 bits (108), Expect = 5e-07
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 17/91 (18%)

Query: 22  IQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHL 81
           ++ A ++ C IC+E  + +   +  +    +    V  L            T C H FHL
Sbjct: 20  LKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRL------------TKCSHAFHL 67

Query: 82  QCVLEWCQRSS-----QCPMCWQPISLKDPT 107
            C+L      +     QCP C      K  T
Sbjct: 68  LCLLAMYCNGNKDGSLQCPSCKTIYGEKTGT 98

>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 = 44.0 bits (103), Expect = 7e-07
 Identities = 14/80 (17%), Positives = 19/80 (23%), Gaps = 26/80 (32%)

Query: 27  DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLE 86
           D  C  C      +                          SL L +  C H     CV  
Sbjct: 3   DQGCPRCKTTKYRNP-------------------------SLKLMVNVCGHTLCESCVDL 37

Query: 87  WCQ-RSSQCPMCWQPISLKD 105
                +  CP C  P+   +
Sbjct: 38  LFVRGAGNCPECGTPLRKSN 57

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 11/74 (14%), Positives = 19/74 (25%), Gaps = 27/74 (36%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEW-C 88
           C +C+EP    D +                              +C ++    C      
Sbjct: 3   CPLCMEPLEIDDINFFP--------------------------CTCGYQICRFCWHRIRT 36

Query: 89  QRSSQCPMCWQPIS 102
             +  CP C +P  
Sbjct: 37  DENGLCPACRKPYP 50

>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 = 40.3 bits (94), Expect = 3e-05
 Identities = 17/77 (22%), Positives = 21/77 (27%), Gaps = 31/77 (40%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C IC    +D                                 TSC+H F   C+L   +
Sbjct: 26  CQICEHILADP------------------------------VETSCKHLFCRICILRCLK 55

Query: 90  -RSSQCPMCWQPISLKD 105
              S CP C  P    D
Sbjct: 56  VMGSYCPSCRYPCFPTD 72

>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 = 39.5 bits (92), Expect = 3e-05
 Identities = 12/75 (16%), Positives = 15/75 (20%), Gaps = 33/75 (44%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C  C                         +L              C H     C+     
Sbjct: 9   CQQCQAEAKC-----------------PKLL-------------PCLHTLCSGCLEAS-- 36

Query: 90  RSSQCPMCWQPISLK 104
              QCP+C  P  L 
Sbjct: 37  -GMQCPICQAPWPLG 50

>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 = 38.3 bits (88), Expect = 7e-05
 Identities = 12/85 (14%), Positives = 20/85 (23%), Gaps = 27/85 (31%)

Query: 22  IQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHL 81
           ++D     C IC E   +                                 T      H 
Sbjct: 1   MEDEDVPVCWICNEELGN-------------------------ERFRACGCTGELENVHR 35

Query: 82  QCVLEWCQRS--SQCPMCWQPISLK 104
            C+  W   S  + C +C    + +
Sbjct: 36  SCLSTWLTISRNTACQICGVVYNTR 60

>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 = 37.4 bits (86), Expect = 1e-04
 Identities = 7/76 (9%), Positives = 20/76 (26%), Gaps = 29/76 (38%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C+I  +                                        R  F    + ++ +
Sbjct: 3   CAISGKVPRRPV-----------------------------LSPKSRTIFEKSLLEQYVK 33

Query: 90  RSSQCPMCWQPISLKD 105
            +   P+  +P+S+++
Sbjct: 34  DTGNDPITNEPLSIEE 49

>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 = 37.7 bits (87), Expect = 3e-04
 Identities = 16/95 (16%), Positives = 25/95 (26%), Gaps = 36/95 (37%)

Query: 30  CSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQ 89
           C ICLE   +                                 T C H F   C+L+   
Sbjct: 24  CPICLELIKEP------------------------------VSTKCDHIFCKFCMLKLLN 53

Query: 90  RSS---QCPMCWQPISLKDPTRFCVNFAARNYLRR 121
           +     QCP+C   I+ +       +      +  
Sbjct: 54  QKKGPSQCPLCKNDITKRS---LQESTRFSQLVEE 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	444
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.4
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.39
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.39
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.23
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.22
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.19
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.18
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.17
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.15
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.15
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.13
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.12
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.04
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.98
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.98
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.96
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.05
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	89.73
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	85.54
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	83.17
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	81.37

>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=99.40  E-value=5e-14  Score=105.06  Aligned_cols=51  Identities=31%  Similarity=0.774  Sum_probs=42.0

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      ++..|+|||+.|..++..                          .+++.|+|.||..||.+|++.+..||+||+.+.
T Consensus         4 d~~~C~ICl~~~~~~~~~--------------------------~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEA--------------------------RFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCC--------------------------EECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEE--------------------------EEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            356799999999876532                          123379999999999999999999999999864

>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=99.39  E-value=6.8e-14  Score=112.21  Aligned_cols=66  Identities=21%  Similarity=0.452  Sum_probs=46.4

Q ss_pred             CCCcccccccCCCCCCCCcccccc-cccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFD-FHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLK  104 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~-~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k  104 (444)
                      .++.|+||++.|.+....+..... ....-..+++             ++|||.||..||.+||+.+.+||+||++|..+
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAW-------------GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEE-------------ETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEE-------------ccccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            466799999999886654322111 1111111233             38999999999999999999999999998653

>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=99.39  E-value=1.1e-13  Score=114.34  Aligned_cols=75  Identities=27%  Similarity=0.406  Sum_probs=49.4

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-----CCCCCc
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-----SQCPMC   97 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-----ssCP~C   97 (444)
                      ....++.|+||++.|...........+..            ......+.+.+|+|.||..||.+|++..     .+||+|
T Consensus        21 ~~~~~~~C~IC~e~l~~~~~~~~~~~~~~------------~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~C   88 (114)
T d1v87a_          21 KVAPEEDCIICMEKLAVASGYSDMTDSKA------------LGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSC   88 (114)
T ss_dssp             SSCCSCEETTTTEETTSCCSTTTTCCCSS------------SCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTT
T ss_pred             cccccccccchhheecccccccccccccc------------cccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccc
Confidence            44557789999999876433221100000            0011223344899999999999999753     379999


Q ss_pred             ccCCCCCCCCcc
Q 013396           98 WQPISLKDPTRF  109 (444)
Q Consensus        98 Rq~i~~k~~~~~  109 (444)
                      |..|..+...++
T Consensus        89 R~~~~~~~~~qP  100 (114)
T d1v87a_          89 KTIYGEKTGTQP  100 (114)
T ss_dssp             CCBSSSCSSSCT
T ss_pred             cchhccCcCCCC
Confidence            999988766554

>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=99.23  E-value=4e-12  Score=100.33  Aligned_cols=49  Identities=31%  Similarity=0.651  Sum_probs=41.3

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLKD  105 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k~  105 (444)
                      +..|+||++.+.+                 ||++             +|||.||..||..|+.. ...||+||+.+....
T Consensus        23 ~~~C~IC~~~~~~-----------------~~~~-------------~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDKD-----------------VKIE-------------PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBCC-----------------EECS-------------SSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCCC-----------------eEEe-------------CCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            4579999998766                 5666             89999999999999974 568999999987654

>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=99.22  E-value=2e-12  Score=98.96  Aligned_cols=47  Identities=34%  Similarity=0.914  Sum_probs=39.6

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPIS  102 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~  102 (444)
                      -+.|+||++.|.+.                ++++             +|||.||..||.+|++.+..||+||+++.
T Consensus         5 ~d~C~IC~~~~~~~----------------~~~~-------------~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSNY----------------SMAL-------------PCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCSC----------------EEET-------------TTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCccCC----------------cEEe-------------CCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            45799999998651                2333             89999999999999999999999999875

>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=99.19  E-value=2.6e-12  Score=95.36  Aligned_cols=50  Identities=16%  Similarity=0.270  Sum_probs=43.4

Q ss_pred             CcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           28 DACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        28 d~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      ..|+||++.|.+                 ||++.            .|||.||..||.+|++.+..||+||+++...+.
T Consensus         1 l~C~Ic~~~~~~-----------------Pv~~~------------~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           1 MLCAISGKVPRR-----------------PVLSP------------KSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCCTTTCSCCSS-----------------EEEET------------TTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCCccCCchHHh-----------------cCccC------------CCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            369999999887                 67662            699999999999999999999999999876654

>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=99.18  E-value=4.7e-12  Score=96.45  Aligned_cols=55  Identities=22%  Similarity=0.495  Sum_probs=40.7

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLK  104 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k  104 (444)
                      +|..|+||++.+......            .++++             +|||.||..||.+|++. +..||+||+++...
T Consensus         2 dd~~CpIC~~~~~~~~~~------------~~~~~-------------~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSL------------KLMVN-------------VCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSC------------CEEEC-------------TTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCce------------EEEeC-------------ccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            478999999976432111            01223             89999999999999965 55899999998655


Q ss_pred             C
Q 013396          105 D  105 (444)
Q Consensus       105 ~  105 (444)
                      +
T Consensus        57 ~   57 (65)
T d1g25a_          57 N   57 (65)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.17  E-value=5.7e-12  Score=92.39  Aligned_cols=49  Identities=22%  Similarity=0.545  Sum_probs=38.6

Q ss_pred             cccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCC
Q 013396           29 ACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISL  103 (444)
Q Consensus        29 ~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~  103 (444)
                      .|+||++.|..++...             +             +.+|||.||..||.+|++.. ..||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~-------------~-------------~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINF-------------F-------------PCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTC-------------C-------------SSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceE-------------E-------------ecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            6999999997644221             1             12799999999999999864 479999999864

>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=99.15  E-value=8.9e-12  Score=101.69  Aligned_cols=53  Identities=32%  Similarity=0.616  Sum_probs=42.8

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC---CCCCCcccCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS---SQCPMCWQPISL  103 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s---ssCP~CRq~i~~  103 (444)
                      +..|+||++.|.+                 ||++             +|||.||..||.+|++..   ..||+||..+..
T Consensus        21 ~l~CpIC~~~~~~-----------------pv~~-------------~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          21 ILECPICLELIKE-----------------PVST-------------KCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HTSCSSSCCCCSS-----------------CCBC-------------TTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CcCCCccCchhCC-----------------eEEc-------------CCCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            4579999999876                 5556             899999999999999664   379999999876


Q ss_pred             CCCCcc
Q 013396          104 KDPTRF  109 (444)
Q Consensus       104 k~~~~~  109 (444)
                      .+...+
T Consensus        71 ~~l~~n   76 (103)
T d1jm7a_          71 RSLQES   76 (103)
T ss_dssp             TTCBCC
T ss_pred             hhCCcC
Confidence            654333

>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=99.15  E-value=3.2e-11  Score=93.83  Aligned_cols=66  Identities=20%  Similarity=0.272  Sum_probs=52.7

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC-CCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS-SQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s-ssCP~CRq~i~~  103 (444)
                      .++..|+||++.|.+                 ||++             +|||.||+.||.+|+... ..||.|+.++..
T Consensus         6 P~~l~CpIc~~~m~d-----------------PV~~-------------~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           6 PEYFRCPISLELMKD-----------------PVIV-------------STGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSS-----------------EEEE-------------TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CccCCCcCcCchhhC-----------------ceEc-------------cCCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            468899999999988                 8888             899999999999999764 579999999987


Q ss_pred             CCCCccchHHHH-HHHHH
Q 013396          104 KDPTRFCVNFAA-RNYLR  120 (444)
Q Consensus       104 k~~~~~~~~~av-r~~lR  120 (444)
                      .+..++..+..+ ..++.
T Consensus        56 ~~l~pN~~L~~~I~~~~~   73 (78)
T d1t1ha_          56 AGLTPNYVLKSLIALWCE   73 (78)
T ss_dssp             CCCEECTTTHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHH
Confidence            776655444433 44443

>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=99.13  E-value=1.7e-11  Score=99.07  Aligned_cols=52  Identities=33%  Similarity=0.597  Sum_probs=43.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISLKD  105 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~k~  105 (444)
                      +..|+||++.|.+                 ||++             +|||.||..||.+|++. ...||+||.++...+
T Consensus        23 ~l~C~IC~~~~~~-----------------pv~~-------------~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          23 SISCQICEHILAD-----------------PVET-------------SCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HTBCTTTCSBCSS-----------------EEEC-------------TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CcCCccCCcchhc-----------------ceec-------------CCCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            4689999999877                 7777             89999999999999975 458999999987665


Q ss_pred             CCc
Q 013396          106 PTR  108 (444)
Q Consensus       106 ~~~  108 (444)
                      ...
T Consensus        73 l~~   75 (86)
T d1rmda2          73 LES   75 (86)
T ss_dssp             CBC
T ss_pred             ccC
Confidence            443

>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=99.12  E-value=2.5e-11  Score=95.03  Aligned_cols=65  Identities=12%  Similarity=0.096  Sum_probs=51.0

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc-CCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR-SSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~-sssCP~CRq~i~~  103 (444)
                      .++..|+||++.|.+                 ||++             +|||.||..||.+|+.. ...||+|++++..
T Consensus         5 P~~l~CpIc~~l~~d-----------------Pv~~-------------~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMRE-----------------PCIT-------------PSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCSS-----------------EEEC-------------SSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhhh-----------------hccc-------------CCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            457899999999988                 8888             89999999999999975 5579999999877


Q ss_pred             CCCCccchHHHH-HHHH
Q 013396          104 KDPTRFCVNFAA-RNYL  119 (444)
Q Consensus       104 k~~~~~~~~~av-r~~l  119 (444)
                      .+..++..+..+ ..++
T Consensus        55 ~~l~pN~~L~~~I~~~l   71 (80)
T d2c2la2          55 EQLIPNLAMKEVIDAFI   71 (80)
T ss_dssp             GGCEECHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHH
Confidence            665555444333 3444

>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=99.04  E-value=3.2e-11  Score=97.34  Aligned_cols=58  Identities=26%  Similarity=0.463  Sum_probs=44.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCCC
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKDP  106 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~~  106 (444)
                      +..|+||++.|.+                 ||++            ++|||.||..||.+|+..  .||+||..+...+.
T Consensus        22 ~l~C~IC~~~~~~-----------------pv~~------------~~CgH~fC~~Ci~~~~~~--~CP~Cr~~~~~~~l   70 (97)
T d1jm7b_          22 LLRCSRCTNILRE-----------------PVCL------------GGCEHIFCSNCVSDCIGT--GCPVCYTPAWIQDL   70 (97)
T ss_dssp             TTSCSSSCSCCSS-----------------CBCC------------CSSSCCBCTTTGGGGTTT--BCSSSCCBCSCSSC
T ss_pred             cCCCccCCchhhc-----------------Ccee------------CCCCCchhHHHHHHHHhc--cccccCCcCchhhC
Confidence            5689999999976                 3332            279999999999999954  59999999887766


Q ss_pred             CccchHHHH
Q 013396          107 TRFCVNFAA  115 (444)
Q Consensus       107 ~~~~~~~av  115 (444)
                      ..+..+..+
T Consensus        71 ~~n~~l~~l   79 (97)
T d1jm7b_          71 KINRQLDSM   79 (97)
T ss_dssp             CCCHHHHHH
T ss_pred             cccHHHHHH
Confidence            555554444

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=4.5e-11  Score=89.39  Aligned_cols=48  Identities=25%  Similarity=0.459  Sum_probs=38.9

Q ss_pred             CCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccCCCCCCcccCCCCCC
Q 013396           26 CDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRSSQCPMCWQPISLKD  105 (444)
Q Consensus        26 ~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~sssCP~CRq~i~~k~  105 (444)
                      ....|+||++.|.+                 ||+|             +|||.||..||.+|   ...||+||+.+....
T Consensus         5 ~~l~C~IC~~~~~~-----------------p~~l-------------pCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKC-----------------PKLL-------------PCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBC-----------------CSCS-------------TTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCC-----------------CEEe-------------cCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            34689999999876                 4455             89999999999876   557999999997654


Q ss_pred             C
Q 013396          106 P  106 (444)
Q Consensus       106 ~  106 (444)
                      .
T Consensus        52 ~   52 (56)
T d1bora_          52 D   52 (56)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=98.98  E-value=3.8e-10  Score=92.19  Aligned_cols=71  Identities=10%  Similarity=0.080  Sum_probs=56.8

Q ss_pred             CCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCC-ChhcHHHHHHHhccCCCCCCcccCCCC
Q 013396           25 ACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCR-HEFHLQCVLEWCQRSSQCPMCWQPISL  103 (444)
Q Consensus        25 ~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~Cg-H~FH~~CI~~Wlk~sssCP~CRq~i~~  103 (444)
                      .++..|+||++.|.+                 ||++             +|+ |.|++.||.+|++.+..||+|++++..
T Consensus        20 P~~f~CPI~~~lm~d-----------------PV~~-------------~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD-----------------PVVL-------------PSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS-----------------EEEC-------------TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHHhCCcCchhHHHH-----------------HHhc-------------ccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            447899999999998                 8888             555 689999999999999999999999988


Q ss_pred             CCCCccchHHHH-HHHHHhcccC
Q 013396          104 KDPTRFCVNFAA-RNYLRRSNKR  125 (444)
Q Consensus       104 k~~~~~~~~~av-r~~lR~~~~r  125 (444)
                      .+..++..+... ..+++....+
T Consensus        70 ~~L~pN~~Lr~~I~~~~~~~~~~   92 (98)
T d1wgma_          70 DQIRPNTELKEKIQRWLAERKQQ   92 (98)
T ss_dssp             TTSEECHHHHHHHHHHHHHSTTC
T ss_pred             hhhcchHHHHHHHHHHHHHHHHh
Confidence            777766555544 5666655543

>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=98.96  E-value=1.8e-10  Score=85.86  Aligned_cols=57  Identities=19%  Similarity=0.389  Sum_probs=41.1

Q ss_pred             CCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhcc--CCCCCCcccC
Q 013396           23 QDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQR--SSQCPMCWQP  100 (444)
Q Consensus        23 qd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~--sssCP~CRq~  100 (444)
                      .+.++..|.||++.+.+....             |            -.-..|+|.||..||.+|+..  +..||+||+.
T Consensus         2 eded~~~C~IC~~~~~~~~~~-------------~------------c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~   56 (60)
T d1vyxa_           2 EDEDVPVCWICNEELGNERFR-------------A------------CGCTGELENVHRSCLSTWLTISRNTACQICGVV   56 (60)
T ss_dssp             TTCSCCEETTTTEECSCCCCC-------------S------------CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCB
T ss_pred             CCCCCCCCccCCccCCCceeE-------------e------------cccCCCCCEEcHHHHHHHHhhCCCCCCcccCCe
Confidence            456778999999987653211             0            011157799999999999954  5689999999


Q ss_pred             CCCC
Q 013396          101 ISLK  104 (444)
Q Consensus       101 i~~k  104 (444)
                      |..+
T Consensus        57 ~~~k   60 (60)
T d1vyxa_          57 YNTR   60 (60)
T ss_dssp             CCCC
T ss_pred             eecC
Confidence            8653

>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=98.05  E-value=3.8e-07  Score=72.06  Aligned_cols=47  Identities=21%  Similarity=0.561  Sum_probs=33.9

Q ss_pred             CCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHHhccC--------CCCCCcc
Q 013396           27 DDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEWCQRS--------SQCPMCW   98 (444)
Q Consensus        27 Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~Wlk~s--------ssCP~CR   98 (444)
                      ...|+||++.+...+.              +++             ..|+|.||..||..|++..        -.||.|+
T Consensus         5 ~~~C~IC~~~~~~~~~--------------~~~-------------~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           5 SSGCKLCLGEYPVEQM--------------TTI-------------AQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             BCCCSSSCCCCBGGGE--------------EEE-------------TTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCcCccCCCcccCCce--------------EEE-------------CCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            4589999998865321              122             2799999999999999531        1599875


Q ss_pred             cC
Q 013396           99 QP  100 (444)
Q Consensus        99 q~  100 (444)
                      ..
T Consensus        58 C~   59 (94)
T d1wima_          58 CP   59 (94)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=89.73  E-value=0.24  Score=39.33  Aligned_cols=38  Identities=21%  Similarity=0.451  Sum_probs=27.6

Q ss_pred             CCCCCCCcccccccCCCCCCCCcccccccccceeeeeeeccCCccccccccCCCCChhcHHHHHHH
Q 013396           22 IQDACDDACSICLEPFSDSDPSTVTSFDFHVRFFRVVILRDLGNFSLLLQLTSCRHEFHLQCVLEW   87 (444)
Q Consensus        22 iqd~~Dd~CsICLE~F~~~~~~~~~~~~~~~~~~~pViL~~~g~~~~~~~l~~CgH~FH~~CI~~W   87 (444)
                      .+..+|+.|.|| +.|......             |-.              -|+-.||..|+.+.
T Consensus        10 e~v~~D~mC~vC-~v~t~~~l~-------------pCR--------------vCtRv~H~~CL~r~   47 (89)
T d1wila_          10 EPVVNDEMCDVC-EVWTAESLF-------------PCR--------------VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCSCCCTTT-CCCCSSCCS-------------SCS--------------SSSSCCCHHHHHHH
T ss_pred             cCCCcCcccccc-Cccccccee-------------cce--------------eecchhhHHHHHHh
Confidence            355679999999 777664321             111              49999999999987

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.54  E-value=0.15  Score=37.82  Aligned_cols=31  Identities=35%  Similarity=0.656  Sum_probs=23.4

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCcccCCCCC
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQPISLK  104 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq~i~~k  104 (444)
                      .|...||..|+...+..    .-.||.|+.....+
T Consensus        24 ~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~   58 (70)
T d1fp0a1          24 QCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLK   58 (70)
T ss_dssp             TSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSC
T ss_pred             CCChhhccccCCCCcCcCCCCCEECcCCcCcCccC
Confidence            69999999999877644    23799997654433

>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=83.17  E-value=0.25  Score=34.15  Aligned_cols=26  Identities=35%  Similarity=0.741  Sum_probs=20.8

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCccc
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQ   99 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq   99 (444)
                      .|...||..|+..-+..    .-.||.|+.
T Consensus        20 ~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_          20 ECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             TTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            79999999999876643    237999975

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.37  E-value=0.19  Score=36.31  Aligned_cols=27  Identities=26%  Similarity=0.699  Sum_probs=20.7

Q ss_pred             CCCChhcHHHHHHHhcc----CCCCCCcccC
Q 013396           74 SCRHEFHLQCVLEWCQR----SSQCPMCWQP  100 (444)
Q Consensus        74 ~CgH~FH~~CI~~Wlk~----sssCP~CRq~  100 (444)
                      .|.-.||..||...+..    .-.||.|+..
T Consensus        26 ~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_          26 TCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            69999999999765543    2379999754